diff --git a/.github/workflows/covr.yaml b/.github/workflows/covr.yaml
index 1f3fd739..81af6c74 100644
--- a/.github/workflows/covr.yaml
+++ b/.github/workflows/covr.yaml
@@ -4,10 +4,10 @@ name: covr
 
 jobs:
   covr:
-    if: "! contains(github.event.head_commit.message, '[ci skip]')"
+    if: "! contains(github.event.head_commit.message, '[ci skip]')"    
+
+    timeout-minutes: 45
 
-    timeout-minutes: 10
-    
     runs-on: ubuntu-latest
 
     name: covr
@@ -17,48 +17,39 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
+      R_KEEP_PKG_SOURCE: yes
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      ## Test in other locale (optional)
+      LANGUAGE: ${{ matrix.config.language }}
       ## R CMD check
+      _R_CHECK_CRAN_INCOMING_: false
       _R_CHECK_LENGTH_1_CONDITION_: true
       _R_CHECK_LENGTH_1_LOGIC2_: true
       _R_CHECK_MATRIX_DATA_: true
-      _R_CHECK_CRAN_INCOMING_: false
+      _R_CHECK_SUGGESTS_ONLY_: true
+      _R_CHECK_THINGS_IN_TEMP_DIR_: true
+      RCMDCHECK_ERROR_ON: note
+      ## Specific to futures
+      R_FUTURE_RNG_ONMISUSE: error
 
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
-
       - uses: r-lib/actions/setup-r@v2
         with:
-          r-version: release
+          use-public-rspm: true
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        uses: actions/cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
+          extra-packages: |
+            any::rcmdcheck
+            any::remotes
+            any::sessioninfo
+            any::covr
+          needs: check
 
       - name: Install dependencies
         run: |
-          install.packages(c("covr", "sessioninfo"))
           remotes::install_deps(dependencies = TRUE)
           install.packages(".", repos=NULL, type="source")
         shell: Rscript {0}
@@ -76,7 +67,7 @@ jobs:
           ##    https://app.codecov.io/gh/<org>/<repo>/settings
           ## 2. Set 'CODECOV_TOKEN' in GitHub Secrets:
           ##    https://github.com/<org>/<repo>/settings/environments/
-          coverage <- covr::package_coverage()
+          coverage <- covr::package_coverage(quiet = FALSE)
           print(coverage)
           covr::codecov(coverage = coverage, token="${{secrets.CODECOV_TOKEN}}")
         shell: Rscript {0}
diff --git a/.github/workflows/revdepcheck-top.yaml b/.github/workflows/revdepcheck-top.yaml
index ec7ffee4..eadca857 100644
--- a/.github/workflows/revdepcheck-top.yaml
+++ b/.github/workflows/revdepcheck-top.yaml
@@ -21,7 +21,6 @@ jobs:
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      RSPM: https://packagemanager.rstudio.com/cran/__linux__/jammy/latest
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       ## R CMD check
       _R_CHECK_LENGTH_1_CONDITION_: true
@@ -39,37 +38,21 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v3
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies (Linux)
-        if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
-        run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
+          extra-packages: |
+            any::rcmdcheck
+            any::remotes
+            any::sessioninfo
+            any::covr
+          needs: check
 
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          install.packages(".", repos=NULL, type="source")  ## needed by parallel workers
-          install.packages("${{ matrix.config.pkg }}", dependencies=TRUE)
+          install.packages(".", repos=NULL, type="source")
         shell: Rscript {0}
 
       - name: Session info
@@ -82,6 +65,7 @@ jobs:
       - name: Check reverse dependency package
         run: |
           pkgname <- "${{ matrix.config.pkg }}"
+          install.packages(pkgname, dependencies = TRUE)
           url <- remotes:::download_version_url(pkgname, version=NULL, repos="https://cloud.r-project.org", type="source")
           tarball <- basename(url)
           utils::download.file(url, destfile = tarball, mode = "wb")
diff --git a/DESCRIPTION b/DESCRIPTION
index cd8902e2..95a4f8a1 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,14 +1,19 @@
 Package: parallelly
-Version: 1.37.1
+Version: 1.38.0
 Title: Enhancing the 'parallel' Package
 Imports:
     parallel,
     tools,
     utils
-Authors@R: c(person("Henrik", "Bengtsson",
-                    role = c("aut", "cre", "cph"),
-                    email = "henrikb@braju.com",
-                    comment = c(ORCID = "0000-0002-7579-5165")))
+Authors@R: c(
+        person("Henrik", "Bengtsson",
+               role = c("aut", "cre", "cph"),
+               email = "henrikb@braju.com",
+               comment = c(ORCID = "0000-0002-7579-5165")),
+        person("Mike", "Cheng",
+               role = c("ctb"),
+               email = "mikefc@coolbutuseless.com")
+    )
 Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package.  For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
 License: LGPL (>= 2.1)
 LazyLoad: TRUE
@@ -16,5 +21,5 @@ ByteCompile: TRUE
 URL: https://parallelly.futureverse.org, https://github.com/HenrikBengtsson/parallelly
 BugReports: https://github.com/HenrikBengtsson/parallelly/issues
 Encoding: UTF-8
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Roxygen: list(markdown = TRUE)
diff --git a/NAMESPACE b/NAMESPACE
index 94d957aa..00c7f2c1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -29,6 +29,8 @@ S3method(print,RichSOCKnode)
 S3method(stopCluster,RichMPIcluster)
 S3method(summary,RichSOCKcluster)
 S3method(summary,RichSOCKnode)
+export(MPI)
+export(PSOCK)
 export(as.cluster)
 export(autoStopCluster)
 export(availableConnections)
@@ -49,7 +51,16 @@ export(killNode)
 export(makeClusterMPI)
 export(makeClusterPSOCK)
 export(makeNodePSOCK)
+export(serializedSize)
 export(supportsMulticore)
+if (getRversion() >= "4.4") S3method(print,sequential_cluster)
+if (getRversion() >= "4.4") S3method(print,sequential_node)
+if (getRversion() >= "4.4") S3method(recvData,sequential_node)
+if (getRversion() >= "4.4") S3method(sendData,sequential_node)
+if (getRversion() >= "4.4") export(SEQ)
+if (getRversion() >= "4.4") export(makeClusterSequential)
+if (getRversion() >= "4.4") importFrom(parallel,recvData)
+if (getRversion() >= "4.4") importFrom(parallel,sendData)
 importFrom(parallel,clusterCall)
 importFrom(parallel,detectCores)
 importFrom(parallel,makeCluster)
diff --git a/NEWS.md b/NEWS.md
index a66a905b..1bec2ab1 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,41 @@
+# Version 1.38.0 [2024-07-27]
+
+## New Features
+
+ * Now argument `rshcmd` of `makeNodePSOCK()` can be a function. It
+   must accept at least two arguments named `rshopts` and
+   `worker`. The `rshopts` argument is a character vector of length
+   zero or more. The `worker` argument is a string hostname. The
+   function must return a single string.
+
+ * Now `makeNodePSOCK()` accepts `rscript_sh = "none"`, which skips
+   quoting the Rscript call.
+   
+ * Now `makeNodePSOCK()` accepts `rscript_sh` of length one or two.
+   If `length(rscript_sh) == 2`, then `rscript_sh[1]` is for the inner
+   and `rscript_sh[2]` is for the outer shell quoting of the Rscript
+   call.  More precisely, `rscript_sh[1]` is for Rscript arguments
+   that need shell quoting (e.g. `Rscript -e "<expr>"`), and
+   `rscript_sh[2]` is for the whole `Rscript ...` call.}
+
+ * Add `makeClusterSequential()` available for R (>= 4.4.0).
+
+ * Starting with R 4.5.0 (currently R-devel), one can use
+   `parallel::makeCluster(n, type = parallelly::PSOCK)` as an
+   alternative to `parallelly::makeClusterPSOCK(n)`.  Similarly, `type
+   = parallelly::MPI` creates a cluster using
+   `parallelly::makeClusterMPI()`, and `type = parallelly::SEQ`
+   creates a cluster using `parallelly::makeClusterSequential()`.
+
+ * Add `serializedSize()` for calculating the size of an object by
+   counting the number of bytes required to serialize it.
+ 
+## Bug Fixes
+
+ * Environment variable `R_PARALLELLY_MAXWORKERS_LOCALHOST` was
+   interpreted as integers rather than doubles.
+
+
 # Version 1.37.1 [2024-02-29]
 
 ## Bug Fixes
diff --git a/R/availableConnections.R b/R/availableConnections.R
index 118e64f1..1fed1173 100644
--- a/R/availableConnections.R
+++ b/R/availableConnections.R
@@ -19,7 +19,11 @@
 #' to a greater number via command-line option `--max-connections=N`, e.g.
 #'
 #' ```r
-#' $ R --max-connection=512
+#' $ Rscript -e "parallelly::availableConnections()"
+#' [1] 128
+#'
+#' $ Rscript --max-connections=512 -e "parallelly::availableConnections()"
+#' [1] 512
 #' ```
 #'
 #' For R (< 4.4.0), the limit can only be changed by rebuilding \R from
diff --git a/R/availableCores.R b/R/availableCores.R
index ca59d2af..64803c4d 100644
--- a/R/availableCores.R
+++ b/R/availableCores.R
@@ -603,7 +603,7 @@ checkNumberOfLocalWorkers <- function(workers) {
   if (length(ignore) > 0) {
     methods <- eval(formals(availableCores)$methods)
     methods <- setdiff(methods, ignore)
-        ncores <- availableCores(methods = methods)
+    ncores <- availableCores(methods = methods)
   } else {
     ncores <- availableCores()
   }
diff --git a/R/makeClusterMPI.R b/R/makeClusterMPI.R
index 7e0198c3..5ae0951f 100644
--- a/R/makeClusterMPI.R
+++ b/R/makeClusterMPI.R
@@ -21,6 +21,15 @@
 #' @return An object of class `c("RichMPIcluster", "MPIcluster", "cluster")` consisting
 #' of a list of `"MPInode"` workers.
 #'
+#' @section Alternative usage:
+#'
+#' In R (>= 4.4.0), an alternatively to using
+#' `cl <- parallelly::makeClusterMPI(workers)` is:
+#'
+#' ```
+#' cl <- parallel::makeCluster(workers, type = parallelly::MPI)
+#' ```
+#'
 #' @examples
 #' \donttest{\dontrun{
 #' if (requireNamespace("Rmpi") && requireNamespace("snow")) {
@@ -38,6 +47,7 @@
 #' @seealso
 #' [makeClusterPSOCK()] and [parallel::makeCluster()].
 #'
+#' @aliases MPI
 #' @importFrom parallel makeCluster
 #' @export
 makeClusterMPI <- function(workers, ..., autoStop = FALSE, verbose = getOption2("parallelly.debug", FALSE)) {
diff --git a/R/makeClusterPSOCK.R b/R/makeClusterPSOCK.R
index 852eda15..1f1e5ad4 100644
--- a/R/makeClusterPSOCK.R
+++ b/R/makeClusterPSOCK.R
@@ -54,8 +54,17 @@
 #' consisting of a list of `"SOCKnode"` or `"SOCK0node"` workers (that also
 #' inherit from `RichSOCKnode`).
 #'
+#' @section Alternative usage:
+#' In R (>= 4.4.0), an alternatively to using
+#' `cl <- parallelly::makeClusterPSOCK(workers)` is:
+#'
+#' ```
+#' cl <- parallel::makeCluster(workers, type = parallelly::PSOCK)
+#' ```
+#'
 #' @example incl/makeClusterPSOCK.R
 #'
+#' @aliases PSOCK
 #' @importFrom parallel stopCluster
 #' @export
 makeClusterPSOCK <- function(workers, makeNode = makeNodePSOCK, port = c("auto", "random"), ..., autoStop = FALSE, tries = getOption2("parallelly.makeNodePSOCK.tries", 3L), delay = getOption2("parallelly.makeNodePSOCK.tries.delay", 15.0), validate = getOption2("parallelly.makeNodePSOCK.validate", TRUE), verbose = getOption2("parallelly.debug", FALSE)) {
@@ -127,7 +136,7 @@ makeClusterPSOCK <- function(workers, makeNode = makeNodePSOCK, port = c("auto",
   nodeOptions <- vector("list", length = n)
   if (verbose) mdebugf("%sGetting setup options for %d cluster nodes ...", verbose_prefix, n)
   for (ii in seq_len(n)) {
-    if (verbose) mdebugf("%s - Node %d of %d ...", verbose_prefix, ii, n)
+    if (verbose) mdebugf("%s - Node #%d of %d ...", verbose_prefix, ii, n)
     options <- makeNode(workers[[ii]], port = port, ..., rank = ii, action = "options", verbose = verbose)
     stop_if_not(inherits(options, "makeNodePSOCKOptions"))
     nodeOptions[[ii]] <- options
@@ -165,7 +174,7 @@ makeClusterPSOCK <- function(workers, makeNode = makeNodePSOCK, port = c("auto",
     setup_strategy <- "sequential"
 
     for (ii in which(is_parallel)) {
-      if (verbose) mdebugf("%s - Node %d of %d ...", verbose_prefix, ii, n)
+      if (verbose) mdebugf("%s - Node #%d of %d ...", verbose_prefix, ii, n)
       args <- list(workers[[ii]], port = port, ..., rank = ii, action = "options", verbose = verbose)
       args$setup_strategy <- "sequential"
       options <- do.call(makeNode, args = args)
@@ -174,6 +183,8 @@ makeClusterPSOCK <- function(workers, makeNode = makeNodePSOCK, port = c("auto",
     }
   }
 
+  stopifnot(length(nodeOptions) == n)
+
   ## Sanity check
   setup_strategy <- lapply(nodeOptions, FUN = function(options) {
     value <- options$setup_strategy
@@ -181,12 +192,14 @@ makeClusterPSOCK <- function(workers, makeNode = makeNodePSOCK, port = c("auto",
     stop_if_not(is.character(value), length(value) == 1L)
     value
   })
+  stopifnot(length(setup_strategy) == n)
   setup_strategy <- unlist(setup_strategy, use.names = FALSE)
   setup_strategy <- unique(setup_strategy)
   stop_if_not(length(setup_strategy) == 1L)
 
   cl <- vector("list", length = length(nodeOptions))
   class(cl) <- c("RichSOCKcluster", "SOCKcluster", "cluster")
+  stopifnot(length(cl) == length(nodeOptions))
   
   ## If an error occurred, make sure to clean up before exiting, i.e.
   ## stop each node
@@ -318,7 +331,7 @@ makeClusterPSOCK <- function(workers, makeNode = makeNodePSOCK, port = c("auto",
     retryPort <- getOption2("parallelly.makeNodePSOCK.tries.port", "same")
     for (ii in seq_along(cl)) {
       if (verbose) {
-        mdebugf("%sCreating node %d of %d ...", verbose_prefix, ii, n)
+        mdebugf("%sCreating node #%d of %d ...", verbose_prefix, ii, n)
         mdebugf("%s- setting up node", verbose_prefix)
       }
 
@@ -363,36 +376,47 @@ makeClusterPSOCK <- function(workers, makeNode = makeNodePSOCK, port = c("auto",
         }
         stop(ex)
       }
-      cl[[ii]] <- node
+
+      ## 'node' is NULL if dryrun = TRUE
+      if (!is.null(node)) cl[[ii]] <- node
+      stopifnot(length(cl) == n)
   
       if (verbose) {
-        mdebugf("%sCreating node %d of %d ... done", verbose_prefix, ii, n)
+        mdebugf("%sCreating node #%d of %d ... done", verbose_prefix, ii, n)
       }
     }
   }
 
-  if (verbose) mdebugf("%sLaunching of workers completed", verbose_prefix)
+  if (verbose) {
+    mdebugf("%sLaunching of %d workers completed", verbose_prefix, n)
+    mdebugf("%sNumber of nodes in cluster: %d", verbose_prefix, length(cl))
+  }
 
   ## Cleanup
   try(close(socket), silent = TRUE)
   socket <- NULL
 
+  ## Sanity check
+  stopifnot(length(cl) == n)
+
   if (validate) {
     ## Attaching session information for each worker.  This is done to assert
     ## that we have a working cluster already here.  It will also collect
     ## useful information otherwise not available, e.g. the PID.
     if (verbose) {
-      mdebugf("%sCollecting session information from workers", verbose_prefix)
+      mdebugf("%sCollecting session information from %d workers", verbose_prefix, length(cl))
     }
     for (ii in seq_along(cl)) {
       cl[ii] <- add_cluster_session_info(cl[ii])
       if (verbose) mdebugf("%s - Worker #%d of %d", verbose_prefix, ii, length(cl))
     }
+    stopifnot(length(cl) == n)
   }
 
   if (autoStop) {
     if (verbose) mdebugf("%sAdding automatic stop of cluster on garbage collection", verbose_prefix)
     cl <- autoStopCluster(cl)
+    stopifnot(length(cl) == n)
   }
 
   if (verbose) {
@@ -400,6 +424,8 @@ makeClusterPSOCK <- function(workers, makeNode = makeNodePSOCK, port = c("auto",
     mdebugf("%smakeClusterPSOCK() ... done", verbose_prefix)
   }
 
+  stopifnot(length(cl) == n)
+
   ## Success, remove automatic cleanup of nodes
   on.exit()
 
diff --git a/R/makeClusterSequential.R b/R/makeClusterSequential.R
new file mode 100644
index 00000000..0d395def
--- /dev/null
+++ b/R/makeClusterSequential.R
@@ -0,0 +1,130 @@
+#' Create a "parallel" cluster running sequentially in the current session
+#'
+#' The created cluster has only one node.
+#'
+#' @examples
+#' \dontshow{if (getRversion() >= "4.4.0") \{}
+#' library(parallel)
+#' 
+#' cl <- makeClusterSequential()
+#' print(cl)
+#' 
+#' y <- parLapply(cl, X = 1:3, fun = sqrt)
+#' str(y)
+#' 
+#' pid <- Sys.getpid()
+#' print(pid)
+#' y <- clusterEvalQ(cl, Sys.getpid())
+#' str(y)
+#'
+#' abc <- 3.14
+#' y <- clusterEvalQ(cl, { abc <- 42; abc })
+#' str(y)
+#' stopifnot(abc == 3.14)
+#' 
+#' \dontshow{\}}
+#'
+#' @details
+#' Expression and function calls are evaluated in a local environment,
+#' inheriting the global environment.
+#'
+#' @section Requirements:
+#' This function is only defined for R (>= 4.4.0).
+#'
+#' @rawNamespace if (getRversion() >= "4.4") export(makeClusterSequential)
+#' @aliases SEQ
+makeClusterSequential <- function() {
+  node <- makeNodeSequential()
+  cl <- list(node)
+  class(cl) <- c("sequential_cluster", "cluster")
+  cl
+}
+
+#' @rawNamespace if (getRversion() >= "4.4") S3method(print,sequential_cluster)
+print.sequential_cluster <- function(x, ...) {
+  cat(sprintf("A %s cluster with %d node\n", sQuote(class(x)[1]), length(x)))
+}
+
+
+makeNodeSequential <- function() {
+  envir <- new.env(parent = globalenv())
+  envir[["...parallelly.valid..."]] <- TRUE
+  
+  node <- list(envir = envir)
+  class(node) <- c("sequential_node")
+  node
+}
+
+#' @rawNamespace if (getRversion() >= "4.4") S3method(print,sequential_node)
+print.sequential_node <- function(x, ...) {
+  cat(sprintf("A %s node\n", sQuote(class(x))))
+}
+
+
+#' @rawNamespace if (getRversion() >= "4.4") importFrom(parallel,sendData)
+#' @rawNamespace if (getRversion() >= "4.4") S3method(sendData,sequential_node)
+sendData.sequential_node <- function(node, data) {
+  envir <- node[["envir"]]
+
+  ## Has the cluster been stopped?
+  if (!isTRUE(envir[["...parallelly.valid..."]])) {
+    stop(sprintf("The %s node is no longer valid, which suggests the cluster it belongs to has been stopped", sQuote(class(node)[1])))
+  }
+  
+  type <- data[["type"]]
+  if (type == "EXEC") {
+    data <- data[["data"]]  ## sic!
+    fun <- data[["fun"]]
+    args <- data[["args"]]
+    ret <- data[["return"]]
+
+    ## Don't evaluate in the global environment, which is the default
+    if (identical(args[["envir"]], globalenv())) {
+      args[["envir"]] <- envir
+    }
+    
+    success <- TRUE
+    t1 <- proc.time()
+    value <- tryCatch({
+      do.call(fun, args = args, quote = TRUE, envir = envir)
+    }, error = function(e) {
+      success <<- FALSE
+      structure(conditionMessage(e), class = c("snow-try-error", "try-error"))
+    })
+    t2 <- proc.time()
+    
+    value <- list(
+      type = "VALUE",
+      value = value,
+      success = success, 
+      time = t2 - t1,
+      tag = data[["tag"]]
+    )
+
+    ## "Send" to internal buffer of current node
+    envir[["value"]] <- value
+  } else if (type == "DONE") {
+    ## Invalidate the local environment
+    envir[["...parallelly.valid..."]] <- FALSE
+  } else {
+    stop(sprintf("sendData(): type = %s not yet implemented", sQuote(type)))
+  }
+}
+
+
+#' @rawNamespace if (getRversion() >= "4.4") importFrom(parallel,recvData)
+#' @rawNamespace if (getRversion() >= "4.4") S3method(recvData,sequential_node)
+recvData.sequential_node <- function(node) {
+  envir <- node[["envir"]]
+
+  ## "Receive" from internal buffer of current node
+  value <- envir[["value"]]
+  if (is.null(value) || !is.list(value) || !identical(value[["type"]], "VALUE")) {
+    stop("INTERNAL ERROR: recvData() for sequential_node expected a value")
+  }
+
+  ## Erase node's buffer
+  envir[["value"]] <- NULL
+
+  value
+}
diff --git a/R/makeNodePSOCK.R b/R/makeNodePSOCK.R
index 0887e621..87db96ce 100644
--- a/R/makeNodePSOCK.R
+++ b/R/makeNodePSOCK.R
@@ -55,11 +55,19 @@
 #' launched via an MS Windows shell.  This controls how shell command-line
 #' options are quoted, via
 #' \code{\link[base:shQuote]{shQuote(..., type = rscript_sh)}}.
+#' If `"none"`, then no quoting is done.
 #' If `"auto"` (default), and the cluster node is launched locally, then it
 #' is set to `"sh"` or `"cmd"` according to the current platform.
 #' _If launched remotely_, then it is set to `"sh"` based on the assumption
 #' remote machines typically launch commands via SSH in a POSIX shell.
 #' If the remote machines run MS Windows, use `rscript_sh = "cmd"`.
+#' If `length(rscript_sh)` is two, then `rscript_sh[1]` is for the inner and
+#' `rscript_sh[2]` is for the outer shell quoting of the Rscript call.
+#' More precisely, `rscript_sh[1]` is for Rscript arguments that need shell
+#' quoting (e.g. `Rscript -e "<expr>"`), and `rscript_sh[2]` is for the whole
+#' `Rscript ...` call.
+#' If `length(rscript_sh)` is one, then it is used for both the inner and the
+#' outer shell quoting.
 #'
 #' @param default_packages A character vector or NULL that controls which R
 #' packages are attached on each cluster node during startup.  An asterisk
@@ -105,7 +113,7 @@
 #' 
 #' @param revtunnel If TRUE, a reverse SSH tunnel is set up for each worker such
 #' that the worker \R process sets up a socket connection to its local port
-#' `(port - rank + 1)` which then reaches the master on port `port`.
+#' `(port + rank - 1)` which then reaches the master on port `port`.
 #' If FALSE, then the worker will try to connect directly to port `port` on
 #' `master`.
 #' If NA, then TRUE or FALSE is inferred from inspection of `rshcmd[1]`.
@@ -369,7 +377,7 @@
 #' @importFrom tools pskill
 #' @importFrom utils flush.console
 #' @export
-makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "localhost"), master = NULL, port, connectTimeout = getOption2("parallelly.makeNodePSOCK.connectTimeout", 2 * 60), timeout = getOption2("parallelly.makeNodePSOCK.timeout", 30 * 24 * 60 * 60), rscript = NULL, homogeneous = NULL, rscript_args = NULL, rscript_envs = NULL, rscript_libs = NULL, rscript_startup = NULL, rscript_sh = c("auto", "cmd", "sh"), default_packages = c("datasets", "utils", "grDevices", "graphics", "stats", if (methods) "methods"), methods = TRUE, socketOptions = getOption2("parallelly.makeNodePSOCK.socketOptions", "no-delay"), useXDR = getOption2("parallelly.makeNodePSOCK.useXDR", FALSE), outfile = "/dev/null", renice = NA_integer_, rshcmd = getOption2("parallelly.makeNodePSOCK.rshcmd", NULL), user = NULL, revtunnel = NA, rshlogfile = NULL, rshopts = getOption2("parallelly.makeNodePSOCK.rshopts", NULL), rank = 1L, manual = FALSE, dryrun = FALSE, quiet = FALSE, setup_strategy = getOption2("parallelly.makeNodePSOCK.setup_strategy", "parallel"), action = c("launch", "options"), verbose = FALSE) {
+makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "localhost"), master = NULL, port, connectTimeout = getOption2("parallelly.makeNodePSOCK.connectTimeout", 2 * 60), timeout = getOption2("parallelly.makeNodePSOCK.timeout", 30 * 24 * 60 * 60), rscript = NULL, homogeneous = NULL, rscript_args = NULL, rscript_envs = NULL, rscript_libs = NULL, rscript_startup = NULL, rscript_sh = c("auto", "cmd", "sh", "none"), default_packages = c("datasets", "utils", "grDevices", "graphics", "stats", if (methods) "methods"), methods = TRUE, socketOptions = getOption2("parallelly.makeNodePSOCK.socketOptions", "no-delay"), useXDR = getOption2("parallelly.makeNodePSOCK.useXDR", FALSE), outfile = "/dev/null", renice = NA_integer_, rshcmd = getOption2("parallelly.makeNodePSOCK.rshcmd", NULL), user = NULL, revtunnel = NA, rshlogfile = NULL, rshopts = getOption2("parallelly.makeNodePSOCK.rshopts", NULL), rank = 1L, manual = FALSE, dryrun = FALSE, quiet = FALSE, setup_strategy = getOption2("parallelly.makeNodePSOCK.setup_strategy", "parallel"), action = c("launch", "options"), verbose = FALSE) {
   verbose <- as.logical(verbose)
   stop_if_not(length(verbose) == 1L, !is.na(verbose))
   verbose_prefix <- "[local output] "
@@ -378,6 +386,9 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
     return(launchNodePSOCK(options = worker, verbose = verbose))
   }
 
+  if (missing(rscript_sh)) rscript_sh <- rscript_sh[1]
+  rscript_sh <- match.arg(rscript_sh, several.ok = TRUE)
+  
   ## Record all the original arguments
   args_org <- list(
     worker = worker,
@@ -426,17 +437,24 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
     attr(worker, "localhost") <- localMachine
   }
 
-  stop_if_not(is.character(rscript_sh), length(rscript_sh) >= 1L, !anyNA(rscript_sh))
-  rscript_sh <- rscript_sh[1]  ## Use the first by default
-  if (rscript_sh == "auto") {
+  stop_if_not(is.character(rscript_sh), length(rscript_sh) >= 1L,
+              length(rscript_sh) <= 2L, !anyNA(rscript_sh))
+  is_auto <- (rscript_sh == "auto")
+  if (any(is_auto)) {
     if (localMachine) {
-      rscript_sh <- if (.Platform$OS.type == "windows") "cmd" else "sh"
+      rscript_sh[is_auto] <- if (.Platform$OS.type == "windows") "cmd" else "sh"
     } else {
       ## Assume remote machine uses as POSIX shell
-      rscript_sh <- "sh"
+     rscript_sh[is_auto] <- "sh"
     }
   }
 
+  ## rscript_sh[1] is for inner and rscript_sh[2] is for the outer shell
+  ## quoting of the Rscript call.  Precisely, rscript_sh[1] is for Rscript
+  ## arguments that need shell quoting (e.g. Rscript -e "<expr>"), and
+  ## rscript_sh[2] is for the the whole 'Rscript ...' call
+  rscript_sh <- rep(rscript_sh, length.out = 2L)
+  
   manual <- as.logical(manual)
   stop_if_not(length(manual) == 1L, !is.na(manual))
 
@@ -452,8 +470,23 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
   if (identical(rshcmd, "")) rshcmd <- NULL
   
   if (!is.null(rshcmd)) {
-    rshcmd <- as.character(rshcmd)
-    stop_if_not(length(rshcmd) >= 1L)
+    if (is.function(rshcmd)) {
+       args <- formals(rshcmd)
+       names <- names(args)
+       stop_if_not(length(args) >= 2)
+       if (!"rshopts" %in% names) {
+         stop("Argument 'rshcmd' specifies a function that does not have an `rshopts` argument: ", paste(sQuote(names), collapse = ", "))
+       } else if (!"worker" %in% names) {
+         stop("Argument 'rshcmd' specifies a function that does not have an `worker` argument: ", paste(sQuote(names), collapse = ", "))
+       }
+       type <- attr(rshcmd, "type")
+       if (is.null(type)) {
+         attr(rshcmd, "type") <- "function"
+       }
+    } else {
+       rshcmd <- as.character(rshcmd)
+       stop_if_not(length(rshcmd) >= 1L)
+    }
   }
 
   if (identical(rshopts, "")) rshopts <- NULL
@@ -466,7 +499,7 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
   assertPort(port)
 
   ## Find default SSH client?
-  if (!localMachine && (is.null(rshcmd) || all(grepl("^<[a-zA-Z-]+>$", rshcmd)))) {
+  if (!is.function(rshcmd) && !localMachine && (is.null(rshcmd) || all(grepl("^<[a-zA-Z-]+>$", rshcmd)))) {
     if (is.null(rshcmd)) {
       which <- NULL
       if (verbose) {
@@ -494,7 +527,7 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
     
     ## Holds a pathname with an optional set of command-line options
     stop_if_not(is.character(rshcmd), length(rshcmd) >= 1L)
-  } else if (!is.null(rshcmd)) {
+  } else if (!is.function(rshcmd) && !is.null(rshcmd)) {
     ## Try to guess "type" of 'rshcmd' from it's basename
     basename <- tolower(basename(rshcmd[1]))
     if (basename %in% c("ssh", "plink")) {
@@ -668,14 +701,14 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
   ## Shell quote the Rscript executable?
   if (!inherits(rscript, "AsIs")) {
     idxs <- grep("^[[:alpha:]_][[:alnum:]_]*=.*", rscript, invert = TRUE)
-    rscript[idxs] <- shQuote(rscript[idxs], type = rscript_sh)
+    rscript[idxs] <- shQuote(rscript[idxs], type = rscript_sh[1])
   }
 
   rscript_args_internal <- character(0L)
 
   ## Can we get the worker's PID during launch?
   if (localMachine && !dryrun) {
-    res <- useWorkerPID(rscript, rank = rank, rscript_sh = rscript_sh, verbose = verbose)
+    res <- useWorkerPID(rscript, rank = rank, rscript_sh = rscript_sh[1], verbose = verbose)
     pidfile <- res$pidfile
     rscript_args_internal <- c(res$rscript_pid_args, rscript_args_internal)
   } else {
@@ -690,7 +723,7 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
       if (is.na(script)) script <- "UNKNOWN"
       rscript_label <- sprintf("%s:%s:%s:%s", script, Sys.getpid(), Sys.info()[["nodename"]], Sys.info()[["user"]])
     }
-    rscript_args_internal <- c("-e", shQuote(paste0("#label=", rscript_label), type = rscript_sh), rscript_args_internal)
+    rscript_args_internal <- c("-e", shQuote(paste0("#label=", rscript_label), type = rscript_sh[1]), rscript_args_internal)
   }
 
   ## In contrast to default_packages=character(0), default_packages = NULL
@@ -706,7 +739,7 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
       arg <- sprintf("R_DEFAULT_PACKAGES=%s", pkgs)
 
       ## Is the cluster node launched in a MS Windows machine?
-      on_MSWindows <- (rscript_sh %in% c("cmd", "cmd2"))
+      on_MSWindows <- (rscript_sh[1] %in% c("cmd", "cmd2"))
       if (on_MSWindows) {
         ## On MS Windows, we have to use special '/path/to/R FOO=1 ...'
         rscript_args <- c(arg, rscript_args)
@@ -719,9 +752,9 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
 
   ## Port that the Rscript should use to connect back to the master
   if (!localMachine && revtunnel && getOption2("parallelly.makeNodePSOCK.port.increment", TRUE)) {
-    rscript_port <- assertPort(port + (rank - 1L))
+    rscript_port <- assertPort(port + rank - 1L)
     if (verbose) {
-      mdebugf("%sRscript port: %d + %d = %d\n", verbose_prefix, port, rank-1L, rscript_port)
+      mdebugf("%sRscript port: %d + %d = %d\n", verbose_prefix, port, rank - 1L, rscript_port)
     }
   } else {
     rscript_port <- port
@@ -732,13 +765,13 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
 
   if (length(socketOptions) == 1L) {
     code <- sprintf("options(socketOptions = \"%s\")", socketOptions)
-    rscript_expr <- c("-e", shQuote(code, type = rscript_sh))
+    rscript_expr <- c("-e", shQuote(code, type = rscript_sh[1]))
     rscript_args_internal <- c(rscript_args_internal, rscript_expr)
   }
 
   if (length(rscript_startup) > 0L) {
     rscript_startup <- paste("invisible({", rscript_startup, "})", sep = "")
-    rscript_startup <- shQuote(rscript_startup, type = rscript_sh)
+    rscript_startup <- shQuote(rscript_startup, type = rscript_sh[1])
     rscript_startup <- lapply(rscript_startup, FUN = function(value) c("-e", value))
     rscript_startup <- unlist(rscript_startup, use.names = FALSE)
     rscript_args_internal <- c(rscript_args_internal, rscript_startup)
@@ -784,7 +817,7 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
       }, error = function(ex) {
         stopf("Argument 'rscript_envs' appears to contain invalid values: %s", paste(sprintf("%s", sQuote(names)), collapse = ", "))
       })
-      rscript_args_internal <- c(rscript_args_internal, "-e", shQuote(code, type = rscript_sh))
+      rscript_args_internal <- c(rscript_args_internal, "-e", shQuote(code, type = rscript_sh[1]))
       rscript_envs <- rscript_envs[-unset]
       names <- names(rscript_envs)
     }
@@ -799,7 +832,7 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
       }, error = function(ex) {
         stopf("Argument 'rscript_envs' appears to contain invalid values: %s", paste(sprintf("%s=%s", sQuote(names), sQuote(rscript_envs)), collapse = ", "))
       })
-      rscript_args_internal <- c(rscript_args_internal, "-e", shQuote(code, type = rscript_sh))
+      rscript_args_internal <- c(rscript_args_internal, "-e", shQuote(code, type = rscript_sh[1]))
     }
   }
 
@@ -815,14 +848,14 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
     }, error = function(ex) {
       stopf("Argument 'rscript_libs' appears to contain invalid values: %s", paste(sQuote(rscript_libs), collapse = ", "))
     })
-    rscript_args_internal <- c(rscript_args_internal, "-e", shQuote(code, type = rscript_sh))
+    rscript_args_internal <- c(rscript_args_internal, "-e", shQuote(code, type = rscript_sh[1]))
   }
   
   ## .{slave,work}RSOCK() command already specified?
   if (!any(grepl("parallel:::[.](slave|work)RSOCK[(][)]", rscript_args))) {
     ## In R (>= 4.1.0), parallel:::.slaveRSOCK() was renamed to .workRSOCK()
     cmd <- "workRSOCK <- tryCatch(parallel:::.workRSOCK, error=function(e) parallel:::.slaveRSOCK); workRSOCK()"
-    rscript_args_internal <- c(rscript_args_internal, "-e", shQuote(cmd, type = rscript_sh))
+    rscript_args_internal <- c(rscript_args_internal, "-e", shQuote(cmd, type = rscript_sh[1]))
   }
 
   ## Append or inject rscript_args_internal?
@@ -858,11 +891,15 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
 
   if (!localMachine) {
     ## Must hold a pathname with an optional set of command-line options
-    stop_if_not(is.character(rshcmd), length(rshcmd) >= 1L)
+    stop_if_not(is.function(rshcmd) || is.character(rshcmd), length(rshcmd) >= 1L)
 
     ## Create label
     s <- sprintf("type=%s, version=%s", sQuote(attr(rshcmd, "type")), sQuote(attr(rshcmd, "version")))
-    rshcmd_label <- sprintf("%s [%s]", paste(sQuote(rshcmd), collapse = ", "), s)
+    if (is.function(rshcmd)) {
+      rshcmd_label <- sprintf("%s [%s]", paste(sQuote("rshcmd-function"), collapse = ", "), s)
+    } else {
+      rshcmd_label <- sprintf("%s [%s]", paste(sQuote(rshcmd), collapse = ", "), s)
+    }
     if (verbose) mdebugf("%sUsing 'rshcmd': %s", verbose_prefix, rshcmd_label)
     
     ## User?
@@ -890,10 +927,14 @@ makeNodePSOCK <- function(worker = getOption2("parallelly.localhost.hostname", "
     }
     
     rshopts <- paste(rshopts, collapse = " ")
-    
+
     ## Local commands
-    rsh_call <- paste(paste(shQuote(rshcmd), collapse = " "), rshopts, worker)
-    local_cmd <- paste(rsh_call, shQuote(cmd, type = rscript_sh))
+    if (is.function(rshcmd)) {
+      rsh_call <- rshcmd(rshopts = rshopts, worker = worker)
+    } else {
+      rsh_call <- paste(paste(shQuote(rshcmd), collapse = " "), rshopts, worker)
+    }
+    local_cmd <- paste(rsh_call, shQuote(cmd, type = rscript_sh[2]))
   } else {
     rshcmd_label <- NULL
     rsh_call <- NULL
diff --git a/R/options.R b/R/options.R
index ee11350c..203c6690 100644
--- a/R/options.R
+++ b/R/options.R
@@ -113,10 +113,10 @@
 #' All of the above \R `parallelly.*` options can be set by
 #' corresponding environment variables \env{R_PARALLELLY_*} _when the
 #' \pkg{parallelly} package is loaded_.
-#' For example, if `R_PARALLELLY_MAKENODEPSOCK_SETUP_STRATEGY = "sequential"`,
+#' For example, if `R_PARALLELLY_MAKENODEPSOCK_SETUP_STRATEGY="sequential"`,
 #' then option `parallelly.makeNodePSOCK.setup_strategy` is set to
 #' `"sequential"` (character).
-#' Similarly, if `R_PARALLELLY_AVAILABLECORES_FALLBACK = "1"`, then option
+#' Similarly, if `R_PARALLELLY_AVAILABLECORES_FALLBACK="1"`, then option
 #' `parallelly.availableCores.fallback` is set to `1` (integer).
 #'
 #'
@@ -140,6 +140,7 @@
 #' parallelly.availableWorkers.methods
 #' parallelly.availableWorkers.custom
 #' parallelly.fork.enable
+#' parallelly.maxWorkers.localhost
 #' parallelly.supportsMulticore.disableOn
 #' parallelly.supportsMulticore.unstable
 #' R_PARALLELLY_AVAILABLECORES_FALLBACK
@@ -310,7 +311,7 @@ update_package_options <- function(debug = FALSE) {
 
   update_package_option("availableWorkers.methods", mode = "character", split = ",", debug = debug)
 
-  update_package_option("maxWorkers.localhost", mode = "integer", split = ",", debug = debug)
+  update_package_option("maxWorkers.localhost", mode = "double", split = ",", debug = debug)
   update_package_option("maxWorkers.localhost.ignore", mode = "character", split = ",", debug = debug)
 
   update_package_option("fork.enable", mode = "logical", debug = debug)
diff --git a/R/registerClusterTypes.R b/R/registerClusterTypes.R
new file mode 100644
index 00000000..2398bf1c
--- /dev/null
+++ b/R/registerClusterTypes.R
@@ -0,0 +1,35 @@
+## Register makeClusterMPI() and makeClusterPSOCK() as a cluster types
+## such that they can be created using parallel::makeCluster(), e.g.
+## cl <- parallel::makeCluster(..., type = parallelly::PSOCK)
+
+#' @rawNamespace export(MPI)
+MPI   <- "parallelly::MPI"
+
+#' @rawNamespace export(PSOCK)
+PSOCK <- "parallelly::PSOCK"
+ 
+#' @rawNamespace if (getRversion() >= "4.4") export(SEQ)
+SEQ <- "parallelly::SEQ"
+
+registerClusterTypes <- local({
+  done <- FALSE
+  
+  function() {
+    if (done) return()
+    
+    ns <- getNamespace("parallel")
+    ## Only available in R (>= 4.5.0)
+    if (!exists("registerClusterType", envir = ns)) return()
+    
+    registerClusterType <- get("registerClusterType", envir = ns)
+
+    ## WORKAROUND: 'R CMD build' somehow creates and calls this function
+    ## twice, resulting in warnings from parallel::registerClusterType().
+    suppressWarnings({
+      registerClusterType(MPI,   makeClusterMPI,        make.default = FALSE)
+      registerClusterType(PSOCK, makeClusterPSOCK,      make.default = FALSE)
+      registerClusterType(SEQ,   makeClusterSequential, make.default = FALSE)
+    })
+    done <<- TRUE
+  }
+})
diff --git a/R/serializedSize.R b/R/serializedSize.R
new file mode 100644
index 00000000..291f28d8
--- /dev/null
+++ b/R/serializedSize.R
@@ -0,0 +1,19 @@
+#' Calculate the size of an R object when it is serialized
+#'
+#' This function goes through all the motions of serializing an object, but
+#' does nothing with the bytes other than to tally the total length.
+#'
+#' @param obj An R object.
+#'
+#' @return (integer or double) Number of bytes needed to serialize this object.
+#'
+#' @examples
+#' object.size(mtcars)
+#' serializedSize(mtcars)
+#'
+#' @author Mike FC
+#' 
+#' @export
+serializedSize <- function(obj) {
+  .Call(C_R_calc_serialized_size, obj)
+}
diff --git a/R/utils,cluster.R b/R/utils,cluster.R
index e160c915..9ee8d518 100644
--- a/R/utils,cluster.R
+++ b/R/utils,cluster.R
@@ -368,3 +368,18 @@ readWorkerPID <- function(pidfile, wait = 0.5, maxTries = 8L, verbose = FALSE) {
   
   pid
 } ## readWorkerPID()
+
+
+# shQuote() that also accepts type = "none"
+shQuote <- local({
+  known_types <- eval(formals(base::shQuote)[["type"]])
+  known_types <- c(known_types, "none")
+  
+  function(string, type = NULL) {
+    if (is.null(type)) type <- known_types
+    type <- match.arg(type, choices = known_types, several.ok = FALSE)
+    if (type == "none") return(string)
+    base::shQuote(string, type = type)
+  }
+})
+
diff --git a/R/zzz.R b/R/zzz.R
index 8c485db7..6a338620 100644
--- a/R/zzz.R
+++ b/R/zzz.R
@@ -1,3 +1,5 @@
+.packageExclude <- c("MPI", "PSOCK")
+
 ## covr: skip=all
 .onLoad <- function(libname, pkgname) {
   debug <- isTRUE(as.logical(getEnvVar2("R_PARALLELLY_DEBUG", "FALSE")))
@@ -56,6 +58,8 @@
     envs <- sprintf("- %s=%s", names(envs), sQuote(envs))
     mdebug(paste(c("parallelly-specific environment variables:", envs), collapse = "\n"))
   }
+
+  registerClusterTypes()
 }
 
 
diff --git a/cran-comments.md b/cran-comments.md
index bce9f2fc..f5204578 100644
--- a/cran-comments.md
+++ b/cran-comments.md
@@ -1,8 +1,8 @@
-# CRAN submission parallelly 1.37.0
+# CRAN submission parallelly 1.38.0
 
-on 2024-02-14
+on 2024-07-27
 
-I've verified this submission has no negative impact on any of the 42 reverse package dependencies available on CRAN (n = 27) and Bioconductor (n = 4), as well as none of the 551 second-level of reverse dependencies on CRAN and Bioconductor.
+I've verified this submission has no negative impact on any of the 55 reverse package dependencies available on CRAN (n = 48) and Bioconductor (n = 7).
 
 Thank you
 
@@ -13,76 +13,12 @@ Thank you
 
 The package has been verified using `R CMD check --as-cran` on:
 
-| R version | GitHub | R-hub | mac/win-builder |
-| --------- | ------ | ----- | --------------- |
-| 3.5.x     | L      |       |                 |
-| 4.0.x     | L      |       |                 |
-| 4.1.x     | L      |       |                 |
-| 4.2.x     | L M  W | L   W |                 |
-| 4.3.x     | L M  W | L   W | M1 W            |
-| devel     | L M1 W | L     |    W            |
+| R version | GitHub | mac/win-builder |
+| --------- | ------ | --------------- |
+| 3.5.x     | L      |                 |
+| 4.2.x     | L      |                 |
+| 4.3.x     | L M  W |                 |
+| 4.4.x     | L M  W | M1 W            |
+| devel     | L M1 W |    W            |
 
 _Legend: OS: L = Linux, M = macOS, M1 = macOS M1, W = Windows_
-
-
-R-hub checks:
-
-```r
-res <- rhub::check(platforms = c(
-  "debian-clang-devel", 
-  "fedora-gcc-devel",
-  "debian-gcc-patched", 
-  "linux-x86_64-rocker-gcc-san",
-  "windows-x86_64-release"
-))
-print(res)
-```
-
-gives
-
-```
-── parallelly 1.37.0: OK
-
-  Build ID:   parallelly_1.37.0.tar.gz-89fbf83779704ccb93e2033a8410f90e
-  Platform:   Debian Linux, R-devel, clang, ISO-8859-15 locale
-  Submitted:  24m 1.9s ago
-  Build time: 10m 4.7s
-
-0 errors ✔ | 0 warnings ✔ | 0 notes ✔
-
-── parallelly 1.37.0: OK
-
-  Build ID:   parallelly_1.37.0.tar.gz-ddd1b2a9c902401d926d62975fd9a52e
-  Platform:   Fedora Linux, R-devel, GCC
-  Submitted:  24m 1.9s ago
-  Build time: 7m 2.9s
-
-0 errors ✔ | 0 warnings ✔ | 0 notes ✔
-
-── parallelly 1.37.0: OK
-
-  Build ID:   parallelly_1.37.0.tar.gz-fcf783d93b984738afe9c1369706a196
-  Platform:   Debian Linux, R-patched, GCC
-  Submitted:  24m 2s ago
-  Build time: 9m 35.9s
-
-0 errors ✔ | 0 warnings ✔ | 0 notes ✔
-
-── parallelly 1.37.0: OK
-
-  Build ID:   parallelly_1.37.0.tar.gz-2f3465f5d0c2400c91045cef9111c81c
-  Platform:   Debian Linux, R-devel, GCC ASAN/UBSAN
-  Submitted:  24m 2s ago
-  Build time: 6m 57.7s
-
-0 errors ✔ | 0 warnings ✔ | 0 notes ✔
-
-── parallelly 1.37.0: OK
-
-  Build ID:   parallelly_1.37.0.tar.gz-137a6008af8646db9b2ff7ac97182790
-  Platform:   Windows Server 2022, R-release, 32/64 bit
-  Submitted:  24m 2s ago
-  Build time: 3m 50.5s
-
-0 errors ✔ | 0 warnings ✔ | 0 notes ✔
-```
diff --git a/incl/makeClusterPSOCK,Slurm.R b/incl/makeClusterPSOCK,Slurm.R
new file mode 100644
index 00000000..4983de8a
--- /dev/null
+++ b/incl/makeClusterPSOCK,Slurm.R
@@ -0,0 +1,35 @@
+## EXAMPLE: 'Slurm' is a high-performance compute (HPC) job scheduler 
+## where one can request compute resources on multiple nodes, each
+## running multiple cores. Here is an example:
+##
+##   ## Request 18 slots on one or more hosts
+##   sbatch --ntasks=18 script.sh
+##
+## This will launch the job script 'script.sh' on one host, while have
+## reserved in total 18 slots (CPU cores) on this host and possible
+## another hosts.
+##
+## This example shows how to use the Slurm command 'srun' to launch
+## 18 parallel workers from R, which is assumed to have been launched
+## by 'script.sh'. The `srun` command does not take a hostname; instead
+## it will automatically launch the work on the next allotted host.
+## The number of workers we want to launch can be inferred from
+## length(availableWorkers()). We will use a dummy hostname for the
+## workers to avoid them being interpreted as a localhost worker.
+##
+## The parallel workers are launched as:
+## 'srun' --ntasks=1 ...
+## 'srun' --ntasks=1 ...
+## ...
+## 'srun' --ntasks=1 ...
+workers <- sub(".*", "<dummy>", availableWorkers())
+
+workers <- c("<dummy>")
+rshcmd_fcn <- function(rshopts, worker) paste(shQuote("srun"), rshopts)
+cl <- makeClusterPSOCK(
+  workers,
+  rshcmd = rshcmd_fcn, rshopts = c("--nodes=1", "--ntasks=1"),
+  rscript_sh = c("auto", "none"),
+  verbose = TRUE,
+  dryrun = TRUE, quiet = FALSE
+)
diff --git a/incl/makeClusterPSOCK.R b/incl/makeClusterPSOCK.R
index a1f37528..749ff32d 100644
--- a/incl/makeClusterPSOCK.R
+++ b/incl/makeClusterPSOCK.R
@@ -13,6 +13,10 @@ cl <- makeClusterPSOCK(workers, dryrun = TRUE, quiet = TRUE)
 ## running on CPU Group #0 and half on CPU Group #1.  
 ## (https://lovickconsulting.com/2021/11/18/
 ##  running-r-clusters-on-an-amd-threadripper-3990x-in-windows-10-2/)
+## The parallel workers are launched as:
+## "%COMSPEC%" /c start /B /NODE 1 /AFFINITY 0xFFFFFFFFFFFFFFFE ...
+## ...
+## "%COMSPEC%" /c start /B /NODE 1 /AFFINITY 0xFFFFFFFFFFFFFFFE ...
 
 ## Temporarily disable CPU load protection for this example
 oopts <- options(parallelly.maxWorkers.localhost = Inf)
@@ -41,6 +45,10 @@ options(oopts)
 ## ---------------------------------------------------------------
 ## EXAMPLE: Three remote workers
 ## Setup of three R workers on two remote machines are set up
+## The parallel workers are launched as:
+## '/usr/bin/ssh' -R 11058:localhost:11058 n1.remote.org ...
+## '/usr/bin/ssh' -R 11059:localhost:11058 n2.remote.org ...
+## '/usr/bin/ssh' -R 11060:localhost:11058 n1.remote.org ...
 workers <- c("n1.remote.org", "n2.remote.org", "n1.remote.org")
 cl <- makeClusterPSOCK(workers, dryrun = TRUE, quiet = TRUE)
 
@@ -48,6 +56,9 @@ cl <- makeClusterPSOCK(workers, dryrun = TRUE, quiet = TRUE)
 ## EXAMPLE: Two remote workers running on MS Windows.  Because the
 ## remote workers are MS Windows machines, we need to use
 ## rscript_sh = "cmd".
+## The parallel workers are launched as:
+## '/usr/bin/ssh' -R 11912:localhost:11912 mswin1.remote.org ...
+## '/usr/bin/ssh' -R 11913:localhost:11912 mswin2.remote.org ...
 workers <- c("mswin1.remote.org", "mswin2.remote.org")
 cl <- makeClusterPSOCK(workers, rscript_sh = "cmd", dryrun = TRUE, quiet = TRUE)
 
@@ -64,6 +75,10 @@ cl <- makeClusterPSOCK(
 
 ## EXAMPLE: Three remote workers 'n1', 'n2', and 'n3' that can only be
 ## accessed via jumphost 'login.remote.org'
+## The parallel workers are launched as:
+## '/usr/bin/ssh' -R 11226:localhost:11226 -J login.remote.org n1 ...
+## '/usr/bin/ssh' -R 11227:localhost:11226 -J login.remote.org n2 ...
+## '/usr/bin/ssh' -R 11228:localhost:11226 -J login.remote.org n1 ...
 workers <- c("n1", "n2", "n1")
 cl <- makeClusterPSOCK(
   workers,
@@ -79,6 +94,8 @@ cl <- makeClusterPSOCK(
 ## Using the explicit special rshcmd = "<putty-plink>", will force
 ## makeClusterPSOCK() to search for and use the PuTTY plink software,
 ## preventing it from using other SSH clients on the system search PATH.
+## The parallel worker is launched as:
+## 'plink' -l bob -P 2200 -i C:/Users/bobby/.ssh/putty.ppk remote.server.org ...
 cl <- makeClusterPSOCK(
   "remote.server.org", user = "bob",
   rshcmd = "<putty-plink>",
@@ -90,6 +107,9 @@ cl <- makeClusterPSOCK(
 ## EXAMPLE: Remote workers with specific setup
 ## Setup of remote worker with more detailed control on
 ## authentication and reverse SSH tunneling
+## The parallel worker is launched as:
+## '/usr/bin/ssh' -l johnny -v -R 11000:gateway:11942 remote.server.org ...
+## "R_DEFAULT_PACKAGES=... 'nice' '/path/to/Rscript' --no-init-file ...
 cl <- makeClusterPSOCK(
   "remote.server.org", user = "johnny",
   ## Manual configuration of reverse SSH tunneling
@@ -109,6 +129,8 @@ cl <- makeClusterPSOCK(
 ## Using the explicit special rshcmd = "<rstudio-ssh>", will force
 ## makeClusterPSOCK() to use the SSH client that comes with RStudio,
 ## preventing it from using other SSH clients on the system search PATH.
+## The parallel worker is launched as:
+## 'ssh' -l bob remote.server.org:2200 ...
 cl <- makeClusterPSOCK(
   "remote.server.org:2200", user = "bob", rshcmd = "<rstudio-ssh>",
   dryrun = TRUE, quiet = TRUE
@@ -139,6 +161,12 @@ cl <- makeClusterPSOCK(
 ## This example shows how to use the SGE command 'qrsh' to launch
 ## 18 parallel workers from R, which is assumed to have been launched
 ## by 'script.sh'.
+##
+## The parallel workers are launched as:
+## 'qrsh' -inherit -nostdin -V comphost01 ...
+## 'qrsh' -inherit -nostdin -V comphost01 ...
+## ...
+## 'qrsh' -inherit -nostdin -V comphost06 ...
 cl <- makeClusterPSOCK(
   availableWorkers(),
   rshcmd = "qrsh", rshopts = c("-inherit", "-nostdin", "-V"),
@@ -157,6 +185,12 @@ cl <- makeClusterPSOCK(
 ## availableWorkers() to return 3 * 18 workers. When the HPC environment
 ## does not support SSH between compute nodes, one can use the 'pjrsh'
 ## command to launch the parallel workers.
+##
+## The parallel workers are launched as:
+## 'pjrsh' comphost01 ...
+## 'pjrsh' comphost01 ...
+## ...
+## 'pjrsh' comphost06 ...
 cl <- makeClusterPSOCK(
   availableWorkers(),
   rshcmd = "pjrsh",
@@ -172,6 +206,11 @@ cl <- makeClusterPSOCK(
 ## Launching worker on Amazon AWS EC2 running one of the
 ## Amazon Machine Images (AMI) provided by RStudio
 ## (https://www.louisaslett.com/RStudio_AMI/)
+##
+## The parallel worker is launched as:
+## '/usr/bin/ssh' -R 11153:localhost:11153 -l ubuntu ...
+## -o StrictHostKeyChecking=no -o IdentitiesOnly=yes ...
+## -i ~/.ssh/my-private-aws-key.pem 1.2.3.4 ...
 public_ip <- "1.2.3.4"
 ssh_private_key_file <- "~/.ssh/my-private-aws-key.pem"
 cl <- makeClusterPSOCK(
@@ -230,6 +269,10 @@ cl <- makeClusterPSOCK(
 ## ---------------------------------------------------------------
 ## EXAMPLE: Two workers running in Docker on the local machine
 ## Setup of 2 Docker workers running rocker/r-parallel
+##
+## The parallel workers are launched as:
+## R_DEFAULT_PACKAGES=... '/usr/bin/docker' 'run' '--net=host' 'rocker/r-parallel' ...
+## R_DEFAULT_PACKAGES=... '/usr/bin/docker' 'run' '--net=host' 'rocker/r-parallel' ...
 cl <- makeClusterPSOCK(
   rep("localhost", times = 2L),
   ## Launch Rscript inside Docker container
@@ -249,6 +292,10 @@ cl <- makeClusterPSOCK(
 
 ## EXAMPLE: Two workers running via Linux container 'rocker/r-parallel' from
 ## DockerHub on the local machine using Apptainer (formerly Singularity)
+##
+## The parallel workers are launched as:
+## R_DEFAULT_PACKAGES=... '/usr/bin/apptainer' 'exec' 'docker://rocker/r-parallel' ...
+## R_DEFAULT_PACKAGES=... '/usr/bin/apptainer' 'exec' 'docker://rocker/r-parallel' ...
 cl <- makeClusterPSOCK(
   rep("localhost", times = 2L),
   ## Launch Rscript inside Linux container
@@ -262,6 +309,9 @@ cl <- makeClusterPSOCK(
 
 ## EXAMPLE: One worker running in udocker on the local machine
 ## Setup of a single udocker.py worker running rocker/r-parallel
+##
+## The parallel worker is launched as:
+## R_DEFAULT_PACKAGES=... 'udocker.py' 'run' 'rocker/r-parallel' ...
 cl <- makeClusterPSOCK(
   "localhost",
   ## Launch Rscript inside Docker container (using udocker)
@@ -281,12 +331,15 @@ cl <- makeClusterPSOCK(
 ## EXAMPLE: One worker running in Wine for Linux on the local machine
 ## To install R for MS Windows in Wine, do something like:
 ##   winecfg  # In GUI, set 'Windows version' to 'Windows 10'
-##   wget https://cran.r-project.org/bin/windows/base/R-4.2.3-win.exe
-##   wine R-4.2.3-win.exe /SILENT
+##   wget https://cran.r-project.org/bin/windows/base/R-4.4.1-win.exe
+##   wine R-4.4.1-win.exe /SILENT
 ## Prevent packages from being installed to R's system library:
-##   chmod ugo-w "$HOME/.wine/drive_c/Program Files/R/R-4.2.3/library/"
+##   chmod ugo-w "$HOME/.wine/drive_c/Program Files/R/R-4.4.1/library/"
 ## Verify it works:
-##   wine "C:/Program Files/R/R-4.2.3/bin/x64/Rscript.exe" --version
+##   wine "C:/Program Files/R/R-4.4.1/bin/x64/Rscript.exe" --version
+##
+## The parallel worker is launched as:
+## R_DEFAULT_PACKAGES=... WINEDEBUG=fixme-all R_LIBS_SITE= R_LIBS_USER= 'wine' ...
 cl <- makeClusterPSOCK(1L,
   rscript = c(
     ## Silence Wine warnings
@@ -294,7 +347,7 @@ cl <- makeClusterPSOCK(1L,
     ## Don't pass LC_* and R_LIBS* environments from host to Wine
     sprintf("%s=", grep("^(LC_|R_LIBS)", names(Sys.getenv()), value = TRUE)),
     "wine",
-    "C:/Program Files/R/R-4.2.3/bin/x64/Rscript.exe"
+    "C:/Program Files/R/R-4.4.1/bin/x64/Rscript.exe"
   ),
   dryrun = TRUE, quiet = TRUE
 )
diff --git a/man/availableConnections.Rd b/man/availableConnections.Rd
index 2be7905d..9bdd7e25 100644
--- a/man/availableConnections.Rd
+++ b/man/availableConnections.Rd
@@ -29,7 +29,11 @@ standard output via text connections (e.g. \code{\link[utils:capture.output]{uti
 In R (>= 4.4.0), it is possible to \emph{increase} the limit of 128 connections
 to a greater number via command-line option \code{--max-connections=N}, e.g.
 
-\if{html}{\out{<div class="sourceCode r">}}\preformatted{$ R --max-connection=512
+\if{html}{\out{<div class="sourceCode r">}}\preformatted{$ Rscript -e "parallelly::availableConnections()"
+[1] 128
+
+$ Rscript --max-connections=512 -e "parallelly::availableConnections()"
+[1] 512
 }\if{html}{\out{</div>}}
 
 For R (< 4.4.0), the limit can only be changed by rebuilding \R from
diff --git a/man/makeClusterMPI.Rd b/man/makeClusterMPI.Rd
index 40832a3d..47e3f3b3 100644
--- a/man/makeClusterMPI.Rd
+++ b/man/makeClusterMPI.Rd
@@ -2,6 +2,7 @@
 % Please edit documentation in R/makeClusterMPI.R
 \name{makeClusterMPI}
 \alias{makeClusterMPI}
+\alias{MPI}
 \title{Create a Message Passing Interface (MPI) Cluster of R Workers for Parallel Processing}
 \usage{
 makeClusterMPI(
@@ -40,6 +41,16 @@ only be used if \code{parallel::makeCluster(..., type = "MPI")} fails.}
 \emph{Creating MPI clusters requires that the \pkg{Rmpi} and \pkg{snow}
 packages are installed.}
 }
+\section{Alternative usage}{
+
+
+In R (>= 4.4.0), an alternatively to using
+\code{cl <- parallelly::makeClusterMPI(workers)} is:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{cl <- parallel::makeCluster(workers, type = parallelly::MPI)
+}\if{html}{\out{</div>}}
+}
+
 \examples{
 \donttest{\dontrun{
 if (requireNamespace("Rmpi") && requireNamespace("snow")) {
diff --git a/man/makeClusterPSOCK.Rd b/man/makeClusterPSOCK.Rd
index cdae6940..e944a4c3 100644
--- a/man/makeClusterPSOCK.Rd
+++ b/man/makeClusterPSOCK.Rd
@@ -4,6 +4,7 @@
 \name{checkNumberOfLocalWorkers}
 \alias{checkNumberOfLocalWorkers}
 \alias{makeClusterPSOCK}
+\alias{PSOCK}
 \alias{makeNodePSOCK}
 \title{Create a PSOCK Cluster of R Workers for Parallel Processing}
 \usage{
@@ -33,7 +34,7 @@ makeNodePSOCK(
   rscript_envs = NULL,
   rscript_libs = NULL,
   rscript_startup = NULL,
-  rscript_sh = c("auto", "cmd", "sh"),
+  rscript_sh = c("auto", "cmd", "sh", "none"),
   default_packages = c("datasets", "utils", "grDevices", "graphics", "stats", if
     (methods) "methods"),
   methods = TRUE,
@@ -153,11 +154,19 @@ which should be \code{"sh"} is launched via a POSIX shell and \code{"cmd"} if
 launched via an MS Windows shell.  This controls how shell command-line
 options are quoted, via
 \code{\link[base:shQuote]{shQuote(..., type = rscript_sh)}}.
+If \code{"none"}, then no quoting is done.
 If \code{"auto"} (default), and the cluster node is launched locally, then it
 is set to \code{"sh"} or \code{"cmd"} according to the current platform.
 \emph{If launched remotely}, then it is set to \code{"sh"} based on the assumption
 remote machines typically launch commands via SSH in a POSIX shell.
-If the remote machines run MS Windows, use \code{rscript_sh = "cmd"}.}
+If the remote machines run MS Windows, use \code{rscript_sh = "cmd"}.
+If \code{length(rscript_sh)} is two, then \code{rscript_sh[1]} is for the inner and
+\code{rscript_sh[2]} is for the outer shell quoting of the Rscript call.
+More precisely, \code{rscript_sh[1]} is for Rscript arguments that need shell
+quoting (e.g. \verb{Rscript -e "<expr>"}), and \code{rscript_sh[2]} is for the whole
+\verb{Rscript ...} call.
+If \code{length(rscript_sh)} is one, then it is used for both the inner and the
+outer shell quoting.}
 
 \item{default_packages}{A character vector or NULL that controls which R
 packages are attached on each cluster node during startup.  An asterisk
@@ -192,7 +201,7 @@ another host.}
 
 \item{revtunnel}{If TRUE, a reverse SSH tunnel is set up for each worker such
 that the worker \R process sets up a socket connection to its local port
-\code{(port - rank + 1)} which then reaches the master on port \code{port}.
+\code{(port + rank - 1)} which then reaches the master on port \code{port}.
 If FALSE, then the worker will try to connect directly to port \code{port} on
 \code{master}.
 If NA, then TRUE or FALSE is inferred from inspection of \code{rshcmd[1]}.
@@ -297,6 +306,15 @@ override this threshold
 See \link{parallelly.options} for how to change the default thresholds.
 }
 
+\section{Alternative usage}{
+
+In R (>= 4.4.0), an alternatively to using
+\code{cl <- parallelly::makeClusterPSOCK(workers)} is:
+
+\if{html}{\out{<div class="sourceCode">}}\preformatted{cl <- parallel::makeCluster(workers, type = parallelly::PSOCK)
+}\if{html}{\out{</div>}}
+}
+
 \section{Definition of \emph{localhost}}{
 
 A hostname is considered to be \emph{localhost} if it equals:
@@ -599,6 +617,10 @@ cl <- makeClusterPSOCK(workers, dryrun = TRUE, quiet = TRUE)
 ## running on CPU Group #0 and half on CPU Group #1.  
 ## (https://lovickconsulting.com/2021/11/18/
 ##  running-r-clusters-on-an-amd-threadripper-3990x-in-windows-10-2/)
+## The parallel workers are launched as:
+## "\%COMSPEC\%" /c start /B /NODE 1 /AFFINITY 0xFFFFFFFFFFFFFFFE ...
+## ...
+## "\%COMSPEC\%" /c start /B /NODE 1 /AFFINITY 0xFFFFFFFFFFFFFFFE ...
 
 ## Temporarily disable CPU load protection for this example
 oopts <- options(parallelly.maxWorkers.localhost = Inf)
@@ -627,6 +649,10 @@ options(oopts)
 ## ---------------------------------------------------------------
 ## EXAMPLE: Three remote workers
 ## Setup of three R workers on two remote machines are set up
+## The parallel workers are launched as:
+## '/usr/bin/ssh' -R 11058:localhost:11058 n1.remote.org ...
+## '/usr/bin/ssh' -R 11059:localhost:11058 n2.remote.org ...
+## '/usr/bin/ssh' -R 11060:localhost:11058 n1.remote.org ...
 workers <- c("n1.remote.org", "n2.remote.org", "n1.remote.org")
 cl <- makeClusterPSOCK(workers, dryrun = TRUE, quiet = TRUE)
 
@@ -634,6 +660,9 @@ cl <- makeClusterPSOCK(workers, dryrun = TRUE, quiet = TRUE)
 ## EXAMPLE: Two remote workers running on MS Windows.  Because the
 ## remote workers are MS Windows machines, we need to use
 ## rscript_sh = "cmd".
+## The parallel workers are launched as:
+## '/usr/bin/ssh' -R 11912:localhost:11912 mswin1.remote.org ...
+## '/usr/bin/ssh' -R 11913:localhost:11912 mswin2.remote.org ...
 workers <- c("mswin1.remote.org", "mswin2.remote.org")
 cl <- makeClusterPSOCK(workers, rscript_sh = "cmd", dryrun = TRUE, quiet = TRUE)
 
@@ -650,6 +679,10 @@ cl <- makeClusterPSOCK(
 
 ## EXAMPLE: Three remote workers 'n1', 'n2', and 'n3' that can only be
 ## accessed via jumphost 'login.remote.org'
+## The parallel workers are launched as:
+## '/usr/bin/ssh' -R 11226:localhost:11226 -J login.remote.org n1 ...
+## '/usr/bin/ssh' -R 11227:localhost:11226 -J login.remote.org n2 ...
+## '/usr/bin/ssh' -R 11228:localhost:11226 -J login.remote.org n1 ...
 workers <- c("n1", "n2", "n1")
 cl <- makeClusterPSOCK(
   workers,
@@ -665,6 +698,8 @@ cl <- makeClusterPSOCK(
 ## Using the explicit special rshcmd = "<putty-plink>", will force
 ## makeClusterPSOCK() to search for and use the PuTTY plink software,
 ## preventing it from using other SSH clients on the system search PATH.
+## The parallel worker is launched as:
+## 'plink' -l bob -P 2200 -i C:/Users/bobby/.ssh/putty.ppk remote.server.org ...
 cl <- makeClusterPSOCK(
   "remote.server.org", user = "bob",
   rshcmd = "<putty-plink>",
@@ -676,6 +711,9 @@ cl <- makeClusterPSOCK(
 ## EXAMPLE: Remote workers with specific setup
 ## Setup of remote worker with more detailed control on
 ## authentication and reverse SSH tunneling
+## The parallel worker is launched as:
+## '/usr/bin/ssh' -l johnny -v -R 11000:gateway:11942 remote.server.org ...
+## "R_DEFAULT_PACKAGES=... 'nice' '/path/to/Rscript' --no-init-file ...
 cl <- makeClusterPSOCK(
   "remote.server.org", user = "johnny",
   ## Manual configuration of reverse SSH tunneling
@@ -695,6 +733,8 @@ cl <- makeClusterPSOCK(
 ## Using the explicit special rshcmd = "<rstudio-ssh>", will force
 ## makeClusterPSOCK() to use the SSH client that comes with RStudio,
 ## preventing it from using other SSH clients on the system search PATH.
+## The parallel worker is launched as:
+## 'ssh' -l bob remote.server.org:2200 ...
 cl <- makeClusterPSOCK(
   "remote.server.org:2200", user = "bob", rshcmd = "<rstudio-ssh>",
   dryrun = TRUE, quiet = TRUE
@@ -725,6 +765,12 @@ cl <- makeClusterPSOCK(
 ## This example shows how to use the SGE command 'qrsh' to launch
 ## 18 parallel workers from R, which is assumed to have been launched
 ## by 'script.sh'.
+##
+## The parallel workers are launched as:
+## 'qrsh' -inherit -nostdin -V comphost01 ...
+## 'qrsh' -inherit -nostdin -V comphost01 ...
+## ...
+## 'qrsh' -inherit -nostdin -V comphost06 ...
 cl <- makeClusterPSOCK(
   availableWorkers(),
   rshcmd = "qrsh", rshopts = c("-inherit", "-nostdin", "-V"),
@@ -743,6 +789,12 @@ cl <- makeClusterPSOCK(
 ## availableWorkers() to return 3 * 18 workers. When the HPC environment
 ## does not support SSH between compute nodes, one can use the 'pjrsh'
 ## command to launch the parallel workers.
+##
+## The parallel workers are launched as:
+## 'pjrsh' comphost01 ...
+## 'pjrsh' comphost01 ...
+## ...
+## 'pjrsh' comphost06 ...
 cl <- makeClusterPSOCK(
   availableWorkers(),
   rshcmd = "pjrsh",
@@ -758,6 +810,11 @@ cl <- makeClusterPSOCK(
 ## Launching worker on Amazon AWS EC2 running one of the
 ## Amazon Machine Images (AMI) provided by RStudio
 ## (https://www.louisaslett.com/RStudio_AMI/)
+##
+## The parallel worker is launched as:
+## '/usr/bin/ssh' -R 11153:localhost:11153 -l ubuntu ...
+## -o StrictHostKeyChecking=no -o IdentitiesOnly=yes ...
+## -i ~/.ssh/my-private-aws-key.pem 1.2.3.4 ...
 public_ip <- "1.2.3.4"
 ssh_private_key_file <- "~/.ssh/my-private-aws-key.pem"
 cl <- makeClusterPSOCK(
@@ -816,6 +873,10 @@ cl <- makeClusterPSOCK(
 ## ---------------------------------------------------------------
 ## EXAMPLE: Two workers running in Docker on the local machine
 ## Setup of 2 Docker workers running rocker/r-parallel
+##
+## The parallel workers are launched as:
+## R_DEFAULT_PACKAGES=... '/usr/bin/docker' 'run' '--net=host' 'rocker/r-parallel' ...
+## R_DEFAULT_PACKAGES=... '/usr/bin/docker' 'run' '--net=host' 'rocker/r-parallel' ...
 cl <- makeClusterPSOCK(
   rep("localhost", times = 2L),
   ## Launch Rscript inside Docker container
@@ -835,6 +896,10 @@ cl <- makeClusterPSOCK(
 
 ## EXAMPLE: Two workers running via Linux container 'rocker/r-parallel' from
 ## DockerHub on the local machine using Apptainer (formerly Singularity)
+##
+## The parallel workers are launched as:
+## R_DEFAULT_PACKAGES=... '/usr/bin/apptainer' 'exec' 'docker://rocker/r-parallel' ...
+## R_DEFAULT_PACKAGES=... '/usr/bin/apptainer' 'exec' 'docker://rocker/r-parallel' ...
 cl <- makeClusterPSOCK(
   rep("localhost", times = 2L),
   ## Launch Rscript inside Linux container
@@ -848,6 +913,9 @@ cl <- makeClusterPSOCK(
 
 ## EXAMPLE: One worker running in udocker on the local machine
 ## Setup of a single udocker.py worker running rocker/r-parallel
+##
+## The parallel worker is launched as:
+## R_DEFAULT_PACKAGES=... 'udocker.py' 'run' 'rocker/r-parallel' ...
 cl <- makeClusterPSOCK(
   "localhost",
   ## Launch Rscript inside Docker container (using udocker)
@@ -867,12 +935,15 @@ cl <- makeClusterPSOCK(
 ## EXAMPLE: One worker running in Wine for Linux on the local machine
 ## To install R for MS Windows in Wine, do something like:
 ##   winecfg  # In GUI, set 'Windows version' to 'Windows 10'
-##   wget https://cran.r-project.org/bin/windows/base/R-4.2.3-win.exe
-##   wine R-4.2.3-win.exe /SILENT
+##   wget https://cran.r-project.org/bin/windows/base/R-4.4.1-win.exe
+##   wine R-4.4.1-win.exe /SILENT
 ## Prevent packages from being installed to R's system library:
-##   chmod ugo-w "$HOME/.wine/drive_c/Program Files/R/R-4.2.3/library/"
+##   chmod ugo-w "$HOME/.wine/drive_c/Program Files/R/R-4.4.1/library/"
 ## Verify it works:
-##   wine "C:/Program Files/R/R-4.2.3/bin/x64/Rscript.exe" --version
+##   wine "C:/Program Files/R/R-4.4.1/bin/x64/Rscript.exe" --version
+##
+## The parallel worker is launched as:
+## R_DEFAULT_PACKAGES=... WINEDEBUG=fixme-all R_LIBS_SITE= R_LIBS_USER= 'wine' ...
 cl <- makeClusterPSOCK(1L,
   rscript = c(
     ## Silence Wine warnings
@@ -880,7 +951,7 @@ cl <- makeClusterPSOCK(1L,
     ## Don't pass LC_* and R_LIBS* environments from host to Wine
     sprintf("\%s=", grep("^(LC_|R_LIBS)", names(Sys.getenv()), value = TRUE)),
     "wine",
-    "C:/Program Files/R/R-4.2.3/bin/x64/Rscript.exe"
+    "C:/Program Files/R/R-4.4.1/bin/x64/Rscript.exe"
   ),
   dryrun = TRUE, quiet = TRUE
 )
diff --git a/man/makeClusterSequential.Rd b/man/makeClusterSequential.Rd
new file mode 100644
index 00000000..7677160e
--- /dev/null
+++ b/man/makeClusterSequential.Rd
@@ -0,0 +1,44 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/makeClusterSequential.R
+\name{makeClusterSequential}
+\alias{makeClusterSequential}
+\alias{SEQ}
+\title{Create a "parallel" cluster running sequentially in the current session}
+\usage{
+makeClusterSequential()
+}
+\description{
+The created cluster has only one node.
+}
+\details{
+Expression and function calls are evaluated in a local environment,
+inheriting the global environment.
+}
+\section{Requirements}{
+
+This function is only defined for R (>= 4.4.0).
+}
+
+\examples{
+\dontshow{if (getRversion() >= "4.4.0") \{}
+library(parallel)
+
+cl <- makeClusterSequential()
+print(cl)
+
+y <- parLapply(cl, X = 1:3, fun = sqrt)
+str(y)
+
+pid <- Sys.getpid()
+print(pid)
+y <- clusterEvalQ(cl, Sys.getpid())
+str(y)
+
+abc <- 3.14
+y <- clusterEvalQ(cl, { abc <- 42; abc })
+str(y)
+stopifnot(abc == 3.14)
+
+\dontshow{\}}
+
+}
diff --git a/man/parallelly.options.Rd b/man/parallelly.options.Rd
index 0e05c572..f5e0e087 100644
--- a/man/parallelly.options.Rd
+++ b/man/parallelly.options.Rd
@@ -12,6 +12,7 @@
 \alias{parallelly.availableWorkers.methods}
 \alias{parallelly.availableWorkers.custom}
 \alias{parallelly.fork.enable}
+\alias{parallelly.maxWorkers.localhost}
 \alias{parallelly.supportsMulticore.disableOn}
 \alias{parallelly.supportsMulticore.unstable}
 \alias{R_PARALLELLY_AVAILABLECORES_FALLBACK}
@@ -173,10 +174,10 @@ The below \R options and environment variables control the default results of \c
 All of the above \R \verb{parallelly.*} options can be set by
 corresponding environment variables \env{R_PARALLELLY_*} \emph{when the
 \pkg{parallelly} package is loaded}.
-For example, if \code{R_PARALLELLY_MAKENODEPSOCK_SETUP_STRATEGY = "sequential"},
+For example, if \code{R_PARALLELLY_MAKENODEPSOCK_SETUP_STRATEGY="sequential"},
 then option \code{parallelly.makeNodePSOCK.setup_strategy} is set to
 \code{"sequential"} (character).
-Similarly, if \code{R_PARALLELLY_AVAILABLECORES_FALLBACK = "1"}, then option
+Similarly, if \code{R_PARALLELLY_AVAILABLECORES_FALLBACK="1"}, then option
 \code{parallelly.availableCores.fallback} is set to \code{1} (integer).
 }
 
diff --git a/man/serializedSize.Rd b/man/serializedSize.Rd
new file mode 100644
index 00000000..cc8701d3
--- /dev/null
+++ b/man/serializedSize.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/serializedSize.R
+\name{serializedSize}
+\alias{serializedSize}
+\title{Calculate the size of an R object when it is serialized}
+\usage{
+serializedSize(obj)
+}
+\arguments{
+\item{obj}{An R object.}
+}
+\value{
+(integer or double) Number of bytes needed to serialize this object.
+}
+\description{
+This function goes through all the motions of serializing an object, but
+does nothing with the bytes other than to tally the total length.
+}
+\examples{
+object.size(mtcars)
+serializedSize(mtcars)
+
+}
+\author{
+Mike FC
+}
diff --git a/pkgdown/_pkgdown.yml b/pkgdown/_pkgdown.yml
index 7bf6698f..ec2492f7 100644
--- a/pkgdown/_pkgdown.yml
+++ b/pkgdown/_pkgdown.yml
@@ -19,18 +19,20 @@ navbar:
     pkgs:
       text: Packages
       menu:
-      - text: doFuture 
+      - text: doFuture (map-reduce)
         href: https://doFuture.futureverse.org
-      - text: furrr 
+      - text: furrr (map-reduce)
         href: https://furrr.futureverse.org
       - text: future 
         href: https://future.futureverse.org
-      - text: future.apply 
+      - text: future.apply (map-reduce)
         href: https://future.apply.futureverse.org
-      - text: future.batchtools 
+      - text: future.batchtools (backend)
         href: https://future.batchtools.futureverse.org
-      - text: future.callr 
+      - text: future.callr (backend)
         href: https://future.callr.futureverse.org
+      - text: future.mirai (backend)
+        href: https://future.mirai.futureverse.org
       - text: future.tests 
         href: https://future.tests.futureverse.org
       - text: globals 
@@ -45,8 +47,6 @@ navbar:
         href: https://BiocParallel.FutureParam.futureverse.org
       - text: future.tools (experimental)
         href: https://future.tools.futureverse.org
-      - text: future.mirai (experimental)
-        href: https://future.mirai.futureverse.org
       - text: future.mapreduce (experimental)
         href: https://future.mapreduce.futureverse.org
       - text: marshal (experimental)
diff --git a/pkgdown/_pkgdown.yml.rsp b/pkgdown/_pkgdown.yml.rsp
index 6d931ca0..fe85ef54 100644
--- a/pkgdown/_pkgdown.yml.rsp
+++ b/pkgdown/_pkgdown.yml.rsp
@@ -1,6 +1,8 @@
 <%
-pkgs <- c("globals", "listenv", "parallelly", "future", "future.apply", "furrr", "future.tests", "future.callr", "future.batchtools", "doFuture", "progressr")
-pkgs_extra <- c("BiocParallel.FutureParam", "future.tools", "future.mirai", "future.mapreduce", "marshal")
+pkgs_mapreduce <- c("future.apply", "doFuture", "furrr")
+pkgs_backend <- c("future.batchtools", "future.callr", "future.mirai")
+pkgs <- c("globals", "listenv", "parallelly", "future", "future.tests", "progressr", pkgs_mapreduce, pkgs_backend)
+pkgs_extra <- c("BiocParallel.FutureParam", "future.tools", "future.mapreduce", "marshal")
 pkgs <- c(sort(pkgs), pkgs_extra)
 urls <- sprintf("https://%s.futureverse.org", pkgs)
 names(urls) <- pkgs
@@ -16,7 +18,7 @@ url: https://<%= pkg %>.futureverse.org
 home:
   links:
   - text: Roadmap/Milestones
-    href: https://github.com/HenrikBengtsson/<%= pkg %>/milestones
+    href: https://github.com/<%= gsub("(^.*:|[.]git$)", "", subset(gert::git_remote_list(), name == "origin")$url) %>/milestones
   - text: The Futureverse Project
     href: https://www.futureverse.org/
   - text: Futureverse User Forum
@@ -33,7 +35,7 @@ navbar:
       text: Packages
       menu:
 <% for (name in names(urls)) { %>
-      - text: <%= name %> <% if (name %in% pkgs_extra) { %>(experimental)<% } %>
+      - text: <%= name %> <% if (name %in% pkgs_extra) { %>(experimental)<% } else if (name %in% pkgs_backend) { %>(backend)<% } else if (name %in% pkgs_mapreduce) { %>(map-reduce)<% } %>
         href: <%= urls[name] %>
 <% } %>
     cran:
diff --git a/revdep/README.md b/revdep/README.md
index fa64bc77..93f50fca 100644
--- a/revdep/README.md
+++ b/revdep/README.md
@@ -1,638 +1,83 @@
 # Platform
 
-|field    |value                                                           |
-|:--------|:---------------------------------------------------------------|
-|version  |R version 4.3.2 (2023-10-31)                                    |
-|os       |CentOS Linux 7 (Core)                                           |
-|system   |x86_64, linux-gnu                                               |
-|ui       |X11                                                             |
-|language |en                                                              |
-|collate  |en_US.UTF-8                                                     |
-|ctype    |en_US.UTF-8                                                     |
-|tz       |America/Los_Angeles                                             |
-|date     |2024-02-14                                                      |
-|pandoc   |3.1.11.1 @ /software/c4/cbi/software/pandoc-3.1.11.1/bin/pandoc |
+|field    |value                                                     |
+|:--------|:---------------------------------------------------------|
+|version  |R version 4.4.1 (2024-06-14)                              |
+|os       |Rocky Linux 8.10 (Green Obsidian)                         |
+|system   |x86_64, linux-gnu                                         |
+|ui       |X11                                                       |
+|language |en                                                        |
+|collate  |en_US.UTF-8                                               |
+|ctype    |en_US.UTF-8                                               |
+|tz       |America/Los_Angeles                                       |
+|date     |2024-07-27                                                |
+|pandoc   |3.2.1 @ /software/c4/cbi/software/pandoc-3.2.1/bin/pandoc |
 
 # Dependencies
 
 |package    |old    |new         |Δ  |
 |:----------|:------|:-----------|:--|
-|parallelly |1.36.0 |1.36.0-9023 |*  |
+|parallelly |1.37.1 |1.37.1-9015 |*  |
 
 # Revdeps
 
-## Failed to check (6)
+## All (55)
 
-|package          |version |error |warning |note |
-|:----------------|:-------|:-----|:-------|:----|
-|[cft](failures.md#cft)|1.0.0   |1     |        |     |
-|[erah](failures.md#erah)|2.0.1   |1     |        |1    |
-|[Prostar](failures.md#prostar)|1.34.5  |1     |        |     |
-|[rmsb](failures.md#rmsb)|1.0-0   |1     |        |1    |
-|[startR](failures.md#startr)|2.3.1   |1     |        |     |
-|[TriDimRegression](failures.md#tridimregression)|1.0.2   |1     |        |     |
-
-## New problems (1)
-
-|package |version |error       |warning |note |
-|:-------|:-------|:-----------|:-------|:----|
-|[stars](problems.md#stars)|0.6-4   |1 -1 __+1__ |        |2    |
-
-## All (593)
-
-|package                    |version    |error       |warning |note |
-|:--------------------------|:----------|:-----------|:-------|:----|
-|accelmissing               |1.4        |            |        |     |
-|[ACE](problems.md#ace)     |1.20.0     |            |        |3    |
-|[adea](problems.md#adea)   |1.5.1      |1           |        |     |
-|adestr                     |0.5.0      |            |        |     |
-|[adjustedCurves](problems.md#adjustedcurves)|0.11.0     |            |1       |     |
-|AICcPermanova              |0.0.2      |            |        |     |
-|[AIPW](problems.md#aipw)   |0.6.3.2    |            |        |1    |
-|airGR                      |1.7.6      |            |        |     |
-|ale                        |0.3.0      |            |        |     |
-|alookr                     |0.3.9      |            |        |     |
-|alphaci                    |1.0.1      |            |        |     |
-|[AlpsNMR](problems.md#alpsnmr)|4.4.0      |1           |        |     |
-|antaresEditObject          |0.6.1      |            |        |     |
-|arkdb                      |0.0.18     |            |        |     |
-|aroma.affymetrix           |3.2.1      |            |        |     |
-|aroma.cn                   |1.7.0      |            |        |     |
-|[aroma.core](problems.md#aromacore)|3.3.0      |            |        |1    |
-|ARPALData                  |1.5.0      |            |        |     |
-|autoReg                    |0.3.3      |            |        |     |
-|BaM                        |1.0.3      |            |        |     |
-|[BAMBI](problems.md#bambi) |2.3.5      |            |1       |1    |
-|[bamm](problems.md#bamm)   |0.4.3      |            |1       |1    |
-|baseballr                  |1.6.0      |            |        |     |
-|BatchGetSymbols            |2.6.4      |            |        |     |
-|[batchtools](problems.md#batchtools)|0.9.17     |            |        |2    |
-|bayesian                   |0.0.9      |            |        |     |
-|BayesianTools              |0.1.8      |            |        |     |
-|[bayesmove](problems.md#bayesmove)|0.2.1      |            |1       |     |
-|[BBEST](problems.md#bbest) |0.1-8      |            |        |1    |
-|bbknnR                     |1.1.1      |            |        |     |
-|bcmaps                     |2.2.0      |            |        |     |
-|[BEKKs](problems.md#bekks) |1.4.4      |            |1       |1    |
-|[BENMMI](problems.md#benmmi)|4.3-7      |            |2       |     |
-|betaMC                     |1.3.1      |            |        |     |
-|bhmbasket                  |0.9.5      |            |        |     |
-|[bigDM](problems.md#bigdm) |0.5.3      |            |        |2    |
-|bigparallelr               |0.3.2      |            |        |     |
-|bigreadr                   |0.2.5      |            |        |     |
-|[bigsnpr](problems.md#bigsnpr)|1.12.2     |            |1       |1    |
-|[bigstatsr](problems.md#bigstatsr)|1.5.12     |            |1       |3    |
-|bigutilsr                  |0.3.4      |            |        |     |
-|BioM2                      |1.0.3      |            |        |     |
-|bipd                       |0.3        |            |        |     |
-|[biscuiteer](problems.md#biscuiteer)|1.16.0     |            |1       |3    |
-|[bistablehistory](problems.md#bistablehistory)|1.1.2      |            |        |2    |
-|bkmrhat                    |1.1.3      |            |        |     |
-|[blavaan](problems.md#blavaan)|0.5-3      |            |        |3    |
-|bolasso                    |0.2.0      |            |        |     |
-|bootImpute                 |1.2.1      |            |        |     |
-|[bootUR](problems.md#bootur)|1.0.3      |            |1       |2    |
-|breathtestcore             |0.8.7      |            |        |     |
-|[breathteststan](problems.md#breathteststan)|0.8.5      |            |        |2    |
-|[brms](problems.md#brms)   |2.20.4     |            |        |2    |
-|brms.mmrm                  |0.0.2      |            |        |     |
-|brokenstick                |2.5.0      |            |        |     |
-|broom.helpers              |1.14.0     |            |        |     |
-|brpop                      |0.3.0      |            |        |     |
-|[bsitar](problems.md#bsitar)|0.1.1      |            |        |1    |
-|bspcov                     |1.0.0      |            |        |     |
-|[bucky](problems.md#bucky) |1.0.7      |            |        |2    |
-|CALIBERrfimpute            |1.0-7      |            |        |     |
-|campsis                    |1.5.0      |            |        |     |
-|canaper                    |1.0.1      |            |        |     |
-|carfima                    |2.0.2      |            |        |     |
-|cati                       |0.99.4     |            |        |     |
-|CEGO                       |2.4.3      |            |        |     |
-|[censcyt](problems.md#censcyt)|1.10.0     |            |        |2    |
-|[ceRNAnetsim](problems.md#cernanetsim)|1.14.1     |3           |        |1    |
-|cfdnakit                   |1.0.0      |            |        |     |
-|[cft](failures.md#cft)     |1.0.0      |1           |        |     |
-|chatAI4R                   |0.2.10     |            |        |     |
-|[ChromSCape](problems.md#chromscape)|1.12.0     |            |4       |4    |
-|civis                      |3.1.2      |            |        |     |
-|[clickR](problems.md#clickr)|0.9.39     |            |        |1    |
-|Clustering                 |1.7.7      |            |        |     |
-|ClustIRR                   |1.0.0      |            |        |     |
-|cobalt                     |4.5.3      |            |        |     |
-|codalm                     |0.1.2      |            |        |     |
-|[codebook](problems.md#codebook)|0.9.2      |            |        |3    |
-|[collinear](problems.md#collinear)|1.1.1      |            |        |1    |
-|condvis2                   |0.1.2      |            |        |     |
-|conformalInference.fd      |1.1.1      |            |        |     |
-|conformalInference.multi   |1.1.1      |            |        |     |
-|ConsReg                    |0.1.0      |            |        |     |
-|[COTAN](problems.md#cotan) |2.2.3      |            |        |3    |
-|counterfactuals            |0.1.2      |            |        |     |
-|[cpi](problems.md#cpi)     |0.1.4      |            |        |1    |
-|CptNonPar                  |0.1.1      |            |        |     |
-|crossmap                   |0.4.0      |            |        |     |
-|CSCNet                     |0.1.2      |            |        |     |
-|[cSEM](problems.md#csem)   |0.5.0      |            |        |1    |
-|[CSGo](problems.md#csgo)   |0.6.7      |            |        |1    |
-|[ctsem](problems.md#ctsem) |3.9.1      |1           |        |4    |
-|cvCovEst                   |1.2.1      |            |        |     |
-|dagHMM                     |0.1.0      |            |        |     |
-|DALEXtra                   |2.3.0      |            |        |     |
-|data.validator             |0.2.1      |            |        |     |
-|dataquieR                  |2.0.1      |            |        |     |
-|[DDD](problems.md#ddd)     |5.2.2      |            |        |1    |
-|DeclareDesign              |1.0.6      |            |        |     |
-|delayed                    |0.4.0      |            |        |     |
-|DEoptim                    |2.2-8      |            |        |     |
-|[deseats](problems.md#deseats)|1.0.0      |            |1       |1    |
-|[desla](problems.md#desla) |0.3.0      |            |1       |1    |
-|[dipsaus](problems.md#dipsaus)|0.2.8      |            |        |1    |
-|Directional                |6.4        |            |        |     |
-|disk.frame                 |0.8.3      |            |        |     |
-|[dispositionEffect](problems.md#dispositioneffect)|1.0.1      |1           |        |     |
-|dlookr                     |0.6.3      |            |        |     |
-|[DMQ](problems.md#dmq)     |0.1.2      |            |1       |     |
-|doFuture                   |1.0.1      |            |        |     |
-|DoubleML                   |0.5.3      |            |        |     |
-|DQAstats                   |0.3.3      |            |        |     |
-|[dragon](problems.md#dragon)|1.2.1      |1           |        |2    |
-|[drake](problems.md#drake) |7.13.8     |            |        |1    |
-|drape                      |0.0.1      |            |        |     |
-|drimmR                     |1.0.1      |            |        |     |
-|drtmle                     |1.1.2      |            |        |     |
-|dsos                       |0.1.2      |            |        |     |
-|[DstarM](problems.md#dstarm)|0.4.0      |            |1       |2    |
-|[DT](problems.md#dt)       |0.31       |            |        |1    |
-|[dynr](problems.md#dynr)   |0.1.16-105 |            |        |2    |
-|easyalluvial               |0.3.2      |            |        |     |
-|eatRep                     |0.14.7     |            |        |     |
-|ecic                       |0.0.3      |            |        |     |
-|eCV                        |0.0.2      |            |        |     |
-|[EFAtools](problems.md#efatools)|0.4.4      |            |1       |3    |
-|EGAnet                     |2.0.4      |            |        |     |
-|elevatr                    |0.99.0     |            |        |     |
-|[emmeans](problems.md#emmeans)|1.10.0     |            |        |1    |
-|[envi](problems.md#envi)   |0.1.19     |            |1       |     |
-|epe4md                     |0.1.4      |            |        |     |
-|[EpiNow2](problems.md#epinow2)|1.4.0      |            |        |2    |
-|[epitweetr](problems.md#epitweetr)|2.2.16     |            |        |2    |
-|epwshiftr                  |0.1.3      |            |        |     |
-|[erah](failures.md#erah)   |2.0.1      |1           |        |1    |
-|EstimationTools            |4.0.0      |            |        |     |
-|[explainer](problems.md#explainer)|1.0.0      |            |        |1    |
-|ezcox                      |1.0.4      |            |        |     |
-|fabletools                 |0.4.0      |            |        |     |
-|FACT                       |0.1.0      |            |        |     |
-|FAMoS                      |0.3.0      |            |        |     |
-|fastRhockey                |0.4.0      |            |        |     |
-|[fdacluster](problems.md#fdacluster)|0.3.0      |            |1       |1    |
-|fdWasserstein              |1.0        |            |        |     |
-|[fect](problems.md#fect)   |1.0.0      |            |1       |3    |
-|fiery                      |1.2.1      |            |        |     |
-|[finalfit](problems.md#finalfit)|1.0.7      |            |        |2    |
-|finbif                     |0.9.4      |            |        |     |
-|finnts                     |0.4.0      |            |        |     |
-|fitlandr                   |0.1.0      |            |        |     |
-|FLAME                      |2.1.1      |            |        |     |
-|[FLAMES](problems.md#flames)|1.8.0      |            |        |5    |
-|flevr                      |0.0.4      |            |        |     |
-|[flowGraph](problems.md#flowgraph)|1.10.0     |            |        |2    |
-|[flowml](problems.md#flowml)|0.1.2      |            |        |1    |
-|[forecastML](problems.md#forecastml)|0.9.0      |            |        |1    |
-|fst4pg                     |1.0.0      |            |        |     |
-|fundiversity               |1.1.1      |            |        |     |
-|fungible                   |2.4.3      |            |        |     |
-|funGp                      |0.3.2      |            |        |     |
-|furrr                      |0.3.1      |            |        |     |
-|future                     |1.33.1     |            |        |     |
-|future.apply               |1.11.1     |            |        |     |
-|future.batchtools          |0.12.1     |            |        |     |
-|future.callr               |0.8.2      |            |        |     |
-|future.tests               |0.7.0      |            |        |     |
-|FuzzyStatProb              |2.0.4      |            |        |     |
-|fxTWAPLS                   |0.1.2      |            |        |     |
-|galts                      |1.3.2      |            |        |     |
-|[genBaRcode](problems.md#genbarcode)|1.2.7      |            |1       |     |
-|[GeneBreak](problems.md#genebreak)|1.32.0     |            |        |1    |
-|GenericML                  |0.2.2      |            |        |     |
-|[geocmeans](problems.md#geocmeans)|0.3.4      |            |1       |1    |
-|gerbil                     |0.1.9      |            |        |     |
-|GetBCBData                 |0.7.0      |            |        |     |
-|gFormulaMI                 |1.0.0      |            |        |     |
-|ggeffects                  |1.4.0      |            |        |     |
-|ggmice                     |0.1.0      |            |        |     |
-|gittargets                 |0.0.7      |            |        |     |
-|[gKRLS](problems.md#gkrls) |1.0.2      |            |        |1    |
-|[googleCloudRunner](problems.md#googlecloudrunner)|0.5.0      |            |        |1    |
-|[googleComputeEngineR](problems.md#googlecomputeenginer)|0.3.0      |            |        |1    |
-|googlePubsubR              |0.0.4      |            |        |     |
-|[googleTagManageR](problems.md#googletagmanager)|0.2.0      |            |        |1    |
-|greatR                     |1.1.0      |            |        |     |
-|[greed](problems.md#greed) |0.6.1      |            |1       |3    |
-|GREENeR                    |1.0.0      |            |        |     |
-|greta                      |0.4.4      |            |        |     |
-|greta.dynamics             |0.2.0      |            |        |     |
-|greta.gp                   |0.2.1      |            |        |     |
-|gsdensity                  |0.1.2      |            |        |     |
-|gstat                      |2.1-1      |            |        |     |
-|GSVA                       |1.50.0     |            |        |     |
-|[gsynth](problems.md#gsynth)|1.2.1      |            |1       |2    |
-|gtfs2emis                  |0.1.0      |            |        |     |
-|gtfs2gps                   |2.1-1      |            |        |     |
-|gtsummary                  |1.7.2      |            |        |     |
-|gWQS                       |3.0.5      |            |        |     |
-|[hackeRnews](problems.md#hackernews)|0.1.0      |            |        |1    |
-|hacksig                    |0.1.2      |            |        |     |
-|[hal9001](problems.md#hal9001)|0.4.6      |            |        |1    |
-|haldensify                 |0.2.3      |            |        |     |
-|[HardyWeinberg](problems.md#hardyweinberg)|1.7.5      |            |        |1    |
-|[hbamr](problems.md#hbamr) |2.1.2      |            |        |2    |
-|healthyR.ai                |0.0.13     |            |        |     |
-|[healthyR.ts](problems.md#healthyrts)|0.3.0      |            |        |1    |
-|[hero](problems.md#hero)   |0.6        |            |        |2    |
-|[heterogen](problems.md#heterogen)|1.2.33     |            |1       |1    |
-|hhsmm                      |0.3.6      |            |        |     |
-|highMLR                    |0.1.1      |            |        |     |
-|[Hmisc](problems.md#hmisc) |5.1-1      |            |        |1    |
-|holodeck                   |0.2.2      |            |        |     |
-|hoopR                      |2.1.0      |            |        |     |
-|hot.deck                   |1.2        |            |        |     |
-|howManyImputations         |0.2.4      |            |        |     |
-|[HSAUR3](problems.md#hsaur3)|1.0-14     |            |        |1    |
-|[hwep](problems.md#hwep)   |2.0.2      |            |        |2    |
-|hydroloom                  |1.0.2      |            |        |     |
-|[IDE](problems.md#ide)     |0.3.1      |            |1       |     |
-|[idem](problems.md#idem)   |5.2        |            |        |2    |
-|idmodelr                   |0.4.0      |            |        |     |
-|[IFAA](problems.md#ifaa)   |1.4.0      |            |1       |     |
-|imagefluency               |0.2.4      |            |        |     |
-|iml                        |0.11.1     |            |        |     |
-|[ImputeRobust](problems.md#imputerobust)|1.3-1      |            |1       |     |
-|incubate                   |1.2.1      |            |        |     |
-|[infercnv](problems.md#infercnv)|1.18.1     |            |        |2    |
-|inlinedocs                 |2023.9.4   |            |        |     |
-|[InPAS](problems.md#inpas) |2.10.0     |            |        |1    |
-|insight                    |0.19.8     |            |        |     |
-|[interflex](problems.md#interflex)|1.2.6      |            |1       |2    |
-|intmed                     |0.1.2      |            |        |     |
-|ipc                        |0.1.4      |            |        |     |
-|IPWboxplot                 |0.1.2      |            |        |     |
-|[ISAnalytics](problems.md#isanalytics)|1.12.0     |            |        |1    |
-|isopam                     |2.0        |            |        |     |
-|ivDiag                     |1.0.6      |            |        |     |
-|[ivmte](problems.md#ivmte) |1.4.0      |            |        |1    |
-|jagstargets                |1.1.0      |            |        |     |
-|jlmerclusterperm           |1.1.1      |            |        |     |
-|[JMbayes2](problems.md#jmbayes2)|0.4-5      |            |1       |1    |
-|jmBIG                      |0.1.1      |            |        |     |
-|[joinet](problems.md#joinet)|0.0.10     |            |        |1    |
-|JointAI                    |1.0.5      |            |        |     |
-|jstor                      |0.3.11     |            |        |     |
-|JuliaConnectoR             |1.1.3      |            |        |     |
-|JWileymisc                 |1.4.1      |            |        |     |
-|kernelboot                 |0.1.10     |            |        |     |
-|[keyATM](problems.md#keyatm)|0.5.1      |            |        |1    |
-|[knitr](problems.md#knitr) |1.45       |1           |1       |     |
-|[konfound](problems.md#konfound)|0.4.0      |            |        |1    |
-|KSPM                       |0.2.1      |            |        |     |
-|LandComp                   |0.0.5      |            |        |     |
-|latentcor                  |2.0.1      |            |        |     |
-|lava                       |1.7.3      |            |        |     |
-|ldaPrototype               |0.3.1      |            |        |     |
-|[ldsr](problems.md#ldsr)   |0.0.2      |            |1       |1    |
-|lemna                      |1.0.1      |            |        |     |
-|LexFindR                   |1.0.2      |            |        |     |
-|lgr                        |0.4.4      |            |        |     |
-|[lidR](problems.md#lidr)   |4.1.0      |1           |1       |1    |
-|lightr                     |1.7.0      |            |        |     |
-|LikertMakeR                |0.1.5      |            |        |     |
-|LMMstar                    |1.0.1      |            |        |     |
-|lmtp                       |1.3.2      |            |        |     |
-|logistf                    |1.26.0     |            |        |     |
-|[LSAmitR](problems.md#lsamitr)|1.0-3      |            |        |2    |
-|LTFHPlus                   |2.1.1      |            |        |     |
-|[Luminescence](problems.md#luminescence)|0.9.23     |            |1       |1    |
-|LWFBrook90R                |0.5.3      |            |        |     |
-|[MAI](problems.md#mai)     |1.8.0      |            |        |1    |
-|malariaAtlas               |1.5.1      |            |        |     |
-|MAMS                       |2.0.1      |            |        |     |
-|MantaID                    |1.0.2      |            |        |     |
-|[manydata](problems.md#manydata)|0.8.3      |            |        |1    |
-|manymome                   |0.1.13     |            |        |     |
-|[manynet](problems.md#manynet)|0.4.1      |            |        |2    |
-|mapme.biodiversity         |0.5.0      |            |        |     |
-|[mappp](problems.md#mappp) |1.0.0      |            |        |1    |
-|marginaleffects            |0.18.0     |            |        |     |
-|MatchThem                  |1.1.0      |            |        |     |
-|matric                     |0.2.0      |            |        |     |
-|mbbe                       |0.1.0      |            |        |     |
-|mcboost                    |0.4.2      |            |        |     |
-|mcmcensemble               |3.0.0      |            |        |     |
-|mcp                        |0.3.3      |            |        |     |
-|[mdmb](problems.md#mdmb)   |1.8-7      |            |1       |1    |
-|[medflex](problems.md#medflex)|0.6-10     |            |        |1    |
-|merTools                   |0.6.2      |            |        |     |
-|[metabolomicsR](problems.md#metabolomicsr)|1.0.0      |            |1       |1    |
-|[metafor](problems.md#metafor)|4.4-0      |            |        |1    |
-|[metaGE](problems.md#metage)|1.0.3      |            |        |1    |
-|metavcov                   |2.1.5      |            |        |     |
-|mi4p                       |1.1        |            |        |     |
-|micd                       |1.1.1      |            |        |     |
-|mice                       |3.16.0     |            |        |     |
-|[miceadds](problems.md#miceadds)|3.17-44    |            |1       |3    |
-|miceafter                  |0.5.0      |            |        |     |
-|micEconCES                 |1.0-2      |            |        |     |
-|[miceFast](problems.md#micefast)|0.8.2      |            |1       |2    |
-|micemd                     |1.10.0     |            |        |     |
-|microeco                   |1.4.0      |            |        |     |
-|[microservices](problems.md#microservices)|0.2.0      |1           |        |     |
-|[midastouch](problems.md#midastouch)|1.3        |            |        |1    |
-|[midfieldr](problems.md#midfieldr)|1.0.1      |            |        |1    |
-|miesmuschel                |0.0.3      |            |        |     |
-|[mifa](problems.md#mifa)   |0.2.0      |            |        |1    |
-|migraph                    |1.3.2      |            |        |     |
-|MIIPW                      |0.1.1      |            |        |     |
-|mikropml                   |1.6.1      |            |        |     |
-|[MineICA](problems.md#mineica)|1.42.0     |            |3       |4    |
-|misaem                     |1.0.1      |            |        |     |
-|miselect                   |0.9.0      |            |        |     |
-|missCompare                |1.0.3      |            |        |     |
-|missDiag                   |1.0.1      |            |        |     |
-|missMDA                    |1.19       |            |        |     |
-|[missSBM](problems.md#misssbm)|1.0.4      |            |1       |1    |
-|[mistyR](problems.md#mistyr)|1.10.0     |-1          |        |1    |
-|mitml                      |0.4-5      |            |        |     |
-|[miWQS](problems.md#miwqs) |0.4.4      |            |1       |     |
-|mixgb                      |1.0.2      |            |        |     |
-|MixtureMissing             |3.0.1      |            |        |     |
-|MKinfer                    |1.1        |            |        |     |
-|mlim                       |0.3.0      |            |        |     |
-|mlr3                       |0.17.2     |            |        |     |
-|mlr3batchmark              |0.1.1      |            |        |     |
-|mlr3benchmark              |0.1.6      |            |        |     |
-|mlr3cluster                |0.1.8      |            |        |     |
-|mlr3data                   |0.7.0      |            |        |     |
-|mlr3db                     |0.5.2      |            |        |     |
-|mlr3fairness               |0.3.2      |            |        |     |
-|mlr3filters                |0.7.1      |            |        |     |
-|mlr3fselect                |0.11.0     |            |        |     |
-|mlr3hyperband              |0.4.5      |            |        |     |
-|mlr3learners               |0.5.8      |            |        |     |
-|mlr3mbo                    |0.2.1      |            |        |     |
-|mlr3oml                    |0.9.0      |            |        |     |
-|mlr3pipelines              |0.5.0-2    |            |        |     |
-|mlr3resampling             |2024.1.23  |            |        |     |
-|[mlr3shiny](problems.md#mlr3shiny)|0.3.0      |            |        |1    |
-|mlr3spatial                |0.4.1      |            |        |     |
-|mlr3spatiotempcv           |2.3.0      |            |        |     |
-|mlr3tuning                 |0.19.2     |            |        |     |
-|mlr3tuningspaces           |0.4.0      |            |        |     |
-|mlr3verse                  |0.2.8      |            |        |     |
-|mlr3viz                    |0.7.0      |            |        |     |
-|[mlrintermbo](problems.md#mlrintermbo)|0.5.0      |            |        |1    |
-|[mmrm](problems.md#mmrm)   |0.3.10     |            |        |1    |
-|modelsummary               |1.4.3      |            |        |     |
-|[modeltime](problems.md#modeltime)|1.2.8      |            |        |1    |
-|[modeltime.ensemble](problems.md#modeltimeensemble)|1.0.3      |            |        |1    |
-|[modeltime.resample](problems.md#modeltimeresample)|0.2.3      |            |        |1    |
-|[momentuHMM](problems.md#momentuhmm)|1.5.5      |            |1       |1    |
-|monoClust                  |1.2.1      |            |        |     |
-|[MOSS](problems.md#moss)   |0.2.2      |            |1       |     |
-|mplusParallel.automation   |0.0.1.1    |            |        |     |
-|mrf                        |0.1.6      |            |        |     |
-|mrgsim.parallel            |0.2.1      |            |        |     |
-|MRPC                       |3.1.0      |            |        |     |
-|MSCMT                      |1.3.9      |            |        |     |
-|[MSiP](problems.md#msip)   |1.3.7      |            |        |1    |
-|mslp                       |1.4.0      |            |        |     |
-|multitool                  |0.1.4      |            |        |     |
-|multiverse                 |0.6.1      |            |        |     |
-|[mvnimpute](problems.md#mvnimpute)|1.0.1      |            |1       |     |
-|[NADIA](problems.md#nadia) |0.4.2      |            |        |1    |
-|[NCC](problems.md#ncc)     |1.0        |            |        |1    |
-|[nebula](problems.md#nebula)|1.4.2      |            |        |1    |
-|netShiny                   |1.0        |            |        |     |
-|NetSimR                    |0.1.5      |            |        |     |
-|[nfl4th](problems.md#nfl4th)|1.0.4      |            |1       |1    |
-|nflfastR                   |4.6.1      |            |        |     |
-|nflseedR                   |1.2.0      |            |        |     |
-|nhdplusTools               |1.0.0      |            |        |     |
-|[NIMAA](problems.md#nimaa) |0.2.1      |            |        |2    |
-|nncc                       |2.0.0      |            |        |     |
-|[oncomsm](problems.md#oncomsm)|0.1.4      |            |        |2    |
-|onemapsgapi                |1.1.0      |            |        |     |
-|[OOS](problems.md#oos)     |1.0.0      |            |        |1    |
-|openEBGM                   |0.9.1      |            |        |     |
-|optic                      |1.0.1      |            |        |     |
-|OptimalGoldstandardDesigns |1.0.1      |            |        |     |
-|optimLanduse               |1.2.0      |            |        |     |
-|[ordbetareg](problems.md#ordbetareg)|0.7.2      |            |        |2    |
-|origami                    |1.0.7      |            |        |     |
-|OSLdecomposition           |1.0.0      |            |        |     |
-|OTrecod                    |0.1.2      |            |        |     |
-|parameters                 |0.21.5     |            |        |     |
-|paramsim                   |0.1.0      |            |        |     |
-|[pareg](problems.md#pareg) |1.6.0      |3           |        |2    |
-|[parseRPDR](problems.md#parserpdr)|1.1.0      |            |        |1    |
-|[partR2](problems.md#partr2)|0.9.1      |            |        |1    |
-|[pavo](problems.md#pavo)   |2.9.0      |            |1       |     |
-|pbapply                    |1.7-2      |            |        |     |
-|[pchc](problems.md#pchc)   |1.2        |            |1       |     |
-|[PCRedux](problems.md#pcredux)|1.1-2      |            |1       |     |
-|PeakSegDisk                |2023.11.27 |            |        |     |
-|[pema](problems.md#pema)   |0.1.3      |            |        |2    |
-|penaltyLearning            |2024.1.25  |            |        |     |
-|pGRN                       |0.3.5      |            |        |     |
-|phenex                     |1.4-5      |            |        |     |
-|[photosynthesis](problems.md#photosynthesis)|2.1.4      |            |        |2    |
-|[phylolm](problems.md#phylolm)|2.6.2      |            |        |2    |
-|phylopath                  |1.2.0      |            |        |     |
-|PINstimation               |0.1.2      |            |        |     |
-|[PLNmodels](problems.md#plnmodels)|1.1.0      |            |1       |1    |
-|plumber                    |1.2.1      |            |        |     |
-|[pmartR](problems.md#pmartr)|2.4.2      |            |1       |2    |
-|polle                      |1.3        |            |        |     |
-|POMADE                     |0.2.0      |            |        |     |
-|[PortfolioAnalytics](problems.md#portfolioanalytics)|1.1.0      |            |        |1    |
-|[portvine](problems.md#portvine)|1.0.3      |            |        |1    |
-|powRICLPM                  |0.1.1      |            |        |     |
-|pre                        |1.0.7      |            |        |     |
-|prodest                    |1.0.1      |            |        |     |
-|proffer                    |0.1.6      |            |        |     |
-|progressr                  |0.14.0     |            |        |     |
-|[projpred](problems.md#projpred)|2.8.0      |            |1       |2    |
-|promises                   |1.2.1      |            |        |     |
-|[Prostar](failures.md#prostar)|1.34.5     |1           |        |     |
-|proteus                    |1.1.4      |            |        |     |
-|protti                     |0.6.0      |            |        |     |
-|PRSPGx                     |0.3.0      |            |        |     |
-|PSCBS                      |0.66.0     |            |        |     |
-|[pseudohouseholds](problems.md#pseudohouseholds)|0.1.1      |            |        |1    |
-|psfmi                      |1.4.0      |            |        |     |
-|PUMP                       |1.0.2      |            |        |     |
-|qape                       |2.1        |            |        |     |
-|[QDNAseq](problems.md#qdnaseq)|1.38.0     |1           |        |1    |
-|[QDNAseq.hg19](problems.md#qdnaseqhg19)|1.32.0     |            |        |1    |
-|[QDNAseq.mm10](problems.md#qdnaseqmm10)|1.32.0     |            |        |1    |
-|qgcomp                     |2.15.2     |            |        |     |
-|qgcompint                  |0.7.0      |            |        |     |
-|[qtl2pleio](problems.md#qtl2pleio)|1.4.3      |            |        |2    |
-|[Qtools](problems.md#qtools)|1.5.9      |            |1       |     |
-|quickpsy                   |0.1.5.1    |            |        |     |
-|[RAINBOWR](problems.md#rainbowr)|0.1.33     |            |        |1    |
-|rangeMapper                |2.0.3      |            |        |     |
-|RapidoPGS                  |2.3.0      |            |        |     |
-|[rattle](problems.md#rattle)|5.5.1      |            |1       |3    |
-|[raveio](problems.md#raveio)|0.9.0      |            |        |1    |
-|rBiasCorrection            |0.3.4      |            |        |     |
-|[rbmi](problems.md#rbmi)   |1.2.6      |            |        |2    |
-|[RBtest](problems.md#rbtest)|1.1        |            |        |1    |
-|[RcppDE](problems.md#rcppde)|0.1.7      |            |1       |1    |
-|Rcurvep                    |1.3.1      |            |        |     |
-|realTimeloads              |1.0.0      |            |        |     |
-|[receptiviti](problems.md#receptiviti)|0.1.6      |1           |        |     |
-|refineR                    |1.6.1      |            |        |     |
-|[regmedint](problems.md#regmedint)|1.0.1      |            |        |1    |
-|remiod                     |1.0.2      |            |        |     |
-|reproducible               |2.0.10     |            |        |     |
-|reqres                     |0.2.5      |            |        |     |
-|reval                      |3.1-0      |            |        |     |
-|[rexposome](problems.md#rexposome)|1.24.1     |            |5       |2    |
-|RfEmpImp                   |2.1.8      |            |        |     |
-|[rgee](problems.md#rgee)   |1.1.7      |            |        |1    |
-|[Riemann](problems.md#riemann)|0.1.4      |            |1       |3    |
-|rkeops                     |2.2.2      |            |        |     |
-|rms                        |6.7-1      |            |        |     |
-|[rmsb](failures.md#rmsb)   |1.0-0      |1           |        |1    |
-|[RNAseqCovarImpute](problems.md#rnaseqcovarimpute)|1.0.2      |            |        |1    |
-|[robotstxt](problems.md#robotstxt)|0.7.13     |            |        |2    |
-|robust2sls                 |0.2.2      |            |        |     |
-|ROI.plugin.deoptim         |1.0-2      |            |        |     |
-|routr                      |0.4.1      |            |        |     |
-|[rpm](problems.md#rpm)     |0.7-1      |            |1       |1    |
-|[rrscale](problems.md#rrscale)|1.0        |            |        |2    |
-|rsi                        |0.1.2      |            |        |     |
-|Rtapas                     |1.1        |            |        |     |
-|RTransferEntropy           |0.2.21     |            |        |     |
-|[runMCMCbtadjust](problems.md#runmcmcbtadjust)|1.0.5      |            |1       |     |
-|s3fs                       |0.1.4      |            |        |     |
-|saeczi                     |0.1.0      |            |        |     |
-|[sapfluxnetr](problems.md#sapfluxnetr)|0.1.4      |            |        |1    |
-|[SCArray.sat](problems.md#scarraysat)|1.2.1      |            |1       |1    |
-|scBubbletree               |1.4.0      |            |        |     |
-|scDiffCom                  |1.0.0      |            |        |     |
-|[scRNAseqApp](problems.md#scrnaseqapp)|1.2.2      |            |        |1    |
-|[scruff](problems.md#scruff)|1.20.0     |            |        |2    |
-|[sctransform](problems.md#sctransform)|0.4.1      |            |1       |1    |
-|[sdmApp](problems.md#sdmapp)|0.0.2      |            |        |1    |
-|[sdmTMB](problems.md#sdmtmb)|0.4.2      |            |        |1    |
-|seer                       |1.1.8      |            |        |     |
-|selectMeta                 |1.0.8      |            |        |     |
-|semmcci                    |1.1.3      |            |        |     |
-|semPower                   |2.1.0      |            |        |     |
-|semTests                   |0.5.0      |            |        |     |
-|semTools                   |0.5-6      |            |        |     |
-|semtree                    |0.9.19     |            |        |     |
-|sense                      |1.0.0      |            |        |     |
-|[sentopics](problems.md#sentopics)|0.7.2      |            |1       |3    |
-|seqimpute                  |1.8        |            |        |     |
-|[seqpac](problems.md#seqpac)|1.2.0      |            |        |1    |
-|[Seurat](problems.md#seurat)|5.0.1      |            |        |3    |
-|[SeuratObject](problems.md#seuratobject)|5.0.1      |            |        |3    |
-|[shapeNA](problems.md#shapena)|0.0.2      |            |        |2    |
-|[sharp](problems.md#sharp) |1.4.6      |            |        |2    |
-|[shiny](problems.md#shiny) |1.8.0      |            |        |1    |
-|[shiny.worker](problems.md#shinyworker)|0.0.1      |            |        |2    |
-|[SIAMCAT](problems.md#siamcat)|2.6.0      |            |        |3    |
-|[sigminer](problems.md#sigminer)|2.3.0      |            |        |1    |
-|[Signac](problems.md#signac)|1.12.0     |            |        |1    |
-|[signeR](problems.md#signer)|2.4.0      |            |1       |4    |
-|[SimDesign](problems.md#simdesign)|2.14       |-1          |        |2    |
-|simfinapi                  |0.2.4      |            |        |     |
-|simglm                     |0.8.9      |            |        |     |
-|simhelpers                 |0.1.2      |            |        |     |
-|simIDM                     |0.1.0      |            |        |     |
-|sims                       |0.0.3      |            |        |     |
-|simtrial                   |0.3.2      |            |        |     |
-|[sits](problems.md#sits)   |1.4.2-1    |            |1       |1    |
-|sjmisc                     |2.8.9      |            |        |     |
-|skewlmm                    |1.1.0      |            |        |     |
-|[skpr](problems.md#skpr)   |1.6.2      |            |        |1    |
-|[SLOPE](problems.md#slope) |0.5.0      |            |1       |3    |
-|[SmCCNet](problems.md#smccnet)|2.0.2      |1           |        |     |
-|smdi                       |0.2.2      |            |        |     |
-|[smoots](problems.md#smoots)|1.1.4      |            |1       |     |
-|sNPLS                      |1.0.27     |            |        |     |
-|sociome                    |2.2.5      |            |        |     |
-|[solitude](problems.md#solitude)|1.1.3      |            |        |1    |
-|sovereign                  |1.2.1      |            |        |     |
-|[SpaDES.core](problems.md#spadescore)|2.0.3      |            |        |2    |
-|[SpaDES.tools](problems.md#spadestools)|2.0.5      |            |        |2    |
-|[spaMM](problems.md#spamm) |4.4.16     |            |        |2    |
-|[sparrpowR](problems.md#sparrpowr)|0.2.8      |            |1       |     |
-|[SPARSEMODr](problems.md#sparsemodr)|1.2.0      |            |        |1    |
-|spatialTIME                |1.3.4-2    |            |        |     |
-|[spatialwarnings](problems.md#spatialwarnings)|3.0.3      |            |2       |1    |
-|spdesign                   |0.0.3      |            |        |     |
-|specr                      |1.0.0      |            |        |     |
-|sperrorest                 |3.0.5      |            |        |     |
-|spFSR                      |2.0.4      |            |        |     |
-|[sphunif](problems.md#sphunif)|1.3.0      |            |1       |2    |
-|[spNetwork](problems.md#spnetwork)|0.4.3.8    |            |1       |1    |
-|SPOT                       |2.11.14    |            |        |     |
-|[spsh](problems.md#spsh)   |1.1.0      |            |        |1    |
-|[squat](problems.md#squat) |0.3.0      |            |1       |1    |
-|[ssdtools](problems.md#ssdtools)|1.0.6      |            |        |1    |
-|[StackImpute](problems.md#stackimpute)|0.1.0      |            |        |1    |
-|[stars](problems.md#stars) |0.6-4      |1 -1 __+1__ |        |2    |
-|[startR](failures.md#startr)|2.3.1      |1           |        |     |
-|steps                      |1.3.0      |            |        |     |
-|[stppSim](problems.md#stppsim)|1.3.2      |            |1       |     |
-|supercells                 |1.0.0      |            |        |     |
-|[superMICE](problems.md#supermice)|1.1.1      |            |        |1    |
-|[survstan](problems.md#survstan)|0.0.6.1    |            |        |3    |
-|[svars](problems.md#svars) |1.3.11     |            |1       |1    |
-|svyweight                  |0.1.0      |            |        |     |
-|[SynDI](problems.md#syndi) |0.1.0      |            |        |1    |
-|[synergyfinder](problems.md#synergyfinder)|3.10.3     |            |1       |3    |
-|[tableschema.r](problems.md#tableschemar)|1.1.2      |            |        |1    |
-|tarchetypes                |0.7.12     |            |        |     |
-|[targeted](problems.md#targeted)|0.4        |            |1       |1    |
-|[targets](problems.md#targets)|1.4.1      |            |        |1    |
-|TaxaNorm                   |2.4        |            |        |     |
-|[TDApplied](problems.md#tdapplied)|3.0.2      |            |        |1    |
-|tealeaves                  |1.0.6      |            |        |     |
-|templr                     |0.2-0      |            |        |     |
-|tern.mmrm                  |0.3.0      |            |        |     |
-|TestDataImputation         |2.3        |            |        |     |
-|[text](problems.md#text)   |1.2.0      |            |        |1    |
-|[tglkmeans](problems.md#tglkmeans)|0.5.4      |            |        |2    |
-|[this.path](problems.md#thispath)|2.3.1      |            |        |2    |
-|tidyMC                     |1.0.0      |            |        |     |
-|tidyqwi                    |0.1.2      |            |        |     |
-|tidySEM                    |0.2.6      |            |        |     |
-|[timetk](problems.md#timetk)|2.9.0      |            |        |1    |
-|tipmap                     |0.5.2      |            |        |     |
-|TKCat                      |1.0.7      |            |        |     |
-|TOU                        |0.1.0      |            |        |     |
-|[trawl](problems.md#trawl) |0.2.2      |            |        |1    |
-|[TreeSearch](problems.md#treesearch)|1.4.0      |            |        |1    |
-|[TriDimRegression](failures.md#tridimregression)|1.0.2      |1           |        |     |
-|tsfeatures                 |1.1.1      |            |        |     |
-|[txshift](problems.md#txshift)|0.3.8      |            |        |1    |
-|uci                        |0.3.0      |            |        |     |
-|[UCSCXenaShiny](problems.md#ucscxenashiny)|1.1.10     |            |        |1    |
-|[updog](problems.md#updog) |2.1.5      |            |1       |1    |
-|vetiver                    |0.2.5      |            |        |     |
-|[vip](problems.md#vip)     |0.4.1      |            |        |2    |
-|vivid                      |0.2.8      |            |        |     |
-|[vmeasur](problems.md#vmeasur)|0.1.4      |            |1       |     |
-|webdeveloper               |1.0.5      |            |        |     |
-|[WeightedCluster](problems.md#weightedcluster)|1.6-4      |            |1       |     |
-|[weights](problems.md#weights)|1.0.4      |            |1       |     |
-|whitewater                 |0.1.3      |            |        |     |
-|wildmeta                   |0.3.2      |            |        |     |
-|[wru](problems.md#wru)     |1.0.1      |            |1       |3    |
-|[XNAString](problems.md#xnastring)|1.10.0     |            |1       |3    |
-|yfR                        |1.1.0      |            |        |     |
+|package             |version |error |warning |note |
+|:-------------------|:-------|:-----|:-------|:----|
+|[adea](problems.md#adea)|1.5.1   |1     |        |     |
+|alookr              |0.3.9   |      |        |     |
+|bigparallelr        |0.3.2   |      |        |     |
+|bigreadr            |0.2.5   |      |        |     |
+|[bootUR](problems.md#bootur)|1.0.4   |      |        |2    |
+|[breathtestcore](problems.md#breathtestcore)|0.8.7   |      |        |2    |
+|[breathteststan](problems.md#breathteststan)|0.8.5   |      |        |2    |
+|[COTAN](problems.md#cotan)|2.4.4   |      |        |3    |
+|CptNonPar           |0.2.1   |      |        |     |
+|dataquieR           |2.1.0   |      |        |     |
+|[decoupleR](problems.md#decoupler)|2.10.0  |1     |1       |1    |
+|DEoptim             |2.2-8   |      |        |     |
+|[desla](problems.md#desla)|0.3.0   |      |        |1    |
+|fiery               |1.2.1   |      |        |     |
+|fmeffects           |0.1.3   |      |        |     |
+|fsemipar            |1.1.1   |      |        |     |
+|future              |1.33.2  |      |        |     |
+|future.batchtools   |0.12.1  |      |        |     |
+|future.mirai        |0.2.2   |      |        |     |
+|GREENeR             |1.0.0   |      |        |     |
+|greta               |0.4.5   |      |        |     |
+|IFAA                |1.6.0   |      |        |     |
+|[InPAS](problems.md#inpas)|2.12.0  |      |1       |2    |
+|[JMbayes2](problems.md#jmbayes2)|0.5-0   |      |        |1    |
+|kernelboot          |0.1.10  |      |        |     |
+|LWFBrook90R         |0.5.3   |      |        |     |
+|[mappp](problems.md#mappp)|1.0.0   |      |        |1    |
+|[mice](problems.md#mice)|3.16.0  |-1    |        |3    |
+|mlr3                |0.20.1  |      |        |     |
+|[mmrm](problems.md#mmrm)|0.3.12  |1     |        |1    |
+|[modeltime](problems.md#modeltime)|1.2.8   |      |        |1    |
+|multilevelmediation |0.3.1   |      |        |     |
+|[NCC](problems.md#ncc)|1.0     |      |        |1    |
+|[nebula](problems.md#nebula)|1.5.3   |      |        |1    |
+|[outliers.ts.oga](problems.md#outlierstsoga)|0.0.1   |      |1       |     |
+|parseRPDR           |1.1.1   |      |        |     |
+|[pgxRpi](problems.md#pgxrpi)|1.0.3   |2     |        |1    |
+|[pmartR](problems.md#pmartr)|2.4.5   |      |        |2    |
+|proffer             |0.1.6   |      |        |     |
+|[QDNAseq](problems.md#qdnaseq)|1.40.0  |      |1       |1    |
+|[qtl2pleio](problems.md#qtl2pleio)|1.4.3   |      |        |2    |
+|Rtapas              |1.2     |      |        |     |
+|SCDB                |0.4.0   |      |        |     |
+|[scruff](problems.md#scruff)|1.22.0  |      |        |5    |
+|simIDM              |0.1.0   |      |        |     |
+|specr               |1.0.0   |      |        |     |
+|[streetscape](problems.md#streetscape)|1.0.2   |      |1       |1    |
+|targets             |1.7.1   |      |        |     |
+|TaxaNorm            |2.4     |      |        |     |
+|[TDApplied](problems.md#tdapplied)|3.0.3   |      |        |1    |
+|tern.mmrm           |0.3.1   |      |        |     |
+|TSEAL               |0.1.3   |      |        |     |
+|wildmeta            |0.3.2   |      |        |     |
+|xega                |0.9.0.0 |      |        |     |
+|xegaPopulation      |1.0.0.0 |      |        |     |
 
diff --git a/revdep/cran.md b/revdep/cran.md
index bf2849e4..d56830e3 100644
--- a/revdep/cran.md
+++ b/revdep/cran.md
@@ -1,22 +1,7 @@
 ## revdepcheck results
 
-We checked 593 reverse dependencies (556 from CRAN + 37 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 55 reverse dependencies (48 from CRAN + 7 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 1 new problems
- * We failed to check 5 packages
+ * We saw 0 new problems
+ * We failed to check 0 packages
 
-Issues with CRAN packages are summarised below.
-
-### New problems
-(This reports the first line of each new failure)
-
-* stars
-  checking examples ...sh: line 1: 48234 Aborted                 (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R'
-
-### Failed to check
-
-* cft              (NA)
-* erah             (NA)
-* rmsb             (NA)
-* startR           (NA)
-* TriDimRegression (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
index 4f3ce353..9a207363 100644
--- a/revdep/failures.md
+++ b/revdep/failures.md
@@ -1,370 +1 @@
-# cft
-
-<details>
-
-* Version: 1.0.0
-* GitHub: https://github.com/earthlab/cft-CRAN
-* Source code: https://github.com/cran/cft
-* Date/Publication: 2022-10-03 07:12:18 UTC
-* Number of recursive dependencies: 90
-
-Run `revdep_details(, "cft")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘cft’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/cft/new/cft.Rcheck/00install.out’ for details.
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘cft’ ...
-** package ‘cft’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘cft’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/cft/new/cft.Rcheck/cft’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘cft’ ...
-** package ‘cft’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘cft’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/cft/old/cft.Rcheck/cft’
-
-
-```
-# erah
-
-<details>
-
-* Version: 2.0.1
-* GitHub: https://github.com/xdomingoal/erah-devel
-* Source code: https://github.com/cran/erah
-* Date/Publication: 2023-12-20 10:10:02 UTC
-* Number of recursive dependencies: 94
-
-Run `revdep_details(, "erah")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘erah’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/erah/new/erah.Rcheck/00install.out’ for details.
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘ncdf4’
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘erah’ ...
-** package ‘erah’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’
-gcc -I"/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
-gcc -I"/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c runfunc.c -o runfunc.o
-gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/lib -lR
-installing to /c4/home/henrik/repositories/parallelly/revdep/checks/erah/new/erah.Rcheck/00LOCK-erah/00new/erah/libs
-** R
-...
-** data
-*** moving datasets to lazyload DB
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘erah’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/erah/new/erah.Rcheck/erah’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘erah’ ...
-** package ‘erah’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’
-gcc -I"/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
-gcc -I"/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c runfunc.c -o runfunc.o
-gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/lib -lR
-installing to /c4/home/henrik/repositories/parallelly/revdep/checks/erah/old/erah.Rcheck/00LOCK-erah/00new/erah/libs
-** R
-...
-** data
-*** moving datasets to lazyload DB
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘erah’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/erah/old/erah.Rcheck/erah’
-
-
-```
-# Prostar
-
-<details>
-
-* Version: 1.34.5
-* GitHub: https://github.com/prostarproteomics/Prostar
-* Source code: https://github.com/cran/Prostar
-* Date/Publication: 2024-01-12
-* Number of recursive dependencies: 332
-
-Run `revdep_details(, "Prostar")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘Prostar’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/Prostar/new/Prostar.Rcheck/00install.out’ for details.
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘Prostar’ ...
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘Prostar’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/Prostar/new/Prostar.Rcheck/Prostar’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘Prostar’ ...
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘Prostar’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/Prostar/old/Prostar.Rcheck/Prostar’
-
-
-```
-# rmsb
-
-<details>
-
-* Version: 1.0-0
-* GitHub: NA
-* Source code: https://github.com/cran/rmsb
-* Date/Publication: 2023-09-26 13:10:02 UTC
-* Number of recursive dependencies: 144
-
-Run `revdep_details(, "rmsb")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘rmsb’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/rmsb/new/rmsb.Rcheck/00install.out’ for details.
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘cmdstanr’
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘rmsb’ ...
-** package ‘rmsb’ successfully unpacked and MD5 sums checked
-** using staged installation
-Error in loadNamespace(x) : there is no package called ‘rstantools’
-Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: configuration failed for package ‘rmsb’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/rmsb/new/rmsb.Rcheck/rmsb’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘rmsb’ ...
-** package ‘rmsb’ successfully unpacked and MD5 sums checked
-** using staged installation
-Error in loadNamespace(x) : there is no package called ‘rstantools’
-Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: configuration failed for package ‘rmsb’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/rmsb/old/rmsb.Rcheck/rmsb’
-
-
-```
-# startR
-
-<details>
-
-* Version: 2.3.1
-* GitHub: NA
-* Source code: https://github.com/cran/startR
-* Date/Publication: 2023-12-21 16:20:02 UTC
-* Number of recursive dependencies: 60
-
-Run `revdep_details(, "startR")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘startR’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/startR/new/startR.Rcheck/00install.out’ for details.
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘startR’ ...
-** package ‘startR’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘startR’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/startR/new/startR.Rcheck/startR’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘startR’ ...
-** package ‘startR’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘startR’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/startR/old/startR.Rcheck/startR’
-
-
-```
-# TriDimRegression
-
-<details>
-
-* Version: 1.0.2
-* GitHub: https://github.com/alexander-pastukhov/tridim-regression
-* Source code: https://github.com/cran/TriDimRegression
-* Date/Publication: 2023-09-13 14:10:03 UTC
-* Number of recursive dependencies: 100
-
-Run `revdep_details(, "TriDimRegression")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘TriDimRegression’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/00install.out’ for details.
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘TriDimRegression’ ...
-** package ‘TriDimRegression’ successfully unpacked and MD5 sums checked
-** using staged installation
-Error in loadNamespace(x) : there is no package called ‘rstantools’
-Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: configuration failed for package ‘TriDimRegression’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/TriDimRegression’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘TriDimRegression’ ...
-** package ‘TriDimRegression’ successfully unpacked and MD5 sums checked
-** using staged installation
-Error in loadNamespace(x) : there is no package called ‘rstantools’
-Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: configuration failed for package ‘TriDimRegression’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/TriDimRegression/old/TriDimRegression.Rcheck/TriDimRegression’
-
-
-```
+*Wow, no problems at all. :)*
\ No newline at end of file
diff --git a/revdep/problems.md b/revdep/problems.md
index 48d4176f..4862a1ce 100644
--- a/revdep/problems.md
+++ b/revdep/problems.md
@@ -1,37 +1,3 @@
-# ACE
-
-<details>
-
-* Version: 1.20.0
-* GitHub: https://github.com/tgac-vumc/ACE
-* Source code: https://github.com/cran/ACE
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 97
-
-Run `revdep_details(, "ACE")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Unexported object imported by a ':::' call: ‘QDNAseq:::sdDiffTrim’
-      See the note in ?`:::` about the use of this operator.
-    ```
-
-*   checking R code for possible problems ... NOTE
-    ```
-    squaremodel: no visible binding for global variable ‘cellularity’
-    Undefined global functions or variables:
-      cellularity
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: ‘corrplot’
-    ```
-
 # adea
 
 <details>
@@ -40,9 +6,9 @@ Run `revdep_details(, "ACE")` for more info
 * GitHub: NA
 * Source code: https://github.com/cran/adea
 * Date/Publication: 2023-11-24 16:00:02 UTC
-* Number of recursive dependencies: 64
+* Number of recursive dependencies: 61
 
-Run `revdep_details(, "adea")` for more info
+Run `revdepcheck::revdep_details(, "adea")` for more info
 
 </details>
 
@@ -56,207 +22,45 @@ Run `revdep_details(, "adea")` for more info
     manual.
     ```
 
-# adjustedCurves
-
-<details>
-
-* Version: 0.11.0
-* GitHub: https://github.com/RobinDenz1/adjustedCurves
-* Source code: https://github.com/cran/adjustedCurves
-* Date/Publication: 2024-02-13 12:40:02 UTC
-* Number of recursive dependencies: 189
-
-Run `revdep_details(, "adjustedCurves")` for more info
-
-</details>
-
-## In both
-
-*   checking Rd cross-references ... WARNING
-    ```
-    Missing link or links in documentation object 'cif_aiptw.Rd':
-      ‘coxph’
-    
-    Missing link or links in documentation object 'cif_aiptw_pseudo.Rd':
-      ‘multinom’
-    
-    Missing link or links in documentation object 'cif_iptw.Rd':
-      ‘multinom’
-    
-    Missing link or links in documentation object 'cif_iptw_pseudo.Rd':
-    ...
-    Missing link or links in documentation object 'surv_iptw_km.Rd':
-      ‘multinom’
-    
-    Missing link or links in documentation object 'surv_iptw_pseudo.Rd':
-      ‘multinom’
-    
-    Missing link or links in documentation object 'surv_km.Rd':
-      ‘survfit’
-    
-    See section 'Cross-references' in the 'Writing R Extensions' manual.
-    ```
-
-# AIPW
-
-<details>
-
-* Version: 0.6.3.2
-* GitHub: https://github.com/yqzhong7/AIPW
-* Source code: https://github.com/cran/AIPW
-* Date/Publication: 2021-06-11 09:30:02 UTC
-* Number of recursive dependencies: 102
-
-Run `revdep_details(, "AIPW")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘Rsolnp’ ‘SuperLearner’ ‘future.apply’ ‘ggplot2’ ‘progressr’ ‘stats’
-      ‘utils’
-      All declared Imports should be used.
-    ```
-
-# AlpsNMR
-
-<details>
-
-* Version: 4.4.0
-* GitHub: https://github.com/sipss/AlpsNMR
-* Source code: https://github.com/cran/AlpsNMR
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 187
-
-Run `revdep_details(, "AlpsNMR")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... ERROR
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘Vig01-introduction-to-alpsnmr.Rmd’ using rmarkdown
-    ! LuaTeX error .../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: b
-    ad argument #1 to 'insert' (table expected, got nil)
-    stack traceback:
-    	[C]: in function 'insert'
-    	.../texlive/texmf-dist/scripts/oberdiek/oberdiek.luatex.lua:55: in main chunk
-    	[C]: in function 'dofile'
-    	[string "\directlua "]:6: in main chunk.
-    l.139   }
-    ...
-    LaTeX failed to compile /c4/home/henrik/repositories/parallelly/revdep/checks/AlpsNMR/new/AlpsNMR.Rcheck/vign_test/AlpsNMR/vignettes/Vig02-handling-metadata-and-annotations.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Vig02-handling-metadata-and-annotations.log for more info.
-    --- failed re-building ‘Vig02-handling-metadata-and-annotations.Rmd’
-    
-    SUMMARY: processing the following files failed:
-      ‘Vig01-introduction-to-alpsnmr.Rmd’
-      ‘Vig01b-introduction-to-alpsnmr-old-api.Rmd’
-      ‘Vig02-handling-metadata-and-annotations.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# aroma.core
-
-<details>
-
-* Version: 3.3.0
-* GitHub: https://github.com/HenrikBengtsson/aroma.core
-* Source code: https://github.com/cran/aroma.core
-* Date/Publication: 2022-11-15 18:30:13 UTC
-* Number of recursive dependencies: 72
-
-Run `revdep_details(, "aroma.core")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages suggested but not available for checking:
-      'sfit', 'expectile', 'HaarSeg', 'mpcbs'
-    ```
-
-# BAMBI
+# bootUR
 
 <details>
 
-* Version: 2.3.5
-* GitHub: https://github.com/c7rishi/BAMBI
-* Source code: https://github.com/cran/BAMBI
-* Date/Publication: 2023-03-08 23:10:05 UTC
-* Number of recursive dependencies: 43
+* Version: 1.0.4
+* GitHub: https://github.com/smeekes/bootUR
+* Source code: https://github.com/cran/bootUR
+* Date/Publication: 2024-05-20 09:30:02 UTC
+* Number of recursive dependencies: 69
 
-Run `revdep_details(, "BAMBI")` for more info
+Run `revdepcheck::revdep_details(, "bootUR")` for more info
 
 </details>
 
 ## In both
 
-*   checking whether package ‘BAMBI’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/BAMBI/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/BAMBI/new/BAMBI.Rcheck/00install.out’ for details.
-    ```
-
 *   checking installed package size ... NOTE
     ```
-      installed size is  7.3Mb
+      installed size is  6.6Mb
       sub-directories of 1Mb or more:
-        libs   6.8Mb
-    ```
-
-# bamm
-
-<details>
-
-* Version: 0.4.3
-* GitHub: https://github.com/luismurao/bamm
-* Source code: https://github.com/cran/bamm
-* Date/Publication: 2022-12-20 11:10:05 UTC
-* Number of recursive dependencies: 109
-
-Run `revdep_details(, "bamm")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘bamm’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/bamm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/bamm/new/bamm.Rcheck/00install.out’ for details.
+        libs   6.2Mb
     ```
 
-*   checking C++ specification ... NOTE
+*   checking for GNU extensions in Makefiles ... NOTE
     ```
-      Specified C++11: please drop specification unless essential
+    GNU make is a SystemRequirements.
     ```
 
-# batchtools
+# breathtestcore
 
 <details>
 
-* Version: 0.9.17
-* GitHub: https://github.com/mllg/batchtools
-* Source code: https://github.com/cran/batchtools
-* Date/Publication: 2023-04-20 14:20:06 UTC
-* Number of recursive dependencies: 84
+* Version: 0.8.7
+* GitHub: https://github.com/dmenne/breathtestcore
+* Source code: https://github.com/cran/breathtestcore
+* Date/Publication: 2024-01-24 15:02:47 UTC
+* Number of recursive dependencies: 130
 
-Run `revdep_details(, "batchtools")` for more info
+Run `revdepcheck::revdep_details(, "breathtestcore")` for more info
 
 </details>
 
@@ -264,7225 +68,239 @@ Run `revdep_details(, "batchtools")` for more info
 
 *   checking package dependencies ... NOTE
     ```
-    Package suggested but not available for checking: ‘doMPI’
+    Package suggested but not available for checking: ‘breathteststan’
     ```
 
 *   checking Rd cross-references ... NOTE
     ```
-    Package unavailable to check Rd xrefs: ‘Rmpi’
+    Package unavailable to check Rd xrefs: ‘breathteststan’
     ```
 
-# bayesmove
+# breathteststan
 
 <details>
 
-* Version: 0.2.1
-* GitHub: https://github.com/joshcullen/bayesmove
-* Source code: https://github.com/cran/bayesmove
-* Date/Publication: 2021-10-22 08:50:09 UTC
-* Number of recursive dependencies: 168
+* Version: 0.8.5
+* GitHub: https://github.com/dmenne/breathteststan
+* Source code: https://github.com/cran/breathteststan
+* Date/Publication: 2024-01-13 17:20:06 UTC
+* Number of recursive dependencies: 153
 
-Run `revdep_details(, "bayesmove")` for more info
+Run `revdepcheck::revdep_details(, "breathteststan")` for more info
 
 </details>
 
 ## In both
 
-*   checking whether package ‘bayesmove’ can be installed ... WARNING
+*   checking installed package size ... NOTE
     ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/bayesmove/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/bayesmove/new/bayesmove.Rcheck/00install.out’ for details.
+      installed size is 64.2Mb
+      sub-directories of 1Mb or more:
+        libs  64.0Mb
     ```
 
-# BBEST
-
-<details>
-
-* Version: 0.1-8
-* GitHub: NA
-* Source code: https://github.com/cran/BBEST
-* Date/Publication: 2020-11-19 13:20:05 UTC
-* Number of recursive dependencies: 60
-
-Run `revdep_details(, "BBEST")` for more info
-
-</details>
-
-## In both
-
-*   checking LazyData ... NOTE
+*   checking for GNU extensions in Makefiles ... NOTE
     ```
-      'LazyData' is specified without a 'data' directory
+    GNU make is a SystemRequirements.
     ```
 
-# BEKKs
+# COTAN
 
 <details>
 
-* Version: 1.4.4
-* GitHub: NA
-* Source code: https://github.com/cran/BEKKs
-* Date/Publication: 2024-01-14 15:50:09 UTC
-* Number of recursive dependencies: 86
+* Version: 2.4.4
+* GitHub: https://github.com/seriph78/COTAN
+* Source code: https://github.com/cran/COTAN
+* Date/Publication: 2024-06-30
+* Number of recursive dependencies: 266
 
-Run `revdep_details(, "BEKKs")` for more info
+Run `revdepcheck::revdep_details(, "COTAN")` for more info
 
 </details>
 
 ## In both
 
-*   checking whether package ‘BEKKs’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/BEKKs/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/BEKKs/new/BEKKs.Rcheck/00install.out’ for details.
-    ```
-
 *   checking installed package size ... NOTE
     ```
-      installed size is 18.5Mb
+      installed size is  9.1Mb
       sub-directories of 1Mb or more:
-        libs  17.6Mb
+        doc   7.4Mb
     ```
 
-# BENMMI
-
-<details>
-
-* Version: 4.3-7
-* GitHub: NA
-* Source code: https://github.com/cran/BENMMI
-* Date/Publication: 2020-10-12 08:20:02 UTC
-* Number of recursive dependencies: 58
-
-Run `revdep_details(, "BENMMI")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘BENMMI’ can be installed ... WARNING
+*   checking dependencies in R code ... NOTE
     ```
-    Found the following significant warnings:
-      Warning: no DISPLAY variable so Tk is not available
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/BENMMI/new/BENMMI.Rcheck/00install.out’ for details.
+    'library' or 'require' call to ‘torch’ in package code.
+      Please use :: or requireNamespace() instead.
+      See section 'Suggested packages' in the 'Writing R Extensions' manual.
+    Unexported object imported by a ':::' call: ‘ggplot2:::ggname’
+      See the note in ?`:::` about the use of this operator.
     ```
 
-*   checking re-building of vignette outputs ... WARNING
+*   checking R code for possible problems ... NOTE
     ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘BENMMI_User_Manual.Rnw’ using knitr
-    Error: processing vignette 'BENMMI_User_Manual.Rnw' failed with diagnostics:
-    Running 'texi2dvi' on 'BENMMI_User_Manual.tex' failed.
-    LaTeX errors:
-    ! LaTeX Error: File `sectsty.sty' not found.
-    
-    Type X to quit or <RETURN> to proceed,
-    or enter new name. (Default extension: sty)
-    
+    GDIPlot: no visible binding for global variable ‘sum.raw.norm’
+    GDIPlot: no visible binding for global variable ‘GDI’
+    UMAPPlot: no visible binding for global variable ‘x’
+    UMAPPlot: no visible binding for global variable ‘y’
+    calculateCoex_Legacy: no visible binding for global variable
+      ‘expectedNN’
+    calculateCoex_Legacy: no visible binding for global variable
+      ‘expectedNY’
+    calculateCoex_Legacy: no visible binding for global variable
+      ‘expectedYN’
     ...
-    l.62 \usepackage
-                    {tocloft} % Required to give customize the table of contents...
-    !  ==> Fatal error occurred, no output PDF file produced!
-    --- failed re-building ‘FAQ.Rnw’
-    
-    SUMMARY: processing the following files failed:
-      ‘BENMMI_User_Manual.Rnw’ ‘FAQ.Rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
+    coerce,COTAN-scCOTAN: no visible binding for global variable
+      ‘clusterData’
+    Undefined global functions or variables:
+      . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 a cl1 cl2
+      clusterData clusters coex condName conditions expectedN expectedNN
+      expectedNY expectedYN expectedYY g2 group hk keys lambda means
+      mit.percentage n nu nuPlot obj objSeurat observedNN observedNY
+      observedY observedYN observedYY permMap rankGenes rawNorm
+      secondaryMarkers sum.raw.norm type useTorch usedMaxResolution values
+      violinwidth width x xmax xmaxv xminv y zoomedNuPlot
     ```
 
-# bigDM
+# decoupleR
 
 <details>
 
-* Version: 0.5.3
-* GitHub: https://github.com/spatialstatisticsupna/bigDM
-* Source code: https://github.com/cran/bigDM
-* Date/Publication: 2023-10-17 12:50:02 UTC
-* Number of recursive dependencies: 135
+* Version: 2.10.0
+* GitHub: https://github.com/saezlab/decoupleR
+* Source code: https://github.com/cran/decoupleR
+* Date/Publication: 2024-05-29
+* Number of recursive dependencies: 267
 
-Run `revdep_details(, "bigDM")` for more info
+Run `revdepcheck::revdep_details(, "decoupleR")` for more info
 
 </details>
 
 ## In both
 
-*   checking package dependencies ... NOTE
+*   checking tests ...
     ```
-    Package suggested but not available for checking: ‘INLA’
+      Running ‘testthat.R’
+     ERROR
+    Running the tests in ‘tests/testthat.R’ failed.
+    Last 50 lines of output:
+        |                                                                      |   0%
+        |                                                                            
+        |===================================                                   |  50%
+        |                                                                            
+        |======================================================================| 100%
+      
+    ...
+      Backtrace:
+          ▆
+       1. ├─decoupleR::get_progeny(organism = "mouse") at test-omnipath.R:19:3
+       2. │ └─... %>% ...
+       3. ├─rlang::set_names(., c("source", "target", "weight", "p_value"))
+       4. └─rlang::abort(message = message)
+      
+      [ FAIL 1 | WARN 4 | SKIP 0 | PASS 34 ]
+      Error: Test failures
+      Execution halted
+    ```
+
+*   checking Rd cross-references ... WARNING
+    ```
+    Missing link or links in Rd file 'run_gsva.Rd':
+      ‘GSVA::gsva’ ‘GeneSetCollection’
+    
+    See section 'Cross-references' in the 'Writing R Extensions' manual.
     ```
 
-*   checking data for non-ASCII characters ... NOTE
+*   checking installed package size ... NOTE
     ```
-      Note: found 940 marked Latin-1 strings
+      installed size is  8.8Mb
+      sub-directories of 1Mb or more:
+        doc       6.6Mb
+        extdata   1.4Mb
     ```
 
-# bigsnpr
+# desla
 
 <details>
 
-* Version: 1.12.2
-* GitHub: https://github.com/privefl/bigsnpr
-* Source code: https://github.com/cran/bigsnpr
-* Date/Publication: 2023-03-28 09:20:02 UTC
-* Number of recursive dependencies: 151
+* Version: 0.3.0
+* GitHub: https://github.com/RobertAdamek/desla
+* Source code: https://github.com/cran/desla
+* Date/Publication: 2023-06-29 11:50:06 UTC
+* Number of recursive dependencies: 35
 
-Run `revdep_details(, "bigsnpr")` for more info
+Run `revdepcheck::revdep_details(, "desla")` for more info
 
 </details>
 
 ## In both
 
-*   checking whether package ‘bigsnpr’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/bigsnpr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/bigsnpr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/bigsnpr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/bigsnpr/new/bigsnpr.Rcheck/00install.out’ for details.
-    ```
-
 *   checking installed package size ... NOTE
     ```
-      installed size is 19.9Mb
+      installed size is 13.1Mb
       sub-directories of 1Mb or more:
-        libs  18.6Mb
+        libs  13.0Mb
     ```
 
-# bigstatsr
+# InPAS
 
 <details>
 
-* Version: 1.5.12
-* GitHub: https://github.com/privefl/bigstatsr
-* Source code: https://github.com/cran/bigstatsr
-* Date/Publication: 2022-10-14 08:32:38 UTC
-* Number of recursive dependencies: 119
+* Version: 2.12.0
+* GitHub: NA
+* Source code: https://github.com/cran/InPAS
+* Date/Publication: 2024-04-30
+* Number of recursive dependencies: 165
 
-Run `revdep_details(, "bigstatsr")` for more info
+Run `revdepcheck::revdep_details(, "InPAS")` for more info
 
 </details>
 
 ## In both
 
-*   checking whether package ‘bigstatsr’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/bigstatsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/bigstatsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/bigstatsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/bigstatsr/new/bigstatsr.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
+*   checking Rd cross-references ... WARNING
     ```
-      Specified C++11: please drop specification unless essential
+    Missing link or links in Rd file 'get_ssRleCov.Rd':
+      ‘[BSgenome:BSgenomeForge]{BSgenome::forgeBSgenomeDataPkg()}’
+    
+    Missing link or links in Rd file 'set_globals.Rd':
+      ‘[BSgenome:BSgenomeForge]{BSgenome::forgeBSgenomeDataPkg()}’
+    
+    See section 'Cross-references' in the 'Writing R Extensions' manual.
     ```
 
-*   checking installed package size ... NOTE
+*   checking dependencies in R code ... NOTE
     ```
-      installed size is 20.9Mb
-      sub-directories of 1Mb or more:
-        extdata   2.3Mb
-        libs     18.0Mb
+    There are ::: calls to the package's namespace in its code. A package
+      almost never needs to use ::: for its own objects:
+      ‘adjust_distalCPs’ ‘adjust_proximalCPs’ ‘adjust_proximalCPsByNBC’
+      ‘adjust_proximalCPsByPWM’ ‘calculate_mse’ ‘find_valleyBySpline’
+      ‘get_PAscore’ ‘get_PAscore2’ ‘remove_convergentUTR3s’
+      ‘search_distalCPs’ ‘search_proximalCPs’
     ```
 
-*   checking dependencies in R code ... NOTE
+*   checking Rd \usage sections ... NOTE
     ```
-    Namespace in Imports field not imported from: ‘rmio’
-      All declared Imports should be used.
+    Documented arguments not in \usage in Rd file 'get_UTR3TotalCov.Rd':
+      ‘gcCompensationensation’
+    
+    Functions with \usage entries need to have the appropriate \alias
+    entries, and all their arguments documented.
+    The \usage entries must correspond to syntactically valid R code.
+    See chapter ‘Writing R documentation files’ in the ‘Writing R
+    Extensions’ manual.
     ```
 
-# biscuiteer
+# JMbayes2
 
 <details>
 
-* Version: 1.16.0
-* GitHub: https://github.com/trichelab/biscuiteer
-* Source code: https://github.com/cran/biscuiteer
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 223
-
-Run `revdep_details(, "biscuiteer")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘biscuiteer’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      Warning: replacing previous import ‘BiocParallel::bpstart’ by ‘QDNAseq::bpstart’ when loading ‘biscuiteer’
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/biscuiteer/new/biscuiteer.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.9Mb
-      sub-directories of 1Mb or more:
-        data      1.1Mb
-        extdata   3.4Mb
-    ```
-
-*   checking package subdirectories ... NOTE
-    ```
-    Problems with news in ‘NEWS.md’:
-    No news entries found.
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Unexported object imported by a ':::' call: ‘QDNAseq:::expectedVariance’
-      See the note in ?`:::` about the use of this operator.
-    ```
-
-# bistablehistory
-
-<details>
-
-* Version: 1.1.2
-* GitHub: https://github.com/alexander-pastukhov/bistablehistory
-* Source code: https://github.com/cran/bistablehistory
-* Date/Publication: 2023-09-13 13:20:09 UTC
-* Number of recursive dependencies: 92
-
-Run `revdep_details(, "bistablehistory")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 65.5Mb
-      sub-directories of 1Mb or more:
-        libs  64.6Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# blavaan
-
-<details>
-
-* Version: 0.5-3
-* GitHub: https://github.com/ecmerkle/blavaan
-* Source code: https://github.com/cran/blavaan
-* Date/Publication: 2024-01-19 22:50:02 UTC
-* Number of recursive dependencies: 98
-
-Run `revdep_details(, "blavaan")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘cmdstanr’
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 165.5Mb
-      sub-directories of 1Mb or more:
-        R           1.2Mb
-        libs      162.6Mb
-        testdata    1.4Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# bootUR
-
-<details>
-
-* Version: 1.0.3
-* GitHub: https://github.com/smeekes/bootUR
-* Source code: https://github.com/cran/bootUR
-* Date/Publication: 2024-01-26 17:40:06 UTC
-* Number of recursive dependencies: 72
-
-Run `revdep_details(, "bootUR")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘bootUR’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/bootUR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/bootUR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/bootUR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/bootUR/new/bootUR.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  6.5Mb
-      sub-directories of 1Mb or more:
-        libs   6.2Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# breathteststan
-
-<details>
-
-* Version: 0.8.5
-* GitHub: https://github.com/dmenne/breathteststan
-* Source code: https://github.com/cran/breathteststan
-* Date/Publication: 2024-01-13 17:20:06 UTC
-* Number of recursive dependencies: 154
-
-Run `revdep_details(, "breathteststan")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 57.4Mb
-      sub-directories of 1Mb or more:
-        libs  57.2Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# brms
-
-<details>
-
-* Version: 2.20.4
-* GitHub: https://github.com/paul-buerkner/brms
-* Source code: https://github.com/cran/brms
-* Date/Publication: 2023-09-25 19:00:09 UTC
-* Number of recursive dependencies: 200
-
-Run `revdep_details(, "brms")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘cmdstanr’
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  7.6Mb
-      sub-directories of 1Mb or more:
-        R     3.0Mb
-        doc   3.5Mb
-    ```
-
-# bsitar
-
-<details>
-
-* Version: 0.1.1
-* GitHub: https://github.com/Sandhu-SS/bsitar
-* Source code: https://github.com/cran/bsitar
-* Date/Publication: 2024-01-25 13:50:09 UTC
-* Number of recursive dependencies: 167
-
-Run `revdep_details(, "bsitar")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.3Mb
-      sub-directories of 1Mb or more:
-        data   2.9Mb
-        doc    1.3Mb
-    ```
-
-# bucky
-
-<details>
-
-* Version: 1.0.7
-* GitHub: https://github.com/atahk/bucky
-* Source code: https://github.com/cran/bucky
-* Date/Publication: 2022-03-25 23:10:02 UTC
-* Number of recursive dependencies: 84
-
-Run `revdep_details(, "bucky")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages which this enhances but not available for checking:
-      'texreg', 'stargazer'
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: ‘mitools’
-    ```
-
-# censcyt
-
-<details>
-
-* Version: 1.10.0
-* GitHub: https://github.com/retogerber/censcyt
-* Source code: https://github.com/cran/censcyt
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 195
-
-Run `revdep_details(, "censcyt")` for more info
-
-</details>
-
-## In both
-
-*   checking for hidden files and directories ... NOTE
-    ```
-    Found the following hidden files and directories:
-      .travis.yml
-    These were most likely included in error. See section ‘Package
-    structure’ in the ‘Writing R Extensions’ manual.
-    ```
-
-*   checking R code for possible problems ... NOTE
-    ```
-    mean_residual_life_imputation: no visible binding for global variable
-      ‘hazard’
-    Undefined global functions or variables:
-      hazard
-    ```
-
-# ceRNAnetsim
-
-<details>
-
-* Version: 1.14.1
-* GitHub: https://github.com/selcenari/ceRNAnetsim
-* Source code: https://github.com/cran/ceRNAnetsim
-* Date/Publication: 2023-12-18
-* Number of recursive dependencies: 101
-
-Run `revdep_details(, "ceRNAnetsim")` for more info
-
-</details>
-
-## In both
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘ceRNAnetsim-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: find_node_perturbation
-    > ### Title: Calculates average expression changes of all (or specified)
-    > ###   nodes except trigger and finds the perturbed node count for all (or
-    > ###   specified) nodes in system.
-    > ### Aliases: find_node_perturbation
-    > 
-    > ### ** Examples
-    ...
-     23. │                 └─dplyr (local) eval()
-     24. └─tidygraph::map_bfs(...)
-     25.   └─tidygraph:::bfs_df(graph, root, mode, unreachable)
-     26.     └─tibble::tibble(...)
-     27.       └─tibble:::tibble_quos(xs, .rows, .name_repair)
-     28.         └─tibble:::vectbl_recycle_rows(...)
-     29.           └─tibble:::abort_incompatible_size(...)
-     30.             └─tibble:::tibble_abort(...)
-     31.               └─rlang::abort(x, class, ..., call = call, parent = parent, use_cli_format = TRUE)
-    Execution halted
-    ```
-
-*   checking tests ...
-    ```
-      Running ‘testthat.R’
-     ERROR
-    Running the tests in ‘tests/testthat.R’ failed.
-    Last 50 lines of output:
-      > library(testthat)
-      > library(ceRNAnetsim)
-      Loading required package: dplyr
-      
-      Attaching package: 'dplyr'
-      
-    ...
-      ══ Failed tests ════════════════════════════════════════════════════════════════
-      ── Failure ('test-iter_perturb.R:33:3'): Could the functions work?  ────────────
-      `node_efficiencies` not equal to c(NA, NA, NA, 3.18, 2.27, 3.18, NA, 32).
-      2/8 mismatches (average diff: 14.9)
-      [5] 3.18 -  2.27 ==   0.91
-      [8] 3.18 - 32.00 == -28.82
-      
-      [ FAIL 1 | WARN 36 | SKIP 0 | PASS 36 ]
-      Error: Test failures
-      Execution halted
-    ```
-
-*   checking re-building of vignette outputs ... ERROR
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘auxiliary_commands.Rmd’ using rmarkdown
-    --- finished re-building ‘auxiliary_commands.Rmd’
-    
-    --- re-building ‘basic_usage.Rmd’ using rmarkdown
-    --- finished re-building ‘basic_usage.Rmd’
-    
-    --- re-building ‘convenient_iteration.Rmd’ using rmarkdown
-    
-    Quitting from lines 226-233 [unnamed-chunk-15] (convenient_iteration.Rmd)
-    ...
-    • Size 5: Existing data.
-    • Size 53: Column `rank`.
-    ℹ Only values of size one are recycled.
-    --- failed re-building ‘mirtarbase_example.Rmd’
-    
-    SUMMARY: processing the following files failed:
-      ‘convenient_iteration.Rmd’ ‘mirtarbase_example.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-*   checking R code for possible problems ... NOTE
-    ```
-    simulate: no visible binding for global variable ‘avg_count_current’
-    simulate: no visible binding for global variable ‘avg_count_pre’
-    Undefined global functions or variables:
-      avg_count_current avg_count_pre
-    ```
-
-# cft
-
-<details>
-
-* Version: 1.0.0
-* GitHub: https://github.com/earthlab/cft-CRAN
-* Source code: https://github.com/cran/cft
-* Date/Publication: 2022-10-03 07:12:18 UTC
-* Number of recursive dependencies: 90
-
-Run `revdep_details(, "cft")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘cft’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/cft/new/cft.Rcheck/00install.out’ for details.
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘cft’ ...
-** package ‘cft’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘cft’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/cft/new/cft.Rcheck/cft’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘cft’ ...
-** package ‘cft’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘cft’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/cft/old/cft.Rcheck/cft’
-
-
-```
-# ChromSCape
-
-<details>
-
-* Version: 1.12.0
-* GitHub: https://github.com/vallotlab/ChromSCape
-* Source code: https://github.com/cran/ChromSCape
-* Date/Publication: 2023-10-25
-* Number of recursive dependencies: 232
-
-Run `revdep_details(, "ChromSCape")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... WARNING
-    ```
-    'library' or 'require' call not declared from: ‘dplyr’
-    'library' or 'require' call to ‘dplyr’ in package code.
-      Please use :: or requireNamespace() instead.
-      See section 'Suggested packages' in the 'Writing R Extensions' manual.
-    ```
-
-*   checking for code/documentation mismatches ... WARNING
-    ```
-    Codoc mismatches from documentation object 'generate_analysis':
-    generate_analysis
-      Code: function(input_data_folder, analysis_name = "Analysis_1",
-                     output_directory = "./", input_data_type = c("scBED",
-                     "DenseMatrix", "SparseMatrix", "scBAM")[1],
-                     feature_count_on = c("bins", "genebody", "peaks")[1],
-                     feature_count_parameter = 50000, rebin_sparse_matrix =
-                     FALSE, ref_genome = c("hg38", "mm10")[1], run =
-                     c("filter", "CNA", "cluster", "consensus", "coverage",
-                     "DA", "GSA", "report")[c(1, 3, 5, 6, 7, 8)],
-    ...
-      Mismatches in argument names:
-        Position: 5 Code: feature_count_on Docs: rebin_sparse_matrix
-        Position: 6 Code: feature_count_parameter Docs: feature_count_on
-        Position: 7 Code: rebin_sparse_matrix Docs: feature_count_parameter
-      Mismatches in argument default values:
-        Name: 'run'
-        Code: c("filter", "CNA", "cluster", "consensus", "coverage", "DA", 
-              "GSA", "report")[c(1, 3, 5, 6, 7, 8)]
-        Docs: c("filter", "CNA", "cluster", "consensus", "peak_call", "coverage", 
-              "DA", "GSA", "report")[c(1, 3, 6, 7, 8, 9)]
-    ```
-
-*   checking Rd \usage sections ... WARNING
-    ```
-    Undocumented arguments in documentation object 'rebin_matrix'
-      ‘rebin_function’
-    
-    Functions with \usage entries need to have the appropriate \alias
-    entries, and all their arguments documented.
-    The \usage entries must correspond to syntactically valid R code.
-    See chapter ‘Writing R documentation files’ in the ‘Writing R
-    Extensions’ manual.
-    ```
-
-*   checking examples ... WARNING
-    ```
-    Found the following significant warnings:
-    
-      Warning: 'as(<matrix>, "dspMatrix")' is deprecated.
-    Deprecated functions may be defunct as soon as of the next release of
-    R.
-    See ?Deprecated.
-    ```
-
-*   checking for hidden files and directories ... NOTE
-    ```
-    Found the following hidden files and directories:
-      .BBSoptions
-    These were most likely included in error. See section ‘Package
-    structure’ in the ‘Writing R Extensions’ manual.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  8.3Mb
-      sub-directories of 1Mb or more:
-        data   1.4Mb
-        doc    2.9Mb
-        libs   1.0Mb
-        www    2.0Mb
-    ```
-
-*   checking R code for possible problems ... NOTE
-    ```
-    bams_to_matrix_indexes: no visible binding for global variable
-      ‘files_dir_list’
-    enrich_TF_ChEA3_genes: no visible binding for global variable
-      ‘CheA3_TF_nTargets’
-    filter_correlated_cell_scExp: no visible binding for global variable
-      ‘run_tsne’
-    generate_analysis: no visible global function definition for ‘head’
-    generate_analysis: no visible binding for global variable ‘k’
-    generate_analysis: no visible binding for global variable
-      ‘clusterConsensus’
-    ...
-    subset_bam_call_peaks: no visible binding for global variable
-      ‘merged_bam’
-    Undefined global functions or variables:
-      CheA3_TF_nTargets Component Fri_cyto Gain_or_Loss Gene TF V1 V2
-      absolute_value cluster clusterConsensus cytoBand files_dir_list genes
-      group head k merged_bam molecule ncells new_row orientation
-      origin_value percent_active run_tsne sample_id total_counts
-    Consider adding
-      importFrom("utils", "head")
-    to your NAMESPACE file.
-    ```
-
-*   checking Rd files ... NOTE
-    ```
-    prepare_Rd: raw_counts_to_sparse_matrix.Rd:6-8: Dropping empty section \source
-    ```
-
-# clickR
-
-<details>
-
-* Version: 0.9.39
-* GitHub: NA
-* Source code: https://github.com/cran/clickR
-* Date/Publication: 2023-08-07 17:40:06 UTC
-* Number of recursive dependencies: 9
-
-Run `revdep_details(, "clickR")` for more info
-
-</details>
-
-## In both
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 1 marked UTF-8 string
-    ```
-
-# codebook
-
-<details>
-
-* Version: 0.9.2
-* GitHub: https://github.com/rubenarslan/codebook
-* Source code: https://github.com/cran/codebook
-* Date/Publication: 2020-06-06 23:40:03 UTC
-* Number of recursive dependencies: 156
-
-Run `revdep_details(, "codebook")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘userfriendlyscience’
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘graphics’ ‘jsonlite’ ‘rlang’ ‘tidyselect’ ‘vctrs’
-      All declared Imports should be used.
-    ```
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 65 marked UTF-8 strings
-    ```
-
-# collinear
-
-<details>
-
-* Version: 1.1.1
-* GitHub: NA
-* Source code: https://github.com/cran/collinear
-* Date/Publication: 2023-12-08 08:50:02 UTC
-* Number of recursive dependencies: 55
-
-Run `revdep_details(, "collinear")` for more info
-
-</details>
-
-## In both
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 89 marked Latin-1 strings
-      Note: found 1203 marked UTF-8 strings
-    ```
-
-# COTAN
-
-<details>
-
-* Version: 2.2.3
-* GitHub: https://github.com/seriph78/COTAN
-* Source code: https://github.com/cran/COTAN
-* Date/Publication: 2024-01-02
-* Number of recursive dependencies: 262
-
-Run `revdep_details(, "COTAN")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  7.2Mb
-      sub-directories of 1Mb or more:
-        doc   5.7Mb
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Unexported object imported by a ':::' call: ‘ggplot2:::ggname’
-      See the note in ?`:::` about the use of this operator.
-    ```
-
-*   checking R code for possible problems ... NOTE
-    ```
-    GDIPlot: no visible binding for global variable ‘sum.raw.norm’
-    GDIPlot: no visible binding for global variable ‘GDI’
-    UMAPPlot: no visible binding for global variable ‘x’
-    UMAPPlot: no visible binding for global variable ‘y’
-    calculateG: no visible binding for global variable ‘observedNN’
-    calculateG: no visible binding for global variable ‘observedNY’
-    calculateG: no visible binding for global variable ‘observedYN’
-    calculateG: no visible binding for global variable ‘observedYY’
-    calculateG: no visible binding for global variable ‘expectedNN’
-    calculateG: no visible binding for global variable ‘expectedNY’
-    ...
-    coerce,COTAN-scCOTAN: no visible binding for global variable
-      ‘clusterData’
-    Undefined global functions or variables:
-      . .x CellNumber Cluster Condition ExpGenes GCS GDI PC1 PC2 a cl1 cl2
-      clusterData clusters condName conditions expectedN expectedNN
-      expectedNY expectedYN expectedYY g2 group hk keys lambda means
-      mit.percentage n nu nuPlot objSeurat observedNN observedNY observedY
-      observedYN observedYY outputCoexDF rankGenes rawNorm secondaryMarkers
-      sum.raw.norm usedMaxResolution values violinwidth width x xmax xmaxv
-      xminv y zoomedNuPlot
-    ```
-
-# cpi
-
-<details>
-
-* Version: 0.1.4
-* GitHub: https://github.com/bips-hb/cpi
-* Source code: https://github.com/cran/cpi
-* Date/Publication: 2022-03-03 09:10:02 UTC
-* Number of recursive dependencies: 88
-
-Run `revdep_details(, "cpi")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘BEST’
-    ```
-
-# cSEM
-
-<details>
-
-* Version: 0.5.0
-* GitHub: https://github.com/M-E-Rademaker/cSEM
-* Source code: https://github.com/cran/cSEM
-* Date/Publication: 2022-11-24 17:50:05 UTC
-* Number of recursive dependencies: 128
-
-Run `revdep_details(, "cSEM")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘Rdpack’
-      All declared Imports should be used.
-    ```
-
-# CSGo
-
-<details>
-
-* Version: 0.6.7
-* GitHub: https://github.com/adsoncostanzifilho/CSGo
-* Source code: https://github.com/cran/CSGo
-* Date/Publication: 2021-05-07 18:50:02 UTC
-* Number of recursive dependencies: 77
-
-Run `revdep_details(, "CSGo")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘extrafont’ ‘future’
-      All declared Imports should be used.
-    ```
-
-# ctsem
-
-<details>
-
-* Version: 3.9.1
-* GitHub: https://github.com/cdriveraus/ctsem
-* Source code: https://github.com/cran/ctsem
-* Date/Publication: 2023-10-30 14:20:02 UTC
-* Number of recursive dependencies: 138
-
-Run `revdep_details(, "ctsem")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... ERROR
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘hierarchicalmanual.rnw’ using knitr_notangle
-    
-    Quitting from lines 194-196 [install] (hierarchicalmanual.rnw)
-    Error: processing vignette 'hierarchicalmanual.rnw' failed with diagnostics:
-    there is no package called 'codetools'
-    --- failed re-building ‘hierarchicalmanual.rnw’
-    
-    SUMMARY: processing the following file failed:
-      ‘hierarchicalmanual.rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 260.0Mb
-      sub-directories of 1Mb or more:
-        R       1.1Mb
-        data    1.7Mb
-        libs  255.9Mb
-    ```
-
-*   checking startup messages can be suppressed ... NOTE
-    ```
-    code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_model_base” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_stan_fit” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_rstantools_model_cov” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_rstantools_model_cov” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_rstantools_model_ctsm” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_rstantools_model_ctsm” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_rstantools_model_ctsmgen” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_rstantools_model_ctsmgen” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    
-    It looks like this package (or a package it requires) has a startup
-    message which cannot be suppressed: see ?packageStartupMessage.
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘rstantools’
-      All declared Imports should be used.
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# DDD
-
-<details>
-
-* Version: 5.2.2
-* GitHub: NA
-* Source code: https://github.com/cran/DDD
-* Date/Publication: 2023-07-10 23:40:47 UTC
-* Number of recursive dependencies: 64
-
-Run `revdep_details(, "DDD")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 14.0Mb
-      sub-directories of 1Mb or more:
-        libs  13.6Mb
-    ```
-
-# deseats
-
-<details>
-
-* Version: 1.0.0
-* GitHub: NA
-* Source code: https://github.com/cran/deseats
-* Date/Publication: 2023-11-08 19:50:02 UTC
-* Number of recursive dependencies: 111
-
-Run `revdep_details(, "deseats")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘deseats’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/deseats/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/deseats/new/deseats.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  8.3Mb
-      sub-directories of 1Mb or more:
-        libs   7.6Mb
-    ```
-
-# desla
-
-<details>
-
-* Version: 0.3.0
-* GitHub: https://github.com/RobertAdamek/desla
-* Source code: https://github.com/cran/desla
-* Date/Publication: 2023-06-29 11:50:06 UTC
-* Number of recursive dependencies: 35
-
-Run `revdep_details(, "desla")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘desla’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/desla/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/desla/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/desla/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/desla/new/desla.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  7.3Mb
-      sub-directories of 1Mb or more:
-        libs   7.3Mb
-    ```
-
-# dipsaus
-
-<details>
-
-* Version: 0.2.8
-* GitHub: https://github.com/dipterix/dipsaus
-* Source code: https://github.com/cran/dipsaus
-* Date/Publication: 2023-07-03 20:00:03 UTC
-* Number of recursive dependencies: 70
-
-Run `revdep_details(, "dipsaus")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.9Mb
-      sub-directories of 1Mb or more:
-        doc    1.1Mb
-        libs   3.5Mb
-    ```
-
-# dispositionEffect
-
-<details>
-
-* Version: 1.0.1
-* GitHub: https://github.com/marcozanotti/dispositionEffect
-* Source code: https://github.com/cran/dispositionEffect
-* Date/Publication: 2022-05-30 07:50:02 UTC
-* Number of recursive dependencies: 136
-
-Run `revdep_details(, "dispositionEffect")` for more info
-
-</details>
-
-## In both
-
-*   checking tests ...
-    ```
-      Running ‘testthat.R’
-     ERROR
-    Running the tests in ‘tests/testthat.R’ failed.
-    Last 50 lines of output:
-      ── Failure ('test-realized_duration.R:113:2'): realized_duration works (realized_only = TRUE) ──
-      realized_duration(...) not equal to c(...).
-      1/4 mismatches
-      [2] 34 - 28 == 6
-      ── Failure ('test-realized_duration.R:116:2'): realized_duration works (realized_only = TRUE) ──
-      realized_duration(...) not equal to c(...).
-    ...
-      1/4 mismatches
-      [2] 34 - 28 == 6
-      ── Failure ('test-realized_duration.R:161:2'): realized_duration works (realized_only = TRUE) ──
-      realized_duration(...) not equal to c(...).
-      1/4 mismatches
-      [1] 34 - 28 == 6
-      
-      [ FAIL 36 | WARN 0 | SKIP 0 | PASS 331 ]
-      Error: Test failures
-      Execution halted
-    ```
-
-# DMQ
-
-<details>
-
-* Version: 0.1.2
-* GitHub: NA
-* Source code: https://github.com/cran/DMQ
-* Date/Publication: 2023-10-28 15:20:05 UTC
-* Number of recursive dependencies: 6
-
-Run `revdep_details(, "DMQ")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘DMQ’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/DMQ/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/DMQ/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/DMQ/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/DMQ/new/DMQ.Rcheck/00install.out’ for details.
-    ```
-
-# dragon
-
-<details>
-
-* Version: 1.2.1
-* GitHub: https://github.com/sjspielman/dragon
-* Source code: https://github.com/cran/dragon
-* Date/Publication: 2022-04-08 08:42:33 UTC
-* Number of recursive dependencies: 131
-
-Run `revdep_details(, "dragon")` for more info
-
-</details>
-
-## In both
-
-*   checking tests ...
-    ```
-      Running ‘testthat.R’
-     ERROR
-    Running the tests in ‘tests/testthat.R’ failed.
-    Complete output:
-      > library(testthat)
-      > library(dragon)
-      > 
-      > test_check("dragon")
-      Error in `FUN()`:
-      ! In path: "/c4/home/henrik/repositories/parallelly/revdep/checks/dragon/new/dragon.Rcheck/tests/testthat/setup_test-settings.R"
-    ...
-       10. │                 └─testthat::source_file(path, env = env, chdir = chdir, wrap = wrap)
-       11. │                   ├─base::withCallingHandlers(...)
-       12. │                   └─base::eval(exprs, env)
-       13. │                     └─base::eval(exprs, env)
-       14. │                       └─igraph::read_graph("graph_by_redox.igraph", format = "ncol") at tests/testthat/setup_test-settings.R:8:1
-       15. │                         └─igraph:::read.graph.ncol(file, ...)
-       16. └─base::.handleSimpleError(...)
-       17.   └─testthat (local) h(simpleError(msg, call))
-       18.     └─rlang::abort(...)
-      Execution halted
-    ```
-
-*   checking package subdirectories ... NOTE
-    ```
-    Problems with news in ‘NEWS.md’:
-    No news entries found.
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘htmltools’
-      All declared Imports should be used.
-    ```
-
-# drake
-
-<details>
-
-* Version: 7.13.8
-* GitHub: https://github.com/ropensci/drake
-* Source code: https://github.com/cran/drake
-* Date/Publication: 2023-11-06 15:40:02 UTC
-* Number of recursive dependencies: 165
-
-Run `revdep_details(, "drake")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘clustermq’
-    ```
-
-# DstarM
-
-<details>
-
-* Version: 0.4.0
-* GitHub: https://github.com/vandenman/DstarM
-* Source code: https://github.com/cran/DstarM
-* Date/Publication: 2020-08-28 18:10:03 UTC
-* Number of recursive dependencies: 57
-
-Run `revdep_details(, "DstarM")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘DstarM’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/DstarM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/DstarM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/DstarM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/DstarM/new/DstarM.Rcheck/00install.out’ for details.
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘Rcpp’
-      All declared Imports should be used.
-    ```
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# DT
-
-<details>
-
-* Version: 0.31
-* GitHub: https://github.com/rstudio/DT
-* Source code: https://github.com/cran/DT
-* Date/Publication: 2023-12-09 06:30:02 UTC
-* Number of recursive dependencies: 55
-
-Run `revdep_details(, "DT")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.4Mb
-      sub-directories of 1Mb or more:
-        htmlwidgets   4.8Mb
-    ```
-
-# dynr
-
-<details>
-
-* Version: 0.1.16-105
-* GitHub: https://github.com/mhunter1/dynr
-* Source code: https://github.com/cran/dynr
-* Date/Publication: 2023-11-28 05:20:05 UTC
-* Number of recursive dependencies: 143
-
-Run `revdep_details(, "dynr")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.6Mb
-      sub-directories of 1Mb or more:
-        data   2.5Mb
-        doc    1.4Mb
-    ```
-
-*   checking re-building of vignette outputs ... NOTE
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘linearSDE.Rmd’ using rmarkdown
-    --- finished re-building ‘linearSDE.Rmd’
-    
-    --- re-building ‘InstallationForDevelopers.Rnw’ using Sweave
-    Error: processing vignette 'InstallationForDevelopers.Rnw' failed with diagnostics:
-    Running 'texi2dvi' on 'InstallationForDevelopers.tex' failed.
-    LaTeX errors:
-    ! LaTeX Error: File `menukeys.sty' not found.
-    
-    ...
-                   {bm}%bm^^M
-    !  ==> Fatal error occurred, no output PDF file produced!
-    --- failed re-building ‘NonlinearContinuousTimeModels.Rnw’
-    
-    SUMMARY: processing the following files failed:
-      ‘InstallationForDevelopers.Rnw’ ‘InstallationForUsers.Rnw’
-      ‘LinearDiscreteTimeModels.Rnw’ ‘NonlinearContinuousTimeModels.Rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# EFAtools
-
-<details>
-
-* Version: 0.4.4
-* GitHub: https://github.com/mdsteiner/EFAtools
-* Source code: https://github.com/cran/EFAtools
-* Date/Publication: 2023-01-06 14:50:40 UTC
-* Number of recursive dependencies: 94
-
-Run `revdep_details(, "EFAtools")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘EFAtools’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/EFAtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/EFAtools/new/EFAtools.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  7.2Mb
-      sub-directories of 1Mb or more:
-        libs   6.0Mb
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘progress’
-      All declared Imports should be used.
-    ```
-
-# emmeans
-
-<details>
-
-* Version: 1.10.0
-* GitHub: https://github.com/rvlenth/emmeans
-* Source code: https://github.com/cran/emmeans
-* Date/Publication: 2024-01-23 23:20:02 UTC
-* Number of recursive dependencies: 169
-
-Run `revdep_details(, "emmeans")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages which this enhances but not available for checking:
-      'CARBayes', 'coxme', 'gee', 'geepack', 'MCMCglmm', 'MCMCpack',
-      'mice', 'pscl', 'rstanarm', 'sommer'
-    ```
-
-# envi
-
-<details>
-
-* Version: 0.1.19
-* GitHub: https://github.com/lance-waller-lab/envi
-* Source code: https://github.com/cran/envi
-* Date/Publication: 2024-01-23 14:40:03 UTC
-* Number of recursive dependencies: 153
-
-Run `revdep_details(, "envi")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘envi’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      Warning: no DISPLAY variable so Tk is not available
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/envi/new/envi.Rcheck/00install.out’ for details.
-    ```
-
-# EpiNow2
-
-<details>
-
-* Version: 1.4.0
-* GitHub: https://github.com/epiforecasts/EpiNow2
-* Source code: https://github.com/cran/EpiNow2
-* Date/Publication: 2023-09-26 12:00:02 UTC
-* Number of recursive dependencies: 126
-
-Run `revdep_details(, "EpiNow2")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 200.5Mb
-      sub-directories of 1Mb or more:
-        help    2.0Mb
-        libs  197.6Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# epitweetr
-
-<details>
-
-* Version: 2.2.16
-* GitHub: https://github.com/EU-ECDC/epitweetr
-* Source code: https://github.com/cran/epitweetr
-* Date/Publication: 2023-11-15 09:30:08 UTC
-* Number of recursive dependencies: 149
-
-Run `revdep_details(, "epitweetr")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘taskscheduleR’
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘httpuv’ ‘knitr’ ‘plyr’ ‘tidyverse’ ‘xml2’
-      All declared Imports should be used.
-    ```
-
-# erah
-
-<details>
-
-* Version: 2.0.1
-* GitHub: https://github.com/xdomingoal/erah-devel
-* Source code: https://github.com/cran/erah
-* Date/Publication: 2023-12-20 10:10:02 UTC
-* Number of recursive dependencies: 94
-
-Run `revdep_details(, "erah")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘erah’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/erah/new/erah.Rcheck/00install.out’ for details.
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘ncdf4’
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘erah’ ...
-** package ‘erah’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’
-gcc -I"/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
-gcc -I"/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c runfunc.c -o runfunc.o
-gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/lib -lR
-installing to /c4/home/henrik/repositories/parallelly/revdep/checks/erah/new/erah.Rcheck/00LOCK-erah/00new/erah/libs
-** R
-...
-** data
-*** moving datasets to lazyload DB
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘erah’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/erah/new/erah.Rcheck/erah’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘erah’ ...
-** package ‘erah’ successfully unpacked and MD5 sums checked
-** using staged installation
-** libs
-using C compiler: ‘gcc (GCC) 10.2.1 20210130 (Red Hat 10.2.1-11)’
-gcc -I"/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c registerDynamicSymbol.c -o registerDynamicSymbol.o
-gcc -I"/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2  -c runfunc.c -o runfunc.o
-gcc -shared -L/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/lib -L/usr/local/lib64 -o erah.so registerDynamicSymbol.o runfunc.o -L/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/lib -lR
-installing to /c4/home/henrik/repositories/parallelly/revdep/checks/erah/old/erah.Rcheck/00LOCK-erah/00new/erah/libs
-** R
-...
-** data
-*** moving datasets to lazyload DB
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘erah’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/erah/old/erah.Rcheck/erah’
-
-
-```
-# explainer
-
-<details>
-
-* Version: 1.0.0
-* GitHub: https://github.com/PERSIMUNE/explainer
-* Source code: https://github.com/cran/explainer
-* Date/Publication: 2023-12-15 12:40:06 UTC
-* Number of recursive dependencies: 194
-
-Run `revdep_details(, "explainer")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘ggpmisc’
-      All declared Imports should be used.
-    ```
-
-# fdacluster
-
-<details>
-
-* Version: 0.3.0
-* GitHub: https://github.com/astamm/fdacluster
-* Source code: https://github.com/cran/fdacluster
-* Date/Publication: 2023-07-04 15:53:04 UTC
-* Number of recursive dependencies: 118
-
-Run `revdep_details(, "fdacluster")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘fdacluster’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/fdacluster/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/fdacluster/new/fdacluster.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 22.2Mb
-      sub-directories of 1Mb or more:
-        R      1.8Mb
-        doc    1.4Mb
-        help   2.1Mb
-        libs  16.4Mb
-    ```
-
-# fect
-
-<details>
-
-* Version: 1.0.0
-* GitHub: NA
-* Source code: https://github.com/cran/fect
-* Date/Publication: 2022-10-14 09:52:32 UTC
-* Number of recursive dependencies: 81
-
-Run `revdep_details(, "fect")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘fect’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/fect/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/fect/new/fect.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 13.9Mb
-      sub-directories of 1Mb or more:
-        libs  12.6Mb
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘panelView’
-      All declared Imports should be used.
-    ```
-
-# finalfit
-
-<details>
-
-* Version: 1.0.7
-* GitHub: https://github.com/ewenharrison/finalfit
-* Source code: https://github.com/cran/finalfit
-* Date/Publication: 2023-11-16 17:40:02 UTC
-* Number of recursive dependencies: 172
-
-Run `revdep_details(, "finalfit")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.4Mb
-      sub-directories of 1Mb or more:
-        doc   4.9Mb
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘tidyselect’
-      All declared Imports should be used.
-    ```
-
-# FLAMES
-
-<details>
-
-* Version: 1.8.0
-* GitHub: https://github.com/OliverVoogd/FLAMES
-* Source code: https://github.com/cran/FLAMES
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 255
-
-Run `revdep_details(, "FLAMES")` for more info
-
-</details>
-
-## In both
-
-*   checking for hidden files and directories ... NOTE
-    ```
-    Found the following hidden files and directories:
-      .BBSoptions
-    These were most likely included in error. See section ‘Package
-    structure’ in the ‘Writing R Extensions’ manual.
-    ```
-
-*   checking whether package ‘FLAMES’ can be installed ... NOTE
-    ```
-    Found the following notes/warnings:
-      Non-staged installation was used
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/FLAMES/new/FLAMES.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  6.2Mb
-      sub-directories of 1Mb or more:
-        data   2.7Mb
-        doc    1.7Mb
-    ```
-
-*   checking R code for possible problems ... NOTE
-    ```
-    annotation_to_fasta: no visible global function definition for
-      'write.table'
-    generate_sc_sce: no visible binding for global variable 'FSM_match'
-    plot_coverage: no visible binding for global variable 'x'
-    plot_coverage: no visible binding for global variable 'transcript'
-    plot_coverage: no visible binding for global variable 'length_bin'
-    plot_demultiplex: no visible binding for global variable 'Freq'
-    plot_demultiplex: no visible binding for global variable '.'
-    plot_demultiplex: no visible binding for global variable 'x'
-    plot_demultiplex: no visible binding for global variable
-    ...
-    sc_umap_expression : plot_idx: no visible binding for global variable
-      'y'
-    transcript_coverage: no visible binding for global variable 'mat'
-    Undefined global functions or variables:
-      . BarcodeEditDist FSM_match FlankEditDist Freq all_vars cell_id cnt
-      everything gene_id heatmap_annotation_colors label length_bin mat n
-      name tr_id transcript transcript_id value write.table x y
-    Consider adding
-      importFrom("utils", "write.table")
-    to your NAMESPACE file.
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# flowGraph
-
-<details>
-
-* Version: 1.10.0
-* GitHub: https://github.com/aya49/flowGraph
-* Source code: https://github.com/cran/flowGraph
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 94
-
-Run `revdep_details(, "flowGraph")` for more info
-
-</details>
-
-## In both
-
-*   checking R code for possible problems ... NOTE
-    ```
-    get_child: no visible binding for global variable ‘no_cores’
-    get_paren: no visible binding for global variable ‘no_cores’
-    ms_psig: no visible binding for global variable ‘meta’
-    Undefined global functions or variables:
-      meta no_cores
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: ‘doParallel’
-    ```
-
-# flowml
-
-<details>
-
-* Version: 0.1.2
-* GitHub: https://github.com/Boehringer-Ingelheim/flowml
-* Source code: https://github.com/cran/flowml
-* Date/Publication: 2023-10-09 12:50:08 UTC
-* Number of recursive dependencies: 277
-
-Run `revdep_details(, "flowml")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘penalizedLDA’
-    ```
-
-# forecastML
-
-<details>
-
-* Version: 0.9.0
-* GitHub: https://github.com/nredell/forecastML
-* Source code: https://github.com/cran/forecastML
-* Date/Publication: 2020-05-07 15:10:17 UTC
-* Number of recursive dependencies: 105
-
-Run `revdep_details(, "forecastML")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘dtplyr’
-      All declared Imports should be used.
-    ```
-
-# genBaRcode
-
-<details>
-
-* Version: 1.2.7
-* GitHub: NA
-* Source code: https://github.com/cran/genBaRcode
-* Date/Publication: 2023-12-11 13:10:05 UTC
-* Number of recursive dependencies: 161
-
-Run `revdep_details(, "genBaRcode")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘genBaRcode_GUI_Vignette.Rmd’ using rmarkdown
-    ! LaTeX Error: File `iftex.sty' not found.
-    
-    ! Emergency stop.
-    <read *> 
-    
-    Error: processing vignette 'genBaRcode_GUI_Vignette.Rmd' failed with diagnostics:
-    LaTeX failed to compile /c4/home/henrik/repositories/parallelly/revdep/checks/genBaRcode/new/genBaRcode.Rcheck/vign_test/genBaRcode/vignettes/genBaRcode_GUI_Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See genBaRcode_GUI_Vignette.log for more info.
-    --- failed re-building ‘genBaRcode_GUI_Vignette.Rmd’
-    ...
-    
-    Error: processing vignette 'genBaRcode_Vignette.Rmd' failed with diagnostics:
-    LaTeX failed to compile /c4/home/henrik/repositories/parallelly/revdep/checks/genBaRcode/new/genBaRcode.Rcheck/vign_test/genBaRcode/vignettes/genBaRcode_Vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See genBaRcode_Vignette.log for more info.
-    --- failed re-building ‘genBaRcode_Vignette.Rmd’
-    
-    SUMMARY: processing the following files failed:
-      ‘genBaRcode_GUI_Vignette.Rmd’ ‘genBaRcode_Vignette.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# GeneBreak
-
-<details>
-
-* Version: 1.32.0
-* GitHub: https://github.com/stefvanlieshout/GeneBreak
-* Source code: https://github.com/cran/GeneBreak
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 43
-
-Run `revdep_details(, "GeneBreak")` for more info
-
-</details>
-
-## In both
-
-*   checking R code for possible problems ... NOTE
-    ```
-    .glmbreak: no visible global function definition for ‘glm’
-    .glmbreak: no visible global function definition for ‘predict’
-    addGeneAnnotation,CopyNumberBreakPoints: no visible global function
-      definition for ‘head’
-    bpStats,CopyNumberBreakPoints: no visible global function definition
-      for ‘sd’
-    bpStats,CopyNumberBreakPoints: no visible global function definition
-      for ‘p.adjust’
-    Undefined global functions or variables:
-      glm head p.adjust predict sd
-    Consider adding
-      importFrom("stats", "glm", "p.adjust", "predict", "sd")
-      importFrom("utils", "head")
-    to your NAMESPACE file.
-    ```
-
-# geocmeans
-
-<details>
-
-* Version: 0.3.4
-* GitHub: https://github.com/JeremyGelb/geocmeans
-* Source code: https://github.com/cran/geocmeans
-* Date/Publication: 2023-09-12 03:10:02 UTC
-* Number of recursive dependencies: 194
-
-Run `revdep_details(, "geocmeans")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘geocmeans’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/geocmeans/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/geocmeans/new/geocmeans.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 13.5Mb
-      sub-directories of 1Mb or more:
-        extdata   3.0Mb
-        libs      8.2Mb
-    ```
-
-# gKRLS
-
-<details>
-
-* Version: 1.0.2
-* GitHub: https://github.com/mgoplerud/gKRLS
-* Source code: https://github.com/cran/gKRLS
-* Date/Publication: 2023-04-20 09:20:05 UTC
-* Number of recursive dependencies: 78
-
-Run `revdep_details(, "gKRLS")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  8.8Mb
-      sub-directories of 1Mb or more:
-        libs   8.6Mb
-    ```
-
-# googleCloudRunner
-
-<details>
-
-* Version: 0.5.0
-* GitHub: https://github.com/MarkEdmondson1234/googleCloudRunner
-* Source code: https://github.com/cran/googleCloudRunner
-* Date/Publication: 2022-02-28 09:40:01 UTC
-* Number of recursive dependencies: 98
-
-Run `revdep_details(, "googleCloudRunner")` for more info
-
-</details>
-
-## In both
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Packages unavailable to check Rd xrefs: ‘rcmdcheck’, ‘covr’, ‘devtools’, ‘pkgdown’
-    ```
-
-# googleComputeEngineR
-
-<details>
-
-* Version: 0.3.0
-* GitHub: https://github.com/cloudyr/googleComputeEngineR
-* Source code: https://github.com/cran/googleComputeEngineR
-* Date/Publication: 2019-05-04 22:40:02 UTC
-* Number of recursive dependencies: 69
-
-Run `revdep_details(, "googleComputeEngineR")` for more info
-
-</details>
-
-## In both
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# googleTagManageR
-
-<details>
-
-* Version: 0.2.0
-* GitHub: NA
-* Source code: https://github.com/cran/googleTagManageR
-* Date/Publication: 2022-04-16 18:12:29 UTC
-* Number of recursive dependencies: 71
-
-Run `revdep_details(, "googleTagManageR")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘assertthat’ ‘future’ ‘httr’
-      All declared Imports should be used.
-    ```
-
-# greed
-
-<details>
-
-* Version: 0.6.1
-* GitHub: https://github.com/comeetie/greed
-* Source code: https://github.com/cran/greed
-* Date/Publication: 2022-10-03 22:00:05 UTC
-* Number of recursive dependencies: 98
-
-Run `revdep_details(, "greed")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘greed’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/greed/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/greed/new/greed.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 36.5Mb
-      sub-directories of 1Mb or more:
-        libs  34.3Mb
-    ```
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 989 marked UTF-8 strings
-    ```
-
-# gsynth
-
-<details>
-
-* Version: 1.2.1
-* GitHub: NA
-* Source code: https://github.com/cran/gsynth
-* Date/Publication: 2021-08-06 07:50:05 UTC
-* Number of recursive dependencies: 77
-
-Run `revdep_details(, "gsynth")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘gsynth’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/gsynth/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/gsynth/new/gsynth.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.2Mb
-      sub-directories of 1Mb or more:
-        libs   4.9Mb
-    ```
-
-# hackeRnews
-
-<details>
-
-* Version: 0.1.0
-* GitHub: https://github.com/szymanskir/hackeRnews
-* Source code: https://github.com/cran/hackeRnews
-* Date/Publication: 2019-12-13 13:20:05 UTC
-* Number of recursive dependencies: 71
-
-Run `revdep_details(, "hackeRnews")` for more info
-
-</details>
-
-## In both
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# hal9001
-
-<details>
-
-* Version: 0.4.6
-* GitHub: https://github.com/tlverse/hal9001
-* Source code: https://github.com/cran/hal9001
-* Date/Publication: 2023-11-14 15:00:02 UTC
-* Number of recursive dependencies: 100
-
-Run `revdep_details(, "hal9001")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.3Mb
-      sub-directories of 1Mb or more:
-        libs   4.9Mb
-    ```
-
-# HardyWeinberg
-
-<details>
-
-* Version: 1.7.5
-* GitHub: NA
-* Source code: https://github.com/cran/HardyWeinberg
-* Date/Publication: 2022-05-07 12:20:06 UTC
-* Number of recursive dependencies: 80
-
-Run `revdep_details(, "HardyWeinberg")` for more info
-
-</details>
-
-## In both
-
-*   checking Rd files ... NOTE
-    ```
-    checkRd: (-1) HWAlr.Rd:25: Escaped LaTeX specials: \&
-    checkRd: (-1) HWAlrPlot.Rd:25: Escaped LaTeX specials: \&
-    checkRd: (-1) HWClr.Rd:23: Escaped LaTeX specials: \&
-    checkRd: (-1) HWClrPlot.Rd:25: Escaped LaTeX specials: \&
-    checkRd: (-1) HWIlr.Rd:30: Escaped LaTeX specials: \&
-    checkRd: (-1) HWf.Rd:25: Escaped LaTeX specials: \&
-    ```
-
-# hbamr
-
-<details>
-
-* Version: 2.1.2
-* GitHub: https://github.com/jbolstad/hbamr
-* Source code: https://github.com/cran/hbamr
-* Date/Publication: 2024-02-07 09:20:02 UTC
-* Number of recursive dependencies: 86
-
-Run `revdep_details(, "hbamr")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 321.9Mb
-      sub-directories of 1Mb or more:
-        libs  320.4Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# healthyR.ts
-
-<details>
-
-* Version: 0.3.0
-* GitHub: https://github.com/spsanderson/healthyR.ts
-* Source code: https://github.com/cran/healthyR.ts
-* Date/Publication: 2023-11-15 06:00:05 UTC
-* Number of recursive dependencies: 217
-
-Run `revdep_details(, "healthyR.ts")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  6.1Mb
-      sub-directories of 1Mb or more:
-        doc   5.2Mb
-    ```
-
-# hero
-
-<details>
-
-* Version: 0.6
-* GitHub: NA
-* Source code: https://github.com/cran/hero
-* Date/Publication: 2023-07-15 21:10:09 UTC
-* Number of recursive dependencies: 160
-
-Run `revdep_details(, "hero")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘Rmpi’
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: ‘Rmpi’
-    ```
-
-# heterogen
-
-<details>
-
-* Version: 1.2.33
-* GitHub: https://github.com/patauchi/heterogen
-* Source code: https://github.com/cran/heterogen
-* Date/Publication: 2023-08-17 07:42:33 UTC
-* Number of recursive dependencies: 56
-
-Run `revdep_details(, "heterogen")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘heterogen’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/heterogen/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/heterogen/new/heterogen.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  7.3Mb
-      sub-directories of 1Mb or more:
-        extdata   2.5Mb
-        libs      4.7Mb
-    ```
-
-# Hmisc
-
-<details>
-
-* Version: 5.1-1
-* GitHub: NA
-* Source code: https://github.com/cran/Hmisc
-* Date/Publication: 2023-09-12 12:52:37 UTC
-* Number of recursive dependencies: 182
-
-Run `revdep_details(, "Hmisc")` for more info
-
-</details>
-
-## In both
-
-*   checking R code for possible problems ... NOTE
-    ```
-    html_describe_con: multiple local function definitions for ‘g’ with
-      different formal arguments
-    ```
-
-# HSAUR3
-
-<details>
-
-* Version: 1.0-14
-* GitHub: NA
-* Source code: https://github.com/cran/HSAUR3
-* Date/Publication: 2023-04-15 07:10:02 UTC
-* Number of recursive dependencies: 126
-
-Run `revdep_details(, "HSAUR3")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... NOTE
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘Ch_analysing_longitudinal_dataI.Rnw’ using Sweave
-    Loading required package: HSAUR3
-    Loading required package: tools
-    Loading required package: Matrix
-    Loading required package: mvtnorm
-    Loading required package: survival
-    Loading required package: TH.data
-    Loading required package: MASS
-    
-    ...
-      ‘Ch_errata.Rnw’ ‘Ch_gam.Rnw’ ‘Ch_graphical_display.Rnw’
-      ‘Ch_introduction_to_R.Rnw’ ‘Ch_logistic_regression_glm.Rnw’
-      ‘Ch_meta_analysis.Rnw’ ‘Ch_missing_values.Rnw’
-      ‘Ch_multidimensional_scaling.Rnw’ ‘Ch_multiple_linear_regression.Rnw’
-      ‘Ch_principal_components_analysis.Rnw’ ‘Ch_quantile_regression.Rnw’
-      ‘Ch_recursive_partitioning.Rnw’ ‘Ch_simple_inference.Rnw’
-      ‘Ch_simultaneous_inference.Rnw’ ‘Ch_survival_analysis.Rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# hwep
-
-<details>
-
-* Version: 2.0.2
-* GitHub: https://github.com/dcgerard/hwep
-* Source code: https://github.com/cran/hwep
-* Date/Publication: 2023-05-16 17:40:02 UTC
-* Number of recursive dependencies: 110
-
-Run `revdep_details(, "hwep")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 72.3Mb
-      sub-directories of 1Mb or more:
-        libs  71.8Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# IDE
-
-<details>
-
-* Version: 0.3.1
-* GitHub: https://github.com/andrewzm/IDE
-* Source code: https://github.com/cran/IDE
-* Date/Publication: 2022-05-30 12:10:14 UTC
-* Number of recursive dependencies: 124
-
-Run `revdep_details(, "IDE")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘IDE_intro.Rnw’ using knitr
-    Error: processing vignette 'IDE_intro.Rnw' failed with diagnostics:
-    Running 'texi2dvi' on 'IDE_intro.tex' failed.
-    LaTeX errors:
-    ! LaTeX Error: File `algpseudocode.sty' not found.
-    
-    Type X to quit or <RETURN> to proceed,
-    or enter new name. (Default extension: sty)
-    ...
-    l.60 \usepackage
-                    {color}^^M
-    !  ==> Fatal error occurred, no output PDF file produced!
-    --- failed re-building ‘IDE_intro.Rnw’
-    
-    SUMMARY: processing the following file failed:
-      ‘IDE_intro.Rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# idem
-
-<details>
-
-* Version: 5.2
-* GitHub: https://github.com/olssol/idem
-* Source code: https://github.com/cran/idem
-* Date/Publication: 2023-08-09 10:30:09 UTC
-* Number of recursive dependencies: 138
-
-Run `revdep_details(, "idem")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 44.1Mb
-      sub-directories of 1Mb or more:
-        doc    1.2Mb
-        libs  42.5Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# IFAA
-
-<details>
-
-* Version: 1.4.0
-* GitHub: https://github.com/quranwu/IFAA
-* Source code: https://github.com/cran/IFAA
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 106
-
-Run `revdep_details(, "IFAA")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘IFAA.Rmd’ using rmarkdown
-    ! LaTeX Error: File `iftex.sty' not found.
-    
-    ! Emergency stop.
-    <read *> 
-    
-    Error: processing vignette 'IFAA.Rmd' failed with diagnostics:
-    LaTeX failed to compile /c4/home/henrik/repositories/parallelly/revdep/checks/IFAA/new/IFAA.Rcheck/vign_test/IFAA/vignettes/IFAA.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See IFAA.log for more info.
-    --- failed re-building ‘IFAA.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘IFAA.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# ImputeRobust
-
-<details>
-
-* Version: 1.3-1
-* GitHub: NA
-* Source code: https://github.com/cran/ImputeRobust
-* Date/Publication: 2018-11-30 12:10:03 UTC
-* Number of recursive dependencies: 87
-
-Run `revdep_details(, "ImputeRobust")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘ImputeRobust’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      Warning: no DISPLAY variable so Tk is not available
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/ImputeRobust/new/ImputeRobust.Rcheck/00install.out’ for details.
-    ```
-
-# infercnv
-
-<details>
-
-* Version: 1.18.1
-* GitHub: https://github.com/broadinstitute/inferCNV
-* Source code: https://github.com/cran/infercnv
-* Date/Publication: 2023-12-01
-* Number of recursive dependencies: 205
-
-Run `revdep_details(, "infercnv")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.1Mb
-      sub-directories of 1Mb or more:
-        extdata   3.1Mb
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Unexported object imported by a ':::' call: ‘HiddenMarkov:::makedensity’
-      See the note in ?`:::` about the use of this operator.
-    ```
-
-# InPAS
-
-<details>
-
-* Version: 2.10.0
-* GitHub: NA
-* Source code: https://github.com/cran/InPAS
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 172
-
-Run `revdep_details(, "InPAS")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    There are ::: calls to the package's namespace in its code. A package
-      almost never needs to use ::: for its own objects:
-      ‘adjust_distalCPs’ ‘adjust_proximalCPs’ ‘adjust_proximalCPsByNBC’
-      ‘adjust_proximalCPsByPWM’ ‘calculate_mse’ ‘find_valleyBySpline’
-      ‘get_PAscore’ ‘get_PAscore2’ ‘remove_convergentUTR3s’
-      ‘search_distalCPs’ ‘search_proximalCPs’
-    ```
-
-# interflex
-
-<details>
-
-* Version: 1.2.6
-* GitHub: NA
-* Source code: https://github.com/cran/interflex
-* Date/Publication: 2021-05-18 11:40:02 UTC
-* Number of recursive dependencies: 103
-
-Run `revdep_details(, "interflex")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘interflex’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/interflex/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/interflex/new/interflex.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.8Mb
-      sub-directories of 1Mb or more:
-        libs   5.1Mb
-    ```
-
-# ISAnalytics
-
-<details>
-
-* Version: 1.12.0
-* GitHub: https://github.com/calabrialab/ISAnalytics
-* Source code: https://github.com/cran/ISAnalytics
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 173
-
-Run `revdep_details(, "ISAnalytics")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  7.2Mb
-      sub-directories of 1Mb or more:
-        data   1.4Mb
-        doc    3.5Mb
-    ```
-
-# ivmte
-
-<details>
-
-* Version: 1.4.0
-* GitHub: NA
-* Source code: https://github.com/cran/ivmte
-* Date/Publication: 2021-09-17 12:20:07 UTC
-* Number of recursive dependencies: 112
-
-Run `revdep_details(, "ivmte")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages suggested but not available for checking: 'gurobi', 'cplexAPI'
-    ```
-
-# JMbayes2
-
-<details>
-
-* Version: 0.4-5
-* GitHub: https://github.com/drizopoulos/JMbayes2
-* Source code: https://github.com/cran/JMbayes2
-* Date/Publication: 2023-06-26 13:30:05 UTC
-* Number of recursive dependencies: 79
-
-Run `revdep_details(, "JMbayes2")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘JMbayes2’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/JMbayes2/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/JMbayes2/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/JMbayes2/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/JMbayes2/new/JMbayes2.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 11.6Mb
-      sub-directories of 1Mb or more:
-        libs  10.9Mb
-    ```
-
-# joinet
-
-<details>
-
-* Version: 0.0.10
-* GitHub: https://github.com/rauschenberger/joinet
-* Source code: https://github.com/cran/joinet
-* Date/Publication: 2021-08-09 07:40:02 UTC
-* Number of recursive dependencies: 64
-
-Run `revdep_details(, "joinet")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages which this enhances but not available for checking:
-      'mice', 'earth', 'spls', 'MRCE', 'remMap',
-      'MultivariateRandomForest', 'SiER', 'mcen', 'GPM', 'RMTL', 'MTPS'
-    ```
-
-# keyATM
-
-<details>
-
-* Version: 0.5.1
-* GitHub: https://github.com/keyATM/keyATM
-* Source code: https://github.com/cran/keyATM
-* Date/Publication: 2024-02-04 23:30:02 UTC
-* Number of recursive dependencies: 107
-
-Run `revdep_details(, "keyATM")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 22.6Mb
-      sub-directories of 1Mb or more:
-        libs  22.2Mb
-    ```
-
-# knitr
-
-<details>
-
-* Version: 1.45
-* GitHub: https://github.com/yihui/knitr
-* Source code: https://github.com/cran/knitr
-* Date/Publication: 2023-10-30 09:10:12 UTC
-* Number of recursive dependencies: 88
-
-Run `revdep_details(, "knitr")` for more info
-
-</details>
-
-## In both
-
-*   checking tests ...
-    ```
-      Running ‘run-all.R’
-     ERROR
-    Running the tests in ‘tests/run-all.R’ failed.
-    Complete output:
-      > library(testit)
-      > test_pkg("knitr")
-      
-      Quitting from lines 4-5 [testfig] (knit-tikzDevice.Rnw)
-      Error in `getMetricsFromLatex()`:
-      ! 
-    ...
-      The TeX and log files used for the calculation can help diagnose the
-      problem. If these files are missing, rerun the plot and make sure to
-      keep the R session open.
-      TeX file: tikzStringWidthCalc.tex
-      Log file: tikzStringWidthCalc.log
-      Backtrace:
-       1. base::plot(runif(100), ylab = "random %")
-       7. tikzDevice (local) `<fn>`(...)
-       8. tikzDevice:::getMetricsFromLatex(TeXMetrics, verbose = verbose)
-      Execution halted
-    ```
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘knit_print.Rmd’ using rmarkdown
-    --- finished re-building ‘knit_print.Rmd’
-    
-    --- re-building ‘knitr-intro.Rmd’ using rmarkdown
-    --- finished re-building ‘knitr-intro.Rmd’
-    
-    --- re-building ‘knitr-refcard.Rmd’ using rmarkdown
-    ! LaTeX Error: Command \textquotesingle unavailable in encoding T1.
-    
-    ...
-    --- finished re-building ‘docco-classic.Rmd’
-    
-    --- re-building ‘docco-linear.Rmd’ using docco_linear
-    --- finished re-building ‘docco-linear.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘knitr-refcard.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# konfound
-
-<details>
-
-* Version: 0.4.0
-* GitHub: https://github.com/jrosen48/konfound
-* Source code: https://github.com/cran/konfound
-* Date/Publication: 2021-06-01 07:40:05 UTC
-* Number of recursive dependencies: 161
-
-Run `revdep_details(, "konfound")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘mice’ ‘tibble’
-      All declared Imports should be used.
-    ```
-
-# ldsr
-
-<details>
-
-* Version: 0.0.2
-* GitHub: https://github.com/ntthung/ldsr
-* Source code: https://github.com/cran/ldsr
-* Date/Publication: 2020-05-04 14:40:09 UTC
-* Number of recursive dependencies: 80
-
-Run `revdep_details(, "ldsr")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘ldsr’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/ldsr/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/ldsr/new/ldsr.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-# lidR
-
-<details>
-
-* Version: 4.1.0
-* GitHub: https://github.com/r-lidar/lidR
-* Source code: https://github.com/cran/lidR
-* Date/Publication: 2024-02-01 19:40:02 UTC
-* Number of recursive dependencies: 156
-
-Run `revdep_details(, "lidR")` for more info
-
-</details>
-
-## In both
-
-*   checking tests ...
-    ```
-      Running ‘testthat.R’/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/bin/BATCH: line 60: 69923 Aborted                 (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
-    
-     ERROR
-    Running the tests in ‘tests/testthat.R’ failed.
-    Complete output:
-      > Sys.setenv("R_TESTS" = "")
-      > 
-      > library(testthat)
-      > library(lidR)
-      > test_check("lidR")
-      Tests using raster: terra 
-      Tests using future: TRUE 
-      Tests using OpenMP thread: 32 
-      OGR: Unsupported geometry type
-      OGR: Unsupported geometry type
-      Chunk 1 of 1 (100%): state ✓
-      terminate called after throwing an instance of 'std::length_error'
-        what():  basic_string::_S_create
-    ```
-
-*   checking whether package ‘lidR’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/lidR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/lidR/new/lidR.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 20.0Mb
-      sub-directories of 1Mb or more:
-        R         1.0Mb
-        extdata   1.1Mb
-        libs     16.3Mb
-    ```
-
-# LSAmitR
-
-<details>
-
-* Version: 1.0-3
-* GitHub: NA
-* Source code: https://github.com/cran/LSAmitR
-* Date/Publication: 2022-06-01 07:50:02 UTC
-* Number of recursive dependencies: 164
-
-Run `revdep_details(, "LSAmitR")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘kerdiest’
-    ```
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 55 marked UTF-8 strings
-    ```
-
-# Luminescence
-
-<details>
-
-* Version: 0.9.23
-* GitHub: https://github.com/R-Lum/Luminescence
-* Source code: https://github.com/cran/Luminescence
-* Date/Publication: 2023-11-03 16:20:08 UTC
-* Number of recursive dependencies: 152
-
-Run `revdep_details(, "Luminescence")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘Luminescence’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/Luminescence/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/Luminescence/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/Luminescence/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/Luminescence/new/Luminescence.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  7.2Mb
-      sub-directories of 1Mb or more:
-        R      1.6Mb
-        libs   3.5Mb
-    ```
-
-# MAI
-
-<details>
-
-* Version: 1.8.0
-* GitHub: https://github.com/KechrisLab/MAI
-* Source code: https://github.com/cran/MAI
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 178
-
-Run `revdep_details(, "MAI")` for more info
-
-</details>
-
-## In both
-
-*   checking top-level files ... NOTE
-    ```
-    File
-      LICENSE
-    is not mentioned in the DESCRIPTION file.
-    ```
-
-# manydata
-
-<details>
-
-* Version: 0.8.3
-* GitHub: https://github.com/globalgov/manydata
-* Source code: https://github.com/cran/manydata
-* Date/Publication: 2023-06-15 11:30:03 UTC
-* Number of recursive dependencies: 134
-
-Run `revdep_details(, "manydata")` for more info
-
-</details>
-
-## In both
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 3 marked UTF-8 strings
-    ```
-
-# manynet
-
-<details>
-
-* Version: 0.4.1
-* GitHub: https://github.com/stocnet/manynet
-* Source code: https://github.com/cran/manynet
-* Date/Publication: 2024-01-24 23:10:06 UTC
-* Number of recursive dependencies: 140
-
-Run `revdep_details(, "manynet")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package which this enhances but not available for checking: ‘Rgraphviz’
-    ```
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 7 marked UTF-8 strings
-    ```
-
-# mappp
-
-<details>
-
-* Version: 1.0.0
-* GitHub: https://github.com/cole-brokamp/mappp
-* Source code: https://github.com/cran/mappp
-* Date/Publication: 2022-01-25 09:22:42 UTC
-* Number of recursive dependencies: 40
-
-Run `revdep_details(, "mappp")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘pbmcapply’
-      All declared Imports should be used.
-    ```
-
-# mdmb
-
-<details>
-
-* Version: 1.8-7
-* GitHub: https://github.com/alexanderrobitzsch/mdmb
-* Source code: https://github.com/cran/mdmb
-* Date/Publication: 2023-02-28 22:02:29 UTC
-* Number of recursive dependencies: 91
-
-Run `revdep_details(, "mdmb")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘mdmb’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/mdmb/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/mdmb/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/mdmb/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/mdmb/new/mdmb.Rcheck/00install.out’ for details.
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages which this enhances but not available for checking:
-      'JointAI', 'smcfcs'
-    ```
-
-# medflex
-
-<details>
-
-* Version: 0.6-10
-* GitHub: https://github.com/jmpsteen/medflex
-* Source code: https://github.com/cran/medflex
-* Date/Publication: 2023-06-22 16:52:38 UTC
-* Number of recursive dependencies: 114
-
-Run `revdep_details(, "medflex")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... NOTE
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘medflex.Rnw’ using Sweave
-    Loading required package: multcomp
-    Loading required package: mvtnorm
-    Loading required package: survival
-    Loading required package: TH.data
-    Loading required package: MASS
-    
-    Attaching package: 'TH.data'
-    
-    ...
-    --- failed re-building 'medflex.Rnw'
-    
-    --- re-building ‘sandwich.Rnw’ using Sweave
-    --- finished re-building ‘sandwich.Rnw’
-    
-    SUMMARY: processing the following file failed:
-      ‘medflex.Rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# metabolomicsR
-
-<details>
-
-* Version: 1.0.0
-* GitHub: https://github.com/XikunHan/metabolomicsR
-* Source code: https://github.com/cran/metabolomicsR
-* Date/Publication: 2022-04-29 07:40:02 UTC
-* Number of recursive dependencies: 182
-
-Run `revdep_details(, "metabolomicsR")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... WARNING
-    ```
-    Missing or unexported object: ‘future::multiprocess’
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘genuMet’
-    ```
-
-# metafor
-
-<details>
-
-* Version: 4.4-0
-* GitHub: https://github.com/wviechtb/metafor
-* Source code: https://github.com/cran/metafor
-* Date/Publication: 2023-09-27 18:40:02 UTC
-* Number of recursive dependencies: 118
-
-Run `revdep_details(, "metafor")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.1Mb
-      sub-directories of 1Mb or more:
-        R      2.1Mb
-        help   2.1Mb
-    ```
-
-# metaGE
-
-<details>
-
-* Version: 1.0.3
-* GitHub: NA
-* Source code: https://github.com/cran/metaGE
-* Date/Publication: 2023-09-28 08:50:02 UTC
-* Number of recursive dependencies: 149
-
-Run `revdep_details(, "metaGE")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.1Mb
-      sub-directories of 1Mb or more:
-        data   4.2Mb
-    ```
-
-# miceadds
-
-<details>
-
-* Version: 3.17-44
-* GitHub: https://github.com/alexanderrobitzsch/miceadds
-* Source code: https://github.com/cran/miceadds
-* Date/Publication: 2024-01-09 10:10:02 UTC
-* Number of recursive dependencies: 166
-
-Run `revdep_details(, "miceadds")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘miceadds’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/miceadds/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/miceadds/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/miceadds/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/miceadds/new/miceadds.Rcheck/00install.out’ for details.
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages which this enhances but not available for checking:
-      'Amelia', 'imputeR', 'micemd', 'simputation'
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 11.5Mb
-      sub-directories of 1Mb or more:
-        libs   9.9Mb
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Packages unavailable to check Rd xrefs: ‘imputeR’, ‘simputation’
-    ```
-
-# miceFast
-
-<details>
-
-* Version: 0.8.2
-* GitHub: https://github.com/Polkas/miceFast
-* Source code: https://github.com/cran/miceFast
-* Date/Publication: 2022-11-17 21:10:02 UTC
-* Number of recursive dependencies: 113
-
-Run `revdep_details(, "miceFast")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘miceFast’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/miceFast/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/miceFast/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/miceFast/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/miceFast/new/miceFast.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 13.8Mb
-      sub-directories of 1Mb or more:
-        libs  12.7Mb
-    ```
-
-# microservices
-
-<details>
-
-* Version: 0.2.0
-* GitHub: https://github.com/tidylab/microservices
-* Source code: https://github.com/cran/microservices
-* Date/Publication: 2022-10-01 09:50:02 UTC
-* Number of recursive dependencies: 72
-
-Run `revdep_details(, "microservices")` for more info
-
-</details>
-
-## In both
-
-*   checking tests ...
-    ```
-      Running ‘testthat.R’
-     ERROR
-    Running the tests in ‘tests/testthat.R’ failed.
-    Complete output:
-      > library(testthat)
-      > library(microservices)
-      > test_check("microservices")
-      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ]
-      
-      ══ Failed tests ════════════════════════════════════════════════════════════════
-    ...
-      Backtrace:
-          ▆
-       1. ├─config::get(...) at test-endpoint-plumber-{route_name}.R:2:1
-       2. │ └─base::normalizePath(file, mustWork = FALSE)
-       3. │   └─base::path.expand(path)
-       4. └─base::system.file(...)
-      
-      [ FAIL 1 | WARN 0 | SKIP 0 | PASS 12 ]
-      Error: Test failures
-      Execution halted
-    ```
-
-# midastouch
-
-<details>
-
-* Version: 1.3
-* GitHub: NA
-* Source code: https://github.com/cran/midastouch
-* Date/Publication: 2016-02-07 09:35:46
-* Number of recursive dependencies: 78
-
-Run `revdep_details(, "midastouch")` for more info
-
-</details>
-
-## In both
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# midfieldr
-
-<details>
-
-* Version: 1.0.1
-* GitHub: https://github.com/MIDFIELDR/midfieldr
-* Source code: https://github.com/cran/midfieldr
-* Date/Publication: 2023-07-08 09:50:06 UTC
-* Number of recursive dependencies: 117
-
-Run `revdep_details(, "midfieldr")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘midfielddata’
-    ```
-
-# mifa
-
-<details>
-
-* Version: 0.2.0
-* GitHub: https://github.com/teebusch/mifa
-* Source code: https://github.com/cran/mifa
-* Date/Publication: 2021-01-22 08:40:08 UTC
-* Number of recursive dependencies: 117
-
-Run `revdep_details(, "mifa")` for more info
-
-</details>
-
-## In both
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# MineICA
-
-<details>
-
-* Version: 1.42.0
-* GitHub: NA
-* Source code: https://github.com/cran/MineICA
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 216
-
-Run `revdep_details(, "MineICA")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... WARNING
-    ```
-    Namespace in Imports field not imported from: ‘lumiHumanAll.db’
-      All declared Imports should be used.
-    Packages in Depends field not imported from:
-      ‘GOstats’ ‘Hmisc’ ‘JADE’ ‘RColorBrewer’ ‘Rgraphviz’ ‘annotate’
-      ‘biomaRt’ ‘cluster’ ‘colorspace’ ‘fastICA’ ‘foreach’ ‘ggplot2’
-      ‘graph’ ‘gtools’ ‘igraph’ ‘marray’ ‘mclust’ ‘methods’ ‘plyr’ ‘scales’
-      ‘xtable’
-      These packages need to be imported from (in the NAMESPACE file)
-      for when this namespace is loaded but not attached.
-    Missing or unexported object: ‘GOstats::geneIdsByCategory’
-    ':::' calls which should be '::':
-      ‘Biobase:::annotation<-’ ‘Biobase:::validMsg’ ‘fpc:::pamk’
-      ‘lumi:::getChipInfo’ ‘mclust:::adjustedRandIndex’
-      See the note in ?`:::` about the use of this operator.
-    Unexported object imported by a ':::' call: ‘Biobase:::isValidVersion’
-      See the note in ?`:::` about the use of this operator.
-    ```
-
-*   checking Rd cross-references ... WARNING
-    ```
-    Missing link or links in documentation object 'Alist.Rd':
-      ‘class-IcaSet’
-    
-    Missing link or links in documentation object 'Slist.Rd':
-      ‘class-IcaSet’
-    
-    Missing link or links in documentation object 'class-IcaSet.Rd':
-      ‘class-IcaSet’
-    
-    Missing link or links in documentation object 'getComp.Rd':
-      ‘class-IcaSet’
-    
-    Missing link or links in documentation object 'runAn.Rd':
-      ‘[Category:class-GOHyperGParams]{GOHyperGParams}’
-    
-    See section 'Cross-references' in the 'Writing R Extensions' manual.
-    ```
-
-*   checking for missing documentation entries ... WARNING
-    ```
-    Undocumented S4 classes:
-      ‘MineICAParams’
-    All user-level objects in a package (including S4 classes and methods)
-    should have documentation entries.
-    See chapter ‘Writing R documentation files’ in the ‘Writing R
-    Extensions’ manual.
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package which this enhances but not available for checking: ‘doMC’
-    
-    Depends: includes the non-default packages:
-      'BiocGenerics', 'Biobase', 'plyr', 'ggplot2', 'scales', 'foreach',
-      'xtable', 'biomaRt', 'gtools', 'GOstats', 'cluster', 'marray',
-      'mclust', 'RColorBrewer', 'colorspace', 'igraph', 'Rgraphviz',
-      'graph', 'annotate', 'Hmisc', 'fastICA', 'JADE'
-    Adding so many packages to the search path is excessive and importing
-    selectively is preferable.
-    ```
-
-*   checking DESCRIPTION meta-information ... NOTE
-    ```
-    Packages listed in more than one of Depends, Imports, Suggests, Enhances:
-      ‘biomaRt’ ‘GOstats’ ‘cluster’ ‘mclust’ ‘igraph’
-    A package should be listed in only one of these fields.
-    ```
-
-*   checking R code for possible problems ... NOTE
-    ```
-    addGenesToGoReport: no visible global function definition for
-      ‘conditional’
-    addGenesToGoReport: no visible global function definition for
-      ‘sigCategories’
-    annot2Color: no visible global function definition for ‘brewer.pal’
-    annot2Color: no visible global function definition for ‘heat_hcl’
-    annot2Color: no visible global function definition for ‘terrain_hcl’
-    annot2Color: no visible global function definition for ‘cm.colors’
-    annot2Color: no visible global function definition for ‘rainbow_hcl’
-    annotFeatures: no visible global function definition for ‘na.omit’
-    ...
-      importFrom("methods", "callNextMethod", "new", "validObject")
-      importFrom("stats", "aggregate", "as.dendrogram", "as.dist",
-                 "as.hclust", "chisq.test", "cor", "cor.test", "cutree",
-                 "dist", "hclust", "kmeans", "kruskal.test", "lm", "median",
-                 "na.omit", "order.dendrogram", "p.adjust", "quantile",
-                 "reorder", "shapiro.test", "wilcox.test")
-      importFrom("utils", "capture.output", "combn", "read.table",
-                 "write.table")
-    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
-    contains 'methods').
-    ```
-
-*   checking re-building of vignette outputs ... NOTE
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘MineICA.Rnw’ using Sweave
-    Loading required package: BiocGenerics
-    
-    Attaching package: ‘BiocGenerics’
-    
-    The following objects are masked from ‘package:stats’:
-    
-        IQR, mad, sd, var, xtabs
-    
-    ...
-    l.23 \usepackage
-                    {subfig}^^M
-    !  ==> Fatal error occurred, no output PDF file produced!
-    --- failed re-building ‘MineICA.Rnw’
-    
-    SUMMARY: processing the following file failed:
-      ‘MineICA.Rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# missSBM
-
-<details>
-
-* Version: 1.0.4
-* GitHub: https://github.com/grossSBM/missSBM
-* Source code: https://github.com/cran/missSBM
-* Date/Publication: 2023-10-24 16:00:05 UTC
-* Number of recursive dependencies: 114
-
-Run `revdep_details(, "missSBM")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘missSBM’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/missSBM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/missSBM/new/missSBM.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  9.8Mb
-      sub-directories of 1Mb or more:
-        libs   7.8Mb
-    ```
-
-# mistyR
-
-<details>
-
-* Version: 1.10.0
-* GitHub: https://github.com/saezlab/mistyR
-* Source code: https://github.com/cran/mistyR
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 156
-
-Run `revdep_details(, "mistyR")` for more info
-
-</details>
-
-## Newly fixed
-
-*   checking tests ...
-    ```
-      Running ‘testthat.R’
-     ERROR
-    Running the tests in ‘tests/testthat.R’ failed.
-    Last 50 lines of output:
-      
-      Collecting contributions
-      
-      Collecting importances
-      
-      Aggregating
-    ...
-      ══ Failed tests ════════════════════════════════════════════════════════════════
-      ── Failure ('test-misty.R:230:3'): k for cv , n.bags for bagging can be changed and approx works ──
-      first.run < second.run is not TRUE
-      
-      `actual`:   FALSE
-      `expected`: TRUE 
-      
-      [ FAIL 1 | WARN 4 | SKIP 0 | PASS 172 ]
-      Error: Test failures
-      Execution halted
-    ```
-
-## In both
-
-*   checking R code for possible problems ... NOTE
-    ```
-    aggregate_results: no visible binding for global variable ‘measure’
-    aggregate_results: no visible binding for global variable ‘target’
-    aggregate_results: no visible binding for global variable ‘value’
-    aggregate_results: no visible binding for global variable ‘sd’
-    aggregate_results: no visible binding for global variable ‘view’
-    aggregate_results: no visible binding for global variable ‘.PT’
-    aggregate_results: no visible binding for global variable ‘Importance’
-    aggregate_results_subset: no visible binding for global variable ‘view’
-    aggregate_results_subset: no visible binding for global variable ‘.PT’
-    aggregate_results_subset: no visible binding for global variable
-    ...
-    run_misty : <anonymous>: no visible binding for global variable
-      ‘multi.R2’
-    svm_model: no visible binding for global variable ‘index’
-    Undefined global functions or variables:
-      .PT Importance Predictor Target fraction index intra.R2 intra.RMSE
-      measure multi.R2 multi.RMSE nsamples p prediction sd target total ts
-      value view
-    Consider adding
-      importFrom("stats", "sd", "ts")
-    to your NAMESPACE file.
-    ```
-
-# miWQS
-
-<details>
-
-* Version: 0.4.4
-* GitHub: https://github.com/phargarten2/miWQS
-* Source code: https://github.com/cran/miWQS
-* Date/Publication: 2021-04-02 21:50:02 UTC
-* Number of recursive dependencies: 152
-
-Run `revdep_details(, "miWQS")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘README.Rmd’ using rmarkdown
-    ! LaTeX Error: File `iftex.sty' not found.
-    
-    ! Emergency stop.
-    <read *> 
-    
-    Error: processing vignette 'README.Rmd' failed with diagnostics:
-    LaTeX failed to compile /c4/home/henrik/repositories/parallelly/revdep/checks/miWQS/new/miWQS.Rcheck/vign_test/miWQS/vignettes/README.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See README.log for more info.
-    --- failed re-building ‘README.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘README.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# mlr3shiny
-
-<details>
-
-* Version: 0.3.0
-* GitHub: NA
-* Source code: https://github.com/cran/mlr3shiny
-* Date/Publication: 2023-09-30 20:30:05 UTC
-* Number of recursive dependencies: 179
-
-Run `revdep_details(, "mlr3shiny")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘DT’ ‘Metrics’ ‘data.table’ ‘dplyr’ ‘mlr3’ ‘mlr3learners’
-      ‘mlr3measures’ ‘mlr3pipelines’ ‘patchwork’ ‘plyr’ ‘purrr’
-      ‘shinyWidgets’ ‘shinyalert’ ‘shinydashboard’ ‘shinyjs’ ‘stats’
-      ‘stringr’
-      All declared Imports should be used.
-    ```
-
-# mlrintermbo
-
-<details>
-
-* Version: 0.5.0
-* GitHub: https://github.com/mb706/mlrintermbo
-* Source code: https://github.com/cran/mlrintermbo
-* Date/Publication: 2021-03-01 09:00:06 UTC
-* Number of recursive dependencies: 90
-
-Run `revdep_details(, "mlrintermbo")` for more info
-
-</details>
-
-## In both
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# mmrm
-
-<details>
-
-* Version: 0.3.10
-* GitHub: https://github.com/openpharma/mmrm
-* Source code: https://github.com/cran/mmrm
-* Date/Publication: 2024-01-26 12:10:04 UTC
-* Number of recursive dependencies: 158
-
-Run `revdep_details(, "mmrm")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 156.6Mb
-      sub-directories of 1Mb or more:
-        libs  155.0Mb
-    ```
-
-# modeltime
-
-<details>
-
-* Version: 1.2.8
-* GitHub: https://github.com/business-science/modeltime
-* Source code: https://github.com/cran/modeltime
-* Date/Publication: 2023-09-02 15:10:02 UTC
-* Number of recursive dependencies: 249
-
-Run `revdep_details(, "modeltime")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘tidymodels’ ‘tidyverse’
-      All declared Imports should be used.
-    ```
-
-# modeltime.ensemble
-
-<details>
-
-* Version: 1.0.3
-* GitHub: https://github.com/business-science/modeltime.ensemble
-* Source code: https://github.com/cran/modeltime.ensemble
-* Date/Publication: 2023-04-18 11:50:02 UTC
-* Number of recursive dependencies: 226
-
-Run `revdep_details(, "modeltime.ensemble")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘parsnip’
-      All declared Imports should be used.
-    ```
-
-# modeltime.resample
-
-<details>
-
-* Version: 0.2.3
-* GitHub: https://github.com/business-science/modeltime.resample
-* Source code: https://github.com/cran/modeltime.resample
-* Date/Publication: 2023-04-12 15:50:02 UTC
-* Number of recursive dependencies: 224
-
-Run `revdep_details(, "modeltime.resample")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘crayon’ ‘dials’ ‘glue’ ‘parsnip’
-      All declared Imports should be used.
-    ```
-
-# momentuHMM
-
-<details>
-
-* Version: 1.5.5
-* GitHub: https://github.com/bmcclintock/momentuHMM
-* Source code: https://github.com/cran/momentuHMM
-* Date/Publication: 2022-10-18 20:52:35 UTC
-* Number of recursive dependencies: 145
-
-Run `revdep_details(, "momentuHMM")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘momentuHMM’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/momentuHMM/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/momentuHMM/new/momentuHMM.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 10.2Mb
-      sub-directories of 1Mb or more:
-        R      1.2Mb
-        doc    1.7Mb
-        libs   6.7Mb
-    ```
-
-# MOSS
-
-<details>
-
-* Version: 0.2.2
-* GitHub: https://github.com/agugonrey/MOSS
-* Source code: https://github.com/cran/MOSS
-* Date/Publication: 2022-03-25 15:50:05 UTC
-* Number of recursive dependencies: 184
-
-Run `revdep_details(, "MOSS")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘MOSS_working_example.Rmd’ using rmarkdown
-    ! LaTeX Error: File `iftex.sty' not found.
-    
-    ! Emergency stop.
-    <read *> 
-    
-    Error: processing vignette 'MOSS_working_example.Rmd' failed with diagnostics:
-    LaTeX failed to compile /c4/home/henrik/repositories/parallelly/revdep/checks/MOSS/new/MOSS.Rcheck/vign_test/MOSS/vignettes/MOSS_working_example.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See MOSS_working_example.log for more info.
-    --- failed re-building ‘MOSS_working_example.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘MOSS_working_example.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# MSiP
-
-<details>
-
-* Version: 1.3.7
-* GitHub: NA
-* Source code: https://github.com/cran/MSiP
-* Date/Publication: 2021-06-17 08:20:05 UTC
-* Number of recursive dependencies: 125
-
-Run `revdep_details(, "MSiP")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘ranger’
-      All declared Imports should be used.
-    ```
-
-# mvnimpute
-
-<details>
-
-* Version: 1.0.1
-* GitHub: https://github.com/hli226/mvnimpute
-* Source code: https://github.com/cran/mvnimpute
-* Date/Publication: 2022-07-06 09:40:02 UTC
-* Number of recursive dependencies: 96
-
-Run `revdep_details(, "mvnimpute")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘mvnimpute’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/mvnimpute/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/mvnimpute/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/mvnimpute/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/mvnimpute/new/mvnimpute.Rcheck/00install.out’ for details.
-    ```
-
-# NADIA
-
-<details>
-
-* Version: 0.4.2
-* GitHub: https://github.com/ModelOriented/EMMA
-* Source code: https://github.com/cran/NADIA
-* Date/Publication: 2022-10-02 19:40:02 UTC
-* Number of recursive dependencies: 180
-
-Run `revdep_details(, "NADIA")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘glmnet’ ‘mlr3learners’ ‘rpart’
-      All declared Imports should be used.
-    ```
-
-# NCC
-
-<details>
-
-* Version: 1.0
-* GitHub: https://github.com/pavlakrotka/NCC
-* Source code: https://github.com/cran/NCC
-* Date/Publication: 2023-03-03 09:10:10 UTC
-* Number of recursive dependencies: 122
-
-Run `revdep_details(, "NCC")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘magick’
-      All declared Imports should be used.
-    ```
-
-# nebula
-
-<details>
-
-* Version: 1.4.2
-* GitHub: NA
-* Source code: https://github.com/cran/nebula
-* Date/Publication: 2023-07-05 23:20:07 UTC
-* Number of recursive dependencies: 74
-
-Run `revdep_details(, "nebula")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 31.4Mb
-      sub-directories of 1Mb or more:
-        libs  30.5Mb
-    ```
-
-# nfl4th
-
-<details>
-
-* Version: 1.0.4
-* GitHub: https://github.com/nflverse/nfl4th
-* Source code: https://github.com/cran/nfl4th
-* Date/Publication: 2023-08-21 09:32:33 UTC
-* Number of recursive dependencies: 111
-
-Run `revdep_details(, "nfl4th")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘nfl4th’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      Warning: GitHub.com seems offline, and `options(nfl4th.keep_games)` is not set to TRUE. Deleting the games cache, and predictions may not be available without an internet connection.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/nfl4th/new/nfl4th.Rcheck/00install.out’ for details.
-    ```
-
-*   checking whether the namespace can be loaded with stated dependencies ... NOTE
-    ```
-    Warning: GitHub.com seems offline, and `options(nfl4th.keep_games)` is not set to TRUE. Deleting the games cache, and predictions may not be available without an internet connection.
-    
-    A namespace must be able to be loaded with just the base namespace
-    loaded: otherwise if the namespace gets loaded by a saved object, the
-    session will be unable to start.
-    
-    Probably some imports need to be declared in the NAMESPACE file.
-    ```
-
-# NIMAA
-
-<details>
-
-* Version: 0.2.1
-* GitHub: https://github.com/jafarilab/NIMAA
-* Source code: https://github.com/cran/NIMAA
-* Date/Publication: 2022-04-11 14:12:45 UTC
-* Number of recursive dependencies: 173
-
-Run `revdep_details(, "NIMAA")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.1Mb
-      sub-directories of 1Mb or more:
-        doc   4.0Mb
-    ```
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 24 marked UTF-8 strings
-    ```
-
-# oncomsm
-
-<details>
-
-* Version: 0.1.4
-* GitHub: https://github.com/Boehringer-Ingelheim/oncomsm
-* Source code: https://github.com/cran/oncomsm
-* Date/Publication: 2023-04-17 07:00:02 UTC
-* Number of recursive dependencies: 123
-
-Run `revdep_details(, "oncomsm")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 57.7Mb
-      sub-directories of 1Mb or more:
-        doc    1.0Mb
-        libs  55.7Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# OOS
-
-<details>
-
-* Version: 1.0.0
-* GitHub: https://github.com/tylerJPike/OOS
-* Source code: https://github.com/cran/OOS
-* Date/Publication: 2021-03-17 13:20:20 UTC
-* Number of recursive dependencies: 137
-
-Run `revdep_details(, "OOS")` for more info
-
-</details>
-
-## In both
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# ordbetareg
-
-<details>
-
-* Version: 0.7.2
-* GitHub: https://github.com/saudiwin/ordbetareg_pack
-* Source code: https://github.com/cran/ordbetareg
-* Date/Publication: 2023-08-10 07:30:02 UTC
-* Number of recursive dependencies: 204
-
-Run `revdep_details(, "ordbetareg")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.2Mb
-      sub-directories of 1Mb or more:
-        data   4.7Mb
-    ```
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 36 marked UTF-8 strings
-    ```
-
-# pareg
-
-<details>
-
-* Version: 1.6.0
-* GitHub: https://github.com/cbg-ethz/pareg
-* Source code: https://github.com/cran/pareg
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 320
-
-Run `revdep_details(, "pareg")` for more info
-
-</details>
-
-## In both
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘pareg-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: as.data.frame.pareg
-    > ### Title: as.data.frame for an object of class 'pareg'.
-    > ### Aliases: as.data.frame.pareg
-    > 
-    > ### ** Examples
-    > 
-    > df_genes <- data.frame(
-    ...
-    + )
-    > fit <- pareg(df_genes, df_terms, max_iterations = 10)
-    Error in py_module_import(module, convert = convert) : 
-      ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so)
-    Run `reticulate::py_last_error()` for details.
-    Error in .activate_fallback(proc, testload, env = env, envpath = envpath,  : 
-      ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so)
-    Run `reticulate::py_last_error()` for details.
-    Calls: pareg -> basiliskStart -> .activate_fallback
-    Execution halted
-    ```
-
-*   checking tests ...
-    ```
-      Running ‘testthat.R’
-     ERROR
-    Running the tests in ‘tests/testthat.R’ failed.
-    Complete output:
-      > library(testthat)
-      > library(pareg)
-      Loading required package: tensorflow
-      Loading required package: tfprobability
-      
-      
-    ...
-      +   testload = c("tensorflow", "tensorflow_probability")
-      + )
-      Error in py_module_import(module, convert = convert) : 
-        ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so)
-      Run `reticulate::py_last_error()` for details.
-      Error in .activate_fallback(proc, testload, env = env, envpath = envpath,  : 
-        ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so)
-      Run `reticulate::py_last_error()` for details.
-      Calls: <Anonymous> -> .activate_fallback
-      Execution halted
-    ```
-
-*   checking re-building of vignette outputs ... ERROR
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘pareg.Rmd’ using rmarkdown
-    The magick package is required to crop "/c4/home/henrik/repositories/parallelly/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-4-1.png" but not available.
-    The magick package is required to crop "/c4/home/henrik/repositories/parallelly/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pareg_files/figure-html/unnamed-chunk-5-1.png" but not available.
-    
-    Quitting from lines 145-150 [unnamed-chunk-9] (pareg.Rmd)
-    Error: processing vignette 'pareg.Rmd' failed with diagnostics:
-    ImportError: /lib64/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /c4/home/henrik/.cache/R/basilisk/1.14.3/pareg/1.6.0/pareg/lib/python3.9/site-packages/tensorflow/python/platform/_pywrap_cpu_feature_guard.so)
-    Run `reticulate::py_last_error()` for details.
-    ...
-    --- re-building ‘pathway_similarities.Rmd’ using rmarkdown
-    The magick package is required to crop "/c4/home/henrik/repositories/parallelly/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-2-1.png" but not available.
-    The magick package is required to crop "/c4/home/henrik/repositories/parallelly/revdep/checks/pareg/new/pareg.Rcheck/vign_test/pareg/vignettes/pathway_similarities_files/figure-html/unnamed-chunk-3-1.png" but not available.
-    --- finished re-building ‘pathway_similarities.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘pareg.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-*   checking for portable file names ... NOTE
-    ```
-    Found the following non-portable file paths:
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/config.yaml
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_ablation_study/params.csv
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/config.yaml
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_dispersion_fitting/params.csv
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/config.yaml
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_real_datasets/params.csv
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/config.yaml
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_effect/params.csv
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter/config.yaml
-    ...
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_response_distribution/params.csv
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/config.yaml
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_similarity_measures/params.csv
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/workflow/scripts/compare_rocauc_vs_loss.R
-      pareg/inst/scripts/synthetic_benchmark/resources/multi_config_workflow/config_regularization_parameter
-    
-    Tarballs are only required to store paths of up to 100 bytes and cannot
-    store those of more than 256 bytes, with restrictions including to 100
-    bytes for the final component.
-    See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
-    ```
-
-*   checking whether package ‘pareg’ can be installed ... NOTE
-    ```
-    Found the following notes/warnings:
-      Non-staged installation was used
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/pareg/new/pareg.Rcheck/00install.out’ for details.
-    ```
-
-# parseRPDR
-
-<details>
-
-* Version: 1.1.0
-* GitHub: https://github.com/martonkolossvary/parseRPDR
-* Source code: https://github.com/cran/parseRPDR
-* Date/Publication: 2024-01-09 12:10:02 UTC
-* Number of recursive dependencies: 89
-
-Run `revdep_details(, "parseRPDR")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘doParallel’
-      All declared Imports should be used.
-    ```
-
-# partR2
-
-<details>
-
-* Version: 0.9.1
-* GitHub: https://github.com/mastoffel/partR2
-* Source code: https://github.com/cran/partR2
-* Date/Publication: 2021-01-18 16:30:04 UTC
-* Number of recursive dependencies: 94
-
-Run `revdep_details(, "partR2")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘methods’
-      All declared Imports should be used.
-    ```
-
-# pavo
-
-<details>
-
-* Version: 2.9.0
-* GitHub: https://github.com/rmaia/pavo
-* Source code: https://github.com/cran/pavo
-* Date/Publication: 2023-09-24 10:10:02 UTC
-* Number of recursive dependencies: 104
-
-Run `revdep_details(, "pavo")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘pavo’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      Warning: no DISPLAY variable so Tk is not available
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/pavo/new/pavo.Rcheck/00install.out’ for details.
-    ```
-
-# pchc
-
-<details>
-
-* Version: 1.2
-* GitHub: NA
-* Source code: https://github.com/cran/pchc
-* Date/Publication: 2023-09-06 16:20:02 UTC
-* Number of recursive dependencies: 62
-
-Run `revdep_details(, "pchc")` for more info
-
-</details>
-
-## In both
-
-*   checking Rd cross-references ... WARNING
-    ```
-    Missing link or links in documentation object 'cat.tests.Rd':
-      ‘loglm’
-    
-    See section 'Cross-references' in the 'Writing R Extensions' manual.
-    ```
-
-# PCRedux
-
-<details>
-
-* Version: 1.1-2
-* GitHub: https://github.com/PCRuniversum/PCRedux
-* Source code: https://github.com/cran/PCRedux
-* Date/Publication: 2022-05-11 11:40:02 UTC
-* Number of recursive dependencies: 153
-
-Run `revdep_details(, "PCRedux")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘PCRedux.Rmd’ using rmarkdown
-    ! LaTeX Error: File `iftex.sty' not found.
-    
-    ! Emergency stop.
-    <read *> 
-    
-    Error: processing vignette 'PCRedux.Rmd' failed with diagnostics:
-    LaTeX failed to compile /c4/home/henrik/repositories/parallelly/revdep/checks/PCRedux/new/PCRedux.Rcheck/vign_test/PCRedux/vignettes/PCRedux.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See PCRedux.log for more info.
-    --- failed re-building ‘PCRedux.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘PCRedux.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# pema
-
-<details>
-
-* Version: 0.1.3
-* GitHub: https://github.com/cjvanlissa/pema
-* Source code: https://github.com/cran/pema
-* Date/Publication: 2023-03-16 11:40:02 UTC
-* Number of recursive dependencies: 129
-
-Run `revdep_details(, "pema")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 324.2Mb
-      sub-directories of 1Mb or more:
-        libs  323.3Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# photosynthesis
-
-<details>
-
-* Version: 2.1.4
-* GitHub: https://github.com/cdmuir/photosynthesis
-* Source code: https://github.com/cran/photosynthesis
-* Date/Publication: 2023-08-15 07:20:05 UTC
-* Number of recursive dependencies: 144
-
-Run `revdep_details(, "photosynthesis")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  7.1Mb
-      sub-directories of 1Mb or more:
-        doc   6.0Mb
-    ```
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 13 marked UTF-8 strings
-    ```
-
-# phylolm
-
-<details>
-
-* Version: 2.6.2
-* GitHub: https://github.com/lamho86/phylolm
-* Source code: https://github.com/cran/phylolm
-* Date/Publication: 2020-06-22 05:10:08 UTC
-* Number of recursive dependencies: 41
-
-Run `revdep_details(, "phylolm")` for more info
-
-</details>
-
-## In both
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Packages unavailable to check Rd xrefs: ‘geiger’, ‘caper’
-    ```
-
-# PLNmodels
-
-<details>
-
-* Version: 1.1.0
-* GitHub: https://github.com/pln-team/PLNmodels
-* Source code: https://github.com/cran/PLNmodels
-* Date/Publication: 2024-01-08 18:30:02 UTC
-* Number of recursive dependencies: 150
-
-Run `revdep_details(, "PLNmodels")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘PLNmodels’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/PLNmodels/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/PLNmodels/new/PLNmodels.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 21.8Mb
-      sub-directories of 1Mb or more:
-        doc    2.0Mb
-        libs  18.4Mb
-    ```
-
-# pmartR
-
-<details>
-
-* Version: 2.4.2
-* GitHub: https://github.com/pmartR/pmartR
-* Source code: https://github.com/cran/pmartR
-* Date/Publication: 2023-12-12 10:50:02 UTC
-* Number of recursive dependencies: 150
-
-Run `revdep_details(, "pmartR")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘pmartR’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/pmartR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/pmartR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/pmartR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/pmartR/new/pmartR.Rcheck/00install.out’ for details.
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘pmartRdata’
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  9.7Mb
-      sub-directories of 1Mb or more:
-        libs   7.4Mb
-    ```
-
-# PortfolioAnalytics
-
-<details>
-
-* Version: 1.1.0
-* GitHub: https://github.com/braverock/PortfolioAnalytics
-* Source code: https://github.com/cran/PortfolioAnalytics
-* Date/Publication: 2018-05-17 22:48:29 UTC
-* Number of recursive dependencies: 73
-
-Run `revdep_details(, "PortfolioAnalytics")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘ROI.plugin.symphony’
-    ```
-
-# portvine
-
-<details>
-
-* Version: 1.0.3
-* GitHub: https://github.com/EmanuelSommer/portvine
-* Source code: https://github.com/cran/portvine
-* Date/Publication: 2024-01-18 16:30:02 UTC
-* Number of recursive dependencies: 130
-
-Run `revdep_details(, "portvine")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 51.1Mb
-      sub-directories of 1Mb or more:
-        libs  50.1Mb
-    ```
-
-# projpred
-
-<details>
-
-* Version: 2.8.0
-* GitHub: https://github.com/stan-dev/projpred
-* Source code: https://github.com/cran/projpred
-* Date/Publication: 2023-12-15 00:00:02 UTC
-* Number of recursive dependencies: 158
-
-Run `revdep_details(, "projpred")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘projpred’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/projpred/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/projpred/new/projpred.Rcheck/00install.out’ for details.
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘cmdstanr’
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.9Mb
-      sub-directories of 1Mb or more:
-        doc    1.4Mb
-        libs   3.6Mb
-    ```
-
-# Prostar
-
-<details>
-
-* Version: 1.34.5
-* GitHub: https://github.com/prostarproteomics/Prostar
-* Source code: https://github.com/cran/Prostar
-* Date/Publication: 2024-01-12
-* Number of recursive dependencies: 332
-
-Run `revdep_details(, "Prostar")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘Prostar’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/Prostar/new/Prostar.Rcheck/00install.out’ for details.
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘Prostar’ ...
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘Prostar’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/Prostar/new/Prostar.Rcheck/Prostar’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘Prostar’ ...
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘Prostar’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/Prostar/old/Prostar.Rcheck/Prostar’
-
-
-```
-# pseudohouseholds
-
-<details>
-
-* Version: 0.1.1
-* GitHub: https://github.com/chris31415926535/pseudohouseholds
-* Source code: https://github.com/cran/pseudohouseholds
-* Date/Publication: 2023-07-19 09:30:02 UTC
-* Number of recursive dependencies: 105
-
-Run `revdep_details(, "pseudohouseholds")` for more info
-
-</details>
-
-## In both
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 596 marked UTF-8 strings
-    ```
-
-# QDNAseq
-
-<details>
-
-* Version: 1.38.0
-* GitHub: https://github.com/ccagc/QDNAseq
-* Source code: https://github.com/cran/QDNAseq
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 93
-
-Run `revdep_details(, "QDNAseq")` for more info
-
-</details>
-
-## In both
-
-*   checking tests ...
-    ```
-      Running ‘QDNAseq,copyneutral.R’
-      Running ‘QDNAseq,gain-copyneutral-gain.R’
-      Running ‘QDNAseq,parallel-reproducibility.R’
-      Running ‘QDNAseq.R’/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/bin/BATCH: line 60:  5009 Segmentation fault      (core dumped) ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1
-    
-     ERROR
-    Running the tests in ‘tests/QDNAseq.R’ failed.
-    Last 50 lines of output:
-      Adjusting normalized data for cellularity ... 
-      
-    ...
-      
-      Traceback:
-       1: diff2(x, differences = diff)
-       2: sdDiff(x, ..., trim = trim)
-       3: FUN(newX[, i], ...)
-       4: apply(copynumber, MARGIN = 2L, FUN = sdFUN, na.rm = TRUE)
-       5: .local(x, y = y, ...)
-       6: plot(fitC)
-       7: plot(fitC)
-      An irrecoverable exception occurred. R is aborting now ...
-    ```
-
-*   checking re-building of vignette outputs ... NOTE
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘QDNAseq.Rnw’ using Sweave
-    EM algorithm started ... 
-    
-    Warning in allprior/tot :
-      Recycling array of length 1 in vector-array arithmetic is deprecated.
-      Use c() or as.vector() instead.
-    
-    Warning in allprior/tot :
-      Recycling array of length 1 in vector-array arithmetic is deprecated.
-    ...
-    l.196 \RequirePackage
-                         {parnotes}^^M
-    !  ==> Fatal error occurred, no output PDF file produced!
-    --- failed re-building ‘QDNAseq.Rnw’
-    
-    SUMMARY: processing the following file failed:
-      ‘QDNAseq.Rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# QDNAseq.hg19
-
-<details>
-
-* Version: 1.32.0
-* GitHub: https://github.com/tgac-vumc/QDNAseq.hg19
-* Source code: https://github.com/cran/QDNAseq.hg19
-* Date/Publication: 2023-10-26
-* Number of recursive dependencies: 43
-
-Run `revdep_details(, "QDNAseq.hg19")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 35.3Mb
-      sub-directories of 1Mb or more:
-        data  35.3Mb
-    ```
-
-# QDNAseq.mm10
-
-<details>
-
-* Version: 1.32.0
-* GitHub: https://github.com/tgac-vumc/QDNAseq.mm10
-* Source code: https://github.com/cran/QDNAseq.mm10
-* Date/Publication: 2023-10-26
-* Number of recursive dependencies: 43
-
-Run `revdep_details(, "QDNAseq.mm10")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 31.2Mb
-      sub-directories of 1Mb or more:
-        data  31.2Mb
-    ```
-
-# qtl2pleio
-
-<details>
-
-* Version: 1.4.3
-* GitHub: https://github.com/fboehm/qtl2pleio
-* Source code: https://github.com/cran/qtl2pleio
-* Date/Publication: 2020-12-02 22:50:02 UTC
-* Number of recursive dependencies: 130
-
-Run `revdep_details(, "qtl2pleio")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 22.9Mb
-      sub-directories of 1Mb or more:
-        libs  22.7Mb
-    ```
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# Qtools
-
-<details>
-
-* Version: 1.5.9
-* GitHub: NA
-* Source code: https://github.com/cran/Qtools
-* Date/Publication: 2023-10-28 15:10:02 UTC
-* Number of recursive dependencies: 117
-
-Run `revdep_details(, "Qtools")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘Qtools’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/Qtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/Qtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/Qtools/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/Qtools/new/Qtools.Rcheck/00install.out’ for details.
-    ```
-
-# RAINBOWR
-
-<details>
-
-* Version: 0.1.33
-* GitHub: NA
-* Source code: https://github.com/cran/RAINBOWR
-* Date/Publication: 2023-09-12 05:40:02 UTC
-* Number of recursive dependencies: 167
-
-Run `revdep_details(, "RAINBOWR")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 38.0Mb
-      sub-directories of 1Mb or more:
-        libs  36.6Mb
-    ```
-
-# rattle
-
-<details>
-
-* Version: 5.5.1
-* GitHub: NA
-* Source code: https://github.com/cran/rattle
-* Date/Publication: 2022-03-21 13:10:02 UTC
-* Number of recursive dependencies: 228
-
-Run `revdep_details(, "rattle")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘rattle.Rnw’ using Sweave
-    Error: processing vignette 'rattle.Rnw' failed with diagnostics:
-    Running 'texi2dvi' on 'rattle.tex' failed.
-    LaTeX errors:
-    ! LaTeX Error: File `lastpage.sty' not found.
-    
-    Type X to quit or <RETURN> to proceed,
-    or enter new name. (Default extension: sty)
-    ...
-    l.13 \usepackage
-                    {algorithm2e}^^M
-    !  ==> Fatal error occurred, no output PDF file produced!
-    --- failed re-building ‘rattle.Rnw’
-    
-    SUMMARY: processing the following file failed:
-      ‘rattle.Rnw’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages suggested but not available for checking: 'cairoDevice', 'RGtk2'
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  9.4Mb
-      sub-directories of 1Mb or more:
-        data   4.6Mb
-        etc    1.9Mb
-        po     1.2Mb
-    ```
-
-*   checking Rd files ... NOTE
-    ```
-    checkRd: (-1) acquireAuditData.Rd:24: Escaped LaTeX specials: \_
-    checkRd: (-1) rattle.Rd:44: Escaped LaTeX specials: \_
-    ```
-
-# raveio
-
-<details>
-
-* Version: 0.9.0
-* GitHub: https://github.com/beauchamplab/raveio
-* Source code: https://github.com/cran/raveio
-* Date/Publication: 2023-07-16 19:10:02 UTC
-* Number of recursive dependencies: 133
-
-Run `revdep_details(, "raveio")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘clustermq’
-    ```
-
-# rbmi
-
-<details>
-
-* Version: 1.2.6
-* GitHub: https://github.com/insightsengineering/rbmi
-* Source code: https://github.com/cran/rbmi
-* Date/Publication: 2023-11-24 14:00:03 UTC
-* Number of recursive dependencies: 103
-
-Run `revdep_details(, "rbmi")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 60.5Mb
-      sub-directories of 1Mb or more:
-        libs  59.4Mb
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# RBtest
-
-<details>
-
-* Version: 1.1
-* GitHub: NA
-* Source code: https://github.com/cran/RBtest
-* Date/Publication: 2020-03-03 15:00:03 UTC
-* Number of recursive dependencies: 80
-
-Run `revdep_details(, "RBtest")` for more info
-
-</details>
-
-## In both
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# RcppDE
-
-<details>
-
-* Version: 0.1.7
-* GitHub: https://github.com/eddelbuettel/rcppde
-* Source code: https://github.com/cran/RcppDE
-* Date/Publication: 2022-12-20 10:40:02 UTC
-* Number of recursive dependencies: 5
-
-Run `revdep_details(, "RcppDE")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘RcppDE’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/RcppDE/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/RcppDE/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/RcppDE/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/RcppDE/new/RcppDE.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-# receptiviti
-
-<details>
-
-* Version: 0.1.6
-* GitHub: https://github.com/Receptiviti/receptiviti-r
-* Source code: https://github.com/cran/receptiviti
-* Date/Publication: 2023-11-27 15:30:02 UTC
-* Number of recursive dependencies: 68
-
-Run `revdep_details(, "receptiviti")` for more info
-
-</details>
-
-## In both
-
-*   checking tests ...
-    ```
-      Running ‘testthat.R’
-     ERROR
-    Running the tests in ‘tests/testthat.R’ failed.
-    Complete output:
-      > library(testthat)
-      > library(receptiviti)
-      > 
-      > test_check("receptiviti")
-      Status: ERROR
-      Message: 400
-    ...
-       7. └─receptiviti::receptiviti(text, url = "http://localhost:0/not_served")
-      ── Failure ('test-receptiviti_status.R:5:3'): failures works ───────────────────
-      receptiviti_status(...) is not NULL
-      
-      `actual` is a list
-      `expected` is NULL
-      
-      [ FAIL 2 | WARN 0 | SKIP 2 | PASS 6 ]
-      Error: Test failures
-      Execution halted
-    ```
-
-# regmedint
-
-<details>
-
-* Version: 1.0.1
-* GitHub: https://github.com/kaz-yos/regmedint
-* Source code: https://github.com/cran/regmedint
-* Date/Publication: 2024-01-13 00:50:02 UTC
-* Number of recursive dependencies: 154
-
-Run `revdep_details(, "regmedint")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘Deriv’
-      All declared Imports should be used.
-    ```
-
-# rexposome
-
-<details>
-
-* Version: 1.24.1
-* GitHub: NA
-* Source code: https://github.com/cran/rexposome
-* Date/Publication: 2023-11-02
-* Number of recursive dependencies: 172
-
-Run `revdep_details(, "rexposome")` for more info
-
-</details>
-
-## In both
-
-*   checking for portable file names ... WARNING
-    ```
-    Found the following file with a non-portable file name:
-      vignettes/rsconnect/documents/exposome_data_analysis.Rmd/rpubs.com/rpubs/Publish Document.dcf
-    These are not fully portable file names.
-    See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
-    Found the following non-portable file path:
-      rexposome/vignettes/rsconnect/documents/exposome_data_analysis.Rmd/rpubs.com/rpubs/Publish Document.dcf
-    
-    Tarballs are only required to store paths of up to 100 bytes and cannot
-    store those of more than 256 bytes, with restrictions including to 100
-    bytes for the final component.
-    See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
-    ```
-
-*   checking dependencies in R code ... WARNING
-    ```
-    '::' or ':::' imports not declared from:
-      ‘missMDA’ ‘nnet’ ‘sandwich’
-    ```
-
-*   checking Rd metadata ... WARNING
-    ```
-    Rd files with duplicated alias 'extract':
-      ‘extract-methods.Rd’ ‘get_robust_sd-methods.Rd’
-    ```
-
-*   checking for code/documentation mismatches ... WARNING
-    ```
-    S4 class codoc mismatches from documentation object 'ExWAS':
-    Slots for class 'ExWAS'
-      Code: comparison description effective formula robust.std.err
-      Docs: comparison description effective formula
-    ```
-
-*   checking Rd \usage sections ... WARNING
-    ```
-    Undocumented arguments in documentation object 'ExposomeSet'
-      ‘robust’
-    
-    Undocumented arguments in documentation object 'exwas'
-      ‘robust’
-    
-    Undocumented arguments in documentation object 'imExposomeSet'
-      ‘robust’
-    
-    Functions with \usage entries need to have the appropriate \alias
-    entries, and all their arguments documented.
-    The \usage entries must correspond to syntactically valid R code.
-    See chapter ‘Writing R documentation files’ in the ‘Writing R
-    Extensions’ manual.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 11.4Mb
-      sub-directories of 1Mb or more:
-        data      2.8Mb
-        doc       5.5Mb
-        extdata   2.2Mb
-    ```
-
-*   checking R code for possible problems ... NOTE
-    ```
-    imputeLOD: multiple local function definitions for ‘faux’ with
-      different formal arguments
-    invExWAS,ExposomeSet : <anonymous>: no visible global function
-      definition for ‘reformulate’
-    invExWAS,ExposomeSet : <anonymous>: no visible global function
-      definition for ‘terms’
-    invExWAS,ExposomeSet : <anonymous>: no visible global function
-      definition for ‘confint’
-    invExWAS,ExposomeSet: no visible global function definition for
-      ‘reformulate’
-    invExWAS,ExposomeSet: no visible global function definition for ‘terms’
-    plotHistogram,ExposomeSet: no visible binding for global variable
-      ‘..density..’
-    Undefined global functions or variables:
-      ..density.. confint reformulate terms
-    Consider adding
-      importFrom("stats", "confint", "reformulate", "terms")
-    to your NAMESPACE file.
-    ```
-
-# rgee
-
-<details>
-
-* Version: 1.1.7
-* GitHub: https://github.com/r-spatial/rgee
-* Source code: https://github.com/cran/rgee
-* Date/Publication: 2023-09-27 08:30:02 UTC
-* Number of recursive dependencies: 146
-
-Run `revdep_details(, "rgee")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  8.2Mb
-      sub-directories of 1Mb or more:
-        doc   6.9Mb
-    ```
-
-# Riemann
-
-<details>
-
-* Version: 0.1.4
-* GitHub: https://github.com/kisungyou/Riemann
-* Source code: https://github.com/cran/Riemann
-* Date/Publication: 2022-02-28 20:30:02 UTC
-* Number of recursive dependencies: 115
-
-Run `revdep_details(, "Riemann")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘Riemann’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/Riemann/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/Riemann/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/Riemann/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/Riemann/new/Riemann.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 27.6Mb
-      sub-directories of 1Mb or more:
-        data   1.6Mb
-        libs  25.3Mb
-    ```
-
-*   checking Rd files ... NOTE
-    ```
-    checkRd: (-1) acg.Rd:72: Escaped LaTeX specials: \&
-    checkRd: (-1) gorilla.Rd:41: Escaped LaTeX specials: \&
-    checkRd: (-1) grassmann.utest.Rd:63: Escaped LaTeX specials: \&
-    checkRd: (-1) macg.Rd:71: Escaped LaTeX specials: \&
-    checkRd: (-1) sphere.utest.Rd:47: Escaped LaTeX specials: \&
-    checkRd: (-1) stiefel.utest.Rd:64: Escaped LaTeX specials: \&
-    checkRd: (-1) wrap.landmark.Rd:41: Escaped LaTeX specials: \&
-    ```
-
-# rmsb
-
-<details>
-
-* Version: 1.0-0
-* GitHub: NA
-* Source code: https://github.com/cran/rmsb
-* Date/Publication: 2023-09-26 13:10:02 UTC
-* Number of recursive dependencies: 144
-
-Run `revdep_details(, "rmsb")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘rmsb’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/rmsb/new/rmsb.Rcheck/00install.out’ for details.
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘cmdstanr’
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘rmsb’ ...
-** package ‘rmsb’ successfully unpacked and MD5 sums checked
-** using staged installation
-Error in loadNamespace(x) : there is no package called ‘rstantools’
-Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: configuration failed for package ‘rmsb’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/rmsb/new/rmsb.Rcheck/rmsb’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘rmsb’ ...
-** package ‘rmsb’ successfully unpacked and MD5 sums checked
-** using staged installation
-Error in loadNamespace(x) : there is no package called ‘rstantools’
-Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: configuration failed for package ‘rmsb’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/rmsb/old/rmsb.Rcheck/rmsb’
-
-
-```
-# RNAseqCovarImpute
-
-<details>
-
-* Version: 1.0.2
-* GitHub: https://github.com/brennanhilton/RNAseqCovarImpute
-* Source code: https://github.com/cran/RNAseqCovarImpute
-* Date/Publication: 2023-10-27
-* Number of recursive dependencies: 111
-
-Run `revdep_details(, "RNAseqCovarImpute")` for more info
-
-</details>
-
-## In both
-
-*   checking R code for possible problems ... NOTE
-    ```
-    combine_rubins: no visible binding for global variable ‘probe’
-    combine_rubins: no visible binding for global variable ‘i’
-    combine_rubins: no visible binding for global variable ‘coef_combined’
-    combine_rubins: no visible binding for global variable ‘rubins_t_bayes’
-    combine_rubins: no visible binding for global variable ‘combined_p’
-    combine_rubins: no visible binding for global variable
-      ‘combined_p_bayes’
-    get_gene_bin_intervals: no visible binding for global variable ‘end’
-    get_gene_bin_intervals: no visible binding for global variable ‘start’
-    limmavoom_imputed_data_list_helper: no visible binding for global
-    ...
-    voom_sx_sy: no visible global function definition for ‘is’
-    voom_sx_sy: no visible global function definition for ‘new’
-    Undefined global functions or variables:
-      approxfun coef_combined combined_p combined_p_bayes end gene_bin i is
-      lm_predictor lowess new probe rubins_t_bayes start
-    Consider adding
-      importFrom("methods", "is", "new")
-      importFrom("stats", "approxfun", "end", "lowess", "start")
-    to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
-    contains 'methods').
-    ```
-
-# robotstxt
-
-<details>
-
-* Version: 0.7.13
-* GitHub: https://github.com/ropensci/robotstxt
-* Source code: https://github.com/cran/robotstxt
-* Date/Publication: 2020-09-03 19:30:02 UTC
-* Number of recursive dependencies: 70
-
-Run `revdep_details(, "robotstxt")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘future’
-      All declared Imports should be used.
-    ```
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# rpm
-
-<details>
-
-* Version: 0.7-1
-* GitHub: https://github.com/handcock/rpm
-* Source code: https://github.com/cran/rpm
-* Date/Publication: 2023-04-21 23:30:02 UTC
-* Number of recursive dependencies: 66
-
-Run `revdep_details(, "rpm")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘rpm’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/rpm/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/rpm/new/rpm.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 11.6Mb
-      sub-directories of 1Mb or more:
-        libs  11.1Mb
-    ```
-
-# rrscale
-
-<details>
-
-* Version: 1.0
-* GitHub: NA
-* Source code: https://github.com/cran/rrscale
-* Date/Publication: 2020-05-26 11:30:02 UTC
-* Number of recursive dependencies: 72
-
-Run `revdep_details(, "rrscale")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘abind’
-      All declared Imports should be used.
-    ```
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# runMCMCbtadjust
-
-<details>
-
-* Version: 1.0.5
-* GitHub: NA
-* Source code: https://github.com/cran/runMCMCbtadjust
-* Date/Publication: 2023-12-13 09:50:13 UTC
-* Number of recursive dependencies: 120
-
-Run `revdep_details(, "runMCMCbtadjust")` for more info
-
-</details>
-
-## In both
-
-*   checking DESCRIPTION meta-information ... WARNING
-    ```
-    Non-standard license specification:
-      CECILL-2.1
-    Standardizable: FALSE
-    ```
-
-# sapfluxnetr
-
-<details>
-
-* Version: 0.1.4
-* GitHub: https://github.com/sapfluxnet/sapfluxnetr
-* Source code: https://github.com/cran/sapfluxnetr
-* Date/Publication: 2023-01-25 15:30:02 UTC
-* Number of recursive dependencies: 83
-
-Run `revdep_details(, "sapfluxnetr")` for more info
-
-</details>
-
-## In both
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 4 marked UTF-8 strings
-    ```
-
-# SCArray.sat
-
-<details>
-
-* Version: 1.2.1
-* GitHub: https://github.com/AbbVie-ComputationalGenomics/SCArray
-* Source code: https://github.com/cran/SCArray.sat
-* Date/Publication: 2024-01-16
-* Number of recursive dependencies: 181
-
-Run `revdep_details(, "SCArray.sat")` for more info
-
-</details>
-
-## In both
-
-*   checking S3 generic/method consistency ... WARNING
-    ```
-    SetAssayData:
-      function(object, layer, new.data, slot, ...)
-    SetAssayData.SCArrayAssay:
-      function(object, slot, new.data, ...)
-    
-    CreateSeuratObject:
-      function(counts, assay, names.field, names.delim, meta.data, project,
-               ...)
-    CreateSeuratObject.DelayedMatrix:
-      function(counts, project, assay, names.field, names.delim, meta.data,
-               min.cells, min.features, row.names, ...)
-    See section ‘Generic functions and methods’ in the ‘Writing R
-    Extensions’ manual.
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Unexported objects imported by ':::' calls:
-      ‘Seurat:::DEmethods_counts’ ‘Seurat:::DEmethods_nocorrect’
-      ‘Seurat:::FastExpMean’ ‘Seurat:::FastLogVMR’ ‘Seurat:::NBResiduals’
-      ‘Seurat:::UpdateKey’ ‘Seurat:::ValidateDataForMerge’
-      See the note in ?`:::` about the use of this operator.
-    ```
-
-# scRNAseqApp
-
-<details>
-
-* Version: 1.2.2
-* GitHub: https://github.com/jianhong/scRNAseqApp
-* Source code: https://github.com/cran/scRNAseqApp
-* Date/Publication: 2023-11-02
-* Number of recursive dependencies: 235
-
-Run `revdep_details(, "scRNAseqApp")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages which this enhances but not available for checking:
-      'celldex', 'SingleR', 'tricycle'
-    ```
-
-# scruff
-
-<details>
-
-* Version: 1.20.0
-* GitHub: https://github.com/campbio/scruff
-* Source code: https://github.com/cran/scruff
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 186
-
-Run `revdep_details(, "scruff")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Unexported object imported by a ':::' call: 'ShortRead:::.set_omp_threads'
-      See the note in ?`:::` about the use of this operator.
-    ```
-
-*   checking foreign function calls ... NOTE
-    ```
-    Foreign function call to a different package:
-      .Call(ShortRead:::.set_omp_threads, ...)
-    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
-    Extensions’ manual.
-    ```
-
-# sctransform
-
-<details>
-
-* Version: 0.4.1
-* GitHub: https://github.com/satijalab/sctransform
-* Source code: https://github.com/cran/sctransform
-* Date/Publication: 2023-10-19 04:40:02 UTC
-* Number of recursive dependencies: 68
-
-Run `revdep_details(, "sctransform")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘sctransform’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/sctransform/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/sctransform/new/sctransform.Rcheck/00install.out’ for details.
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package which this enhances but not available for checking: ‘glmGamPoi’
-    ```
-
-# sdmApp
-
-<details>
-
-* Version: 0.0.2
-* GitHub: https://github.com/Abson-dev/sdmApp
-* Source code: https://github.com/cran/sdmApp
-* Date/Publication: 2021-07-07 08:30:02 UTC
-* Number of recursive dependencies: 177
-
-Run `revdep_details(, "sdmApp")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘sp’
-      All declared Imports should be used.
-    ```
-
-# sdmTMB
-
-<details>
-
-* Version: 0.4.2
-* GitHub: https://github.com/pbs-assess/sdmTMB
-* Source code: https://github.com/cran/sdmTMB
-* Date/Publication: 2024-01-18 04:30:02 UTC
-* Number of recursive dependencies: 117
-
-Run `revdep_details(, "sdmTMB")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 87.1Mb
-      sub-directories of 1Mb or more:
-        libs  85.3Mb
-    ```
-
-# sentopics
-
-<details>
-
-* Version: 0.7.2
-* GitHub: https://github.com/odelmarcelle/sentopics
-* Source code: https://github.com/cran/sentopics
-* Date/Publication: 2023-05-28 09:50:02 UTC
-* Number of recursive dependencies: 173
-
-Run `revdep_details(, "sentopics")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘sentopics’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/sentopics/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/sentopics/new/sentopics.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  8.1Mb
-      sub-directories of 1Mb or more:
-        data   1.2Mb
-        libs   6.2Mb
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: ‘lexicon’
-    ```
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 3128 marked UTF-8 strings
-    ```
-
-# seqpac
-
-<details>
-
-* Version: 1.2.0
-* GitHub: https://github.com/Danis102/seqpac
-* Source code: https://github.com/cran/seqpac
-* Date/Publication: 2023-11-03
-* Number of recursive dependencies: 201
-
-Run `revdep_details(, "seqpac")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.1Mb
-      sub-directories of 1Mb or more:
-        doc       1.6Mb
-        extdata   2.7Mb
-    ```
-
-# Seurat
-
-<details>
-
-* Version: 5.0.1
-* GitHub: https://github.com/satijalab/seurat
-* Source code: https://github.com/cran/Seurat
-* Date/Publication: 2023-11-17 23:10:06 UTC
-* Number of recursive dependencies: 266
-
-Run `revdep_details(, "Seurat")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages suggested but not available for checking: 'BPCells', 'presto'
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 15.1Mb
-      sub-directories of 1Mb or more:
-        R      1.7Mb
-        libs  12.6Mb
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: ‘Signac’
-    ```
-
-# SeuratObject
-
-<details>
-
-* Version: 5.0.1
-* GitHub: https://github.com/mojaveazure/seurat-object
-* Source code: https://github.com/cran/SeuratObject
-* Date/Publication: 2023-11-17 22:40:16 UTC
-* Number of recursive dependencies: 105
-
-Run `revdep_details(, "SeuratObject")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘BPCells’
-    
-    Package which this enhances but not available for checking: ‘Seurat’
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.4Mb
-      sub-directories of 1Mb or more:
-        R      1.5Mb
-        libs   3.2Mb
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: ‘plotly’
-    ```
-
-# shapeNA
-
-<details>
-
-* Version: 0.0.2
-* GitHub: NA
-* Source code: https://github.com/cran/shapeNA
-* Date/Publication: 2021-03-15 09:10:02 UTC
-* Number of recursive dependencies: 96
-
-Run `revdep_details(, "shapeNA")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘stats’
-      All declared Imports should be used.
-    ```
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# sharp
-
-<details>
-
-* Version: 1.4.6
-* GitHub: https://github.com/barbarabodinier/sharp
-* Source code: https://github.com/cran/sharp
-* Date/Publication: 2024-02-03 17:30:02 UTC
-* Number of recursive dependencies: 157
-
-Run `revdep_details(, "sharp")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘rCOSA’
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: ‘rCOSA’
-    ```
-
-# shiny
-
-<details>
-
-* Version: 1.8.0
-* GitHub: https://github.com/rstudio/shiny
-* Source code: https://github.com/cran/shiny
-* Date/Publication: 2023-11-17 23:40:02 UTC
-* Number of recursive dependencies: 92
-
-Run `revdep_details(, "shiny")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 11.4Mb
-      sub-directories of 1Mb or more:
-        R     1.4Mb
-        www   8.9Mb
-    ```
-
-# shiny.worker
-
-<details>
-
-* Version: 0.0.1
-* GitHub: NA
-* Source code: https://github.com/cran/shiny.worker
-* Date/Publication: 2021-01-21 11:00:02 UTC
-* Number of recursive dependencies: 65
-
-Run `revdep_details(, "shiny.worker")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘R6’ ‘shiny’
-      All declared Imports should be used.
-    ```
-
-*   checking LazyData ... NOTE
-    ```
-      'LazyData' is specified without a 'data' directory
-    ```
-
-# SIAMCAT
-
-<details>
-
-* Version: 2.6.0
-* GitHub: NA
-* Source code: https://github.com/cran/SIAMCAT
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 202
-
-Run `revdep_details(, "SIAMCAT")` for more info
-
-</details>
-
-## In both
-
-*   checking for hidden files and directories ... NOTE
-    ```
-    Found the following hidden files and directories:
-      .travis.yml
-    These were most likely included in error. See section ‘Package
-    structure’ in the ‘Writing R Extensions’ manual.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 23.4Mb
-      sub-directories of 1Mb or more:
-        doc      18.4Mb
-        extdata   2.1Mb
-        help      1.9Mb
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: ‘ranger’
-    ```
-
-# sigminer
-
-<details>
-
-* Version: 2.3.0
-* GitHub: https://github.com/ShixiangWang/sigminer
-* Source code: https://github.com/cran/sigminer
-* Date/Publication: 2023-12-12 11:50:03 UTC
-* Number of recursive dependencies: 205
-
-Run `revdep_details(, "sigminer")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.9Mb
-      sub-directories of 1Mb or more:
-        help   1.7Mb
-        libs   1.4Mb
-    ```
-
-# Signac
-
-<details>
-
-* Version: 1.12.0
-* GitHub: https://github.com/stuart-lab/signac
-* Source code: https://github.com/cran/Signac
-* Date/Publication: 2023-11-08 09:30:02 UTC
-* Number of recursive dependencies: 254
-
-Run `revdep_details(, "Signac")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.1Mb
-      sub-directories of 1Mb or more:
-        R      1.1Mb
-        libs   2.9Mb
-    ```
-
-# signeR
-
-<details>
-
-* Version: 2.4.0
-* GitHub: https://github.com/TojalLab/signeR
-* Source code: https://github.com/cran/signeR
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 244
-
-Run `revdep_details(, "signeR")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘signeR’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/signeR/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/signeR/new/signeR.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  6.6Mb
-      sub-directories of 1Mb or more:
-        R     1.2Mb
-        doc   4.5Mb
-    ```
-
-*   checking R code for possible problems ... NOTE
-    ```
-    covariate: no visible binding for global variable ‘.’
-    explorepage: no visible binding for global variable ‘.’
-    genCountMatrixFromMAF: no visible binding for global variable
-      ‘Variant_Type’
-    genCountMatrixFromMAF: no visible binding for global variable
-      ‘Reference_Allele’
-    genCountMatrixFromMAF: no visible binding for global variable
-      ‘Tumor_Seq_Allele2’
-    genCountMatrixFromMAF: no visible binding for global variable
-      ‘Tumor_Seq_Allele1’
-    ...
-    ExposureCorrelation,SignExp-numeric: no visible binding for global
-      variable ‘exposure’
-    ExposureCorrelation,matrix-numeric: no visible binding for global
-      variable ‘Feature’
-    ExposureCorrelation,matrix-numeric: no visible binding for global
-      variable ‘exposure’
-    Undefined global functions or variables:
-      . Col Feature Frequency Reference_Allele Row Samples Signatures
-      Tumor_Seq_Allele1 Tumor_Seq_Allele2 Variant_Type alt<- exposure fc
-      project sig sig_test
-    ```
-
-*   checking Rd files ... NOTE
-    ```
-    prepare_Rd: cosmic_data.Rd:91-93: Dropping empty section \details
-    prepare_Rd: cosmic_data.Rd:98-100: Dropping empty section \references
-    prepare_Rd: cosmic_data.Rd:101-102: Dropping empty section \examples
-    prepare_Rd: tcga_similarities.Rd:96-98: Dropping empty section \details
-    prepare_Rd: tcga_similarities.Rd:99-101: Dropping empty section \source
-    prepare_Rd: tcga_similarities.Rd:102-104: Dropping empty section \references
-    prepare_Rd: tcga_similarities.Rd:105-106: Dropping empty section \examples
-    prepare_Rd: tcga_tumors.Rd:18-20: Dropping empty section \details
-    prepare_Rd: tcga_tumors.Rd:21-23: Dropping empty section \source
-    prepare_Rd: tcga_tumors.Rd:24-26: Dropping empty section \references
-    prepare_Rd: tcga_tumors.Rd:27-28: Dropping empty section \examples
-    ```
-
-# SimDesign
-
-<details>
-
-* Version: 2.14
-* GitHub: https://github.com/philchalmers/SimDesign
-* Source code: https://github.com/cran/SimDesign
-* Date/Publication: 2024-01-09 09:10:11 UTC
-* Number of recursive dependencies: 124
-
-Run `revdep_details(, "SimDesign")` for more info
-
-</details>
-
-## Newly fixed
-
-*   checking re-building of vignette outputs ... ERROR
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘Catch_errors.Rmd’ using rmarkdown
-    --- finished re-building ‘Catch_errors.Rmd’
-    
-    --- re-building ‘Fixed_obj_fun.Rmd’ using rmarkdown
-    
-    Quitting from lines 65-69 [unnamed-chunk-5] (Fixed_obj_fun.Rmd)
-    Error: processing vignette 'Fixed_obj_fun.Rmd' failed with diagnostics:
-    creation of server socket failed: port 11284 cannot be opened
-    --- failed re-building ‘Fixed_obj_fun.Rmd’
-    ...
-    --- finished re-building ‘Saving-results.Rmd’
-    
-    --- re-building ‘SimDesign-intro.Rmd’ using rmarkdown
-    --- finished re-building ‘SimDesign-intro.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘Fixed_obj_fun.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘doMPI’
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.8Mb
-      sub-directories of 1Mb or more:
-        doc   5.2Mb
-    ```
-
-# sits
-
-<details>
-
-* Version: 1.4.2-1
-* GitHub: https://github.com/e-sensing/sits
-* Source code: https://github.com/cran/sits
-* Date/Publication: 2023-11-02 15:10:02 UTC
-* Number of recursive dependencies: 220
-
-Run `revdep_details(, "sits")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘sits’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/sits/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/sits/new/sits.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 13.2Mb
-      sub-directories of 1Mb or more:
-        R         1.1Mb
-        extdata   1.5Mb
-        libs      9.9Mb
-    ```
-
-# skpr
-
-<details>
-
-* Version: 1.6.2
-* GitHub: https://github.com/tylermorganwall/skpr
-* Source code: https://github.com/cran/skpr
-* Date/Publication: 2024-02-06 19:50:02 UTC
-* Number of recursive dependencies: 149
-
-Run `revdep_details(, "skpr")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 55.9Mb
-      sub-directories of 1Mb or more:
-        libs  55.3Mb
-    ```
-
-# SLOPE
-
-<details>
-
-* Version: 0.5.0
-* GitHub: https://github.com/jolars/SLOPE
-* Source code: https://github.com/cran/SLOPE
-* Date/Publication: 2022-06-09 22:40:18 UTC
-* Number of recursive dependencies: 151
-
-Run `revdep_details(, "SLOPE")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘SLOPE’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/SLOPE/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/SLOPE/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/SLOPE/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/SLOPE/new/SLOPE.Rcheck/00install.out’ for details.
-    ```
-
-*   checking C++ specification ... NOTE
-    ```
-      Specified C++11: please drop specification unless essential
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 13.1Mb
-      sub-directories of 1Mb or more:
-        libs  12.6Mb
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘checkmate’ ‘glmnet’ ‘mice’
-      All declared Imports should be used.
-    ```
-
-# SmCCNet
-
-<details>
-
-* Version: 2.0.2
-* GitHub: https://github.com/KechrisLab/SmCCNet
-* Source code: https://github.com/cran/SmCCNet
-* Date/Publication: 2024-01-13 21:50:17 UTC
-* Number of recursive dependencies: 162
-
-Run `revdep_details(, "SmCCNet")` for more info
-
-</details>
-
-## In both
-
-*   checking re-building of vignette outputs ... ERROR
-    ```
-    Error(s) in re-building vignettes:
-    --- re-building ‘SmCCNet_Vignette_AutoSmCCNet.Rmd’ using rmarkdown
-    ! kpathsea: Running mktexfmt xelatex.fmt
-    
-    Error: processing vignette 'SmCCNet_Vignette_AutoSmCCNet.Rmd' failed with diagnostics:
-    LaTeX failed to compile /c4/home/henrik/repositories/parallelly/revdep/checks/SmCCNet/new/SmCCNet.Rcheck/vign_test/SmCCNet/vignettes/SmCCNet_Vignette_AutoSmCCNet.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SmCCNet_Vignette_AutoSmCCNet.log for more info.
-    --- failed re-building ‘SmCCNet_Vignette_AutoSmCCNet.Rmd’
-    
-    --- re-building ‘SmCCNet_Vignette_MultiOmics.Rmd’ using rmarkdown
-    ! kpathsea: Running mktexfmt xelatex.fmt
-    ...
-    Error: processing vignette 'SmCCNet_Vignette_SingleOmics.Rmd' failed with diagnostics:
-    LaTeX failed to compile /c4/home/henrik/repositories/parallelly/revdep/checks/SmCCNet/new/SmCCNet.Rcheck/vign_test/SmCCNet/vignettes/SmCCNet_Vignette_SingleOmics.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SmCCNet_Vignette_SingleOmics.log for more info.
-    --- failed re-building ‘SmCCNet_Vignette_SingleOmics.Rmd’
-    
-    SUMMARY: processing the following files failed:
-      ‘SmCCNet_Vignette_AutoSmCCNet.Rmd’ ‘SmCCNet_Vignette_MultiOmics.Rmd’
-      ‘SmCCNet_Vignette_SingleOmics.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
-# smoots
-
-<details>
-
-* Version: 1.1.4
-* GitHub: NA
-* Source code: https://github.com/cran/smoots
-* Date/Publication: 2023-09-11 08:50:02 UTC
-* Number of recursive dependencies: 78
-
-Run `revdep_details(, "smoots")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘smoots’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/smoots/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/smoots/new/smoots.Rcheck/00install.out’ for details.
-    ```
-
-# solitude
-
-<details>
-
-* Version: 1.1.3
-* GitHub: https://github.com/talegari/solitude
-* Source code: https://github.com/cran/solitude
-* Date/Publication: 2021-07-29 20:00:02 UTC
-* Number of recursive dependencies: 131
-
-Run `revdep_details(, "solitude")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘R6’ ‘lgr’
-      All declared Imports should be used.
-    ```
-
-# SpaDES.core
-
-<details>
-
-* Version: 2.0.3
-* GitHub: https://github.com/PredictiveEcology/SpaDES.core
-* Source code: https://github.com/cran/SpaDES.core
-* Date/Publication: 2023-11-10 10:20:02 UTC
-* Number of recursive dependencies: 136
-
-Run `revdep_details(, "SpaDES.core")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘NLMR’
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  6.2Mb
-      sub-directories of 1Mb or more:
-        R   4.7Mb
-    ```
-
-# SpaDES.tools
-
-<details>
-
-* Version: 2.0.5
-* GitHub: https://github.com/PredictiveEcology/SpaDES.tools
-* Source code: https://github.com/cran/SpaDES.tools
-* Date/Publication: 2023-11-10 23:23:24 UTC
-* Number of recursive dependencies: 94
-
-Run `revdep_details(, "SpaDES.tools")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘NLMR’
-    ```
-
-*   checking startup messages can be suppressed ... NOTE
-    ```
-    code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    ...
-    code for methods in class “Rcpp_SpatTime_v” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatVector” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatVectorCollection” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
-    
-    It looks like this package (or a package it requires) has a startup
-    message which cannot be suppressed: see ?packageStartupMessage.
-    ```
-
-# spaMM
-
-<details>
-
-* Version: 4.4.16
-* GitHub: NA
-* Source code: https://github.com/cran/spaMM
-* Date/Publication: 2023-12-20 13:50:02 UTC
-* Number of recursive dependencies: 102
-
-Run `revdep_details(, "spaMM")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Packages suggested but not available for checking: 'Infusion', 'blackbox'
-    
-    Packages which this enhances but not available for checking:
-      'multcomp', 'RLRsim', 'lmerTest'
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 56.2Mb
-      sub-directories of 1Mb or more:
-        R      2.7Mb
-        libs  52.2Mb
-    ```
-
-# sparrpowR
-
-<details>
-
-* Version: 0.2.8
-* GitHub: https://github.com/machiela-lab/sparrpowR
-* Source code: https://github.com/cran/sparrpowR
-* Date/Publication: 2024-01-23 15:20:02 UTC
-* Number of recursive dependencies: 130
-
-Run `revdep_details(, "sparrpowR")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘sparrpowR’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      Warning: no DISPLAY variable so Tk is not available
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/sparrpowR/new/sparrpowR.Rcheck/00install.out’ for details.
-    ```
-
-# SPARSEMODr
-
-<details>
-
-* Version: 1.2.0
-* GitHub: https://github.com/NAU-CCL/SPARSEMODr
-* Source code: https://github.com/cran/SPARSEMODr
-* Date/Publication: 2022-07-19 20:50:02 UTC
-* Number of recursive dependencies: 127
-
-Run `revdep_details(, "SPARSEMODr")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘future’ ‘geosphere’ ‘lubridate’ ‘tidyverse’ ‘viridis’
-      All declared Imports should be used.
-    ```
-
-# spatialwarnings
-
-<details>
-
-* Version: 3.0.3
-* GitHub: https://github.com/spatial-ews/spatialwarnings
-* Source code: https://github.com/cran/spatialwarnings
-* Date/Publication: 2022-03-21 13:00:02 UTC
-* Number of recursive dependencies: 97
-
-Run `revdep_details(, "spatialwarnings")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘spatialwarnings’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/spatialwarnings/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/spatialwarnings/new/spatialwarnings.Rcheck/00install.out’ for details.
-    ```
-
-*   checking Rd cross-references ... WARNING
-    ```
-    Missing link or links in documentation object 'indictest.Rd':
-      ‘mgcv’
-    
-    See section 'Cross-references' in the 'Writing R Extensions' manual.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  7.0Mb
-      sub-directories of 1Mb or more:
-        libs   6.0Mb
-    ```
-
-# sphunif
-
-<details>
-
-* Version: 1.3.0
-* GitHub: https://github.com/egarpor/sphunif
-* Source code: https://github.com/cran/sphunif
-* Date/Publication: 2023-12-04 19:50:02 UTC
-* Number of recursive dependencies: 79
-
-Run `revdep_details(, "sphunif")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘sphunif’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/sphunif/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/sphunif/new/sphunif.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 24.7Mb
-      sub-directories of 1Mb or more:
-        libs  23.8Mb
-    ```
-
-*   checking data for non-ASCII characters ... NOTE
-    ```
-      Note: found 189 marked UTF-8 strings
-    ```
-
-# spNetwork
-
-<details>
-
-* Version: 0.4.3.8
-* GitHub: https://github.com/JeremyGelb/spNetwork
-* Source code: https://github.com/cran/spNetwork
-* Date/Publication: 2023-08-24 11:20:05 UTC
-* Number of recursive dependencies: 146
-
-Run `revdep_details(, "spNetwork")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘spNetwork’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/spNetwork/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/spNetwork/new/spNetwork.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 25.5Mb
-      sub-directories of 1Mb or more:
-        doc       1.0Mb
-        extdata   2.6Mb
-        libs     20.5Mb
-    ```
-
-# spsh
-
-<details>
-
-* Version: 1.1.0
-* GitHub: NA
-* Source code: https://github.com/cran/spsh
-* Date/Publication: 2020-04-06 16:30:02 UTC
-* Number of recursive dependencies: 17
-
-Run `revdep_details(, "spsh")` for more info
-
-</details>
-
-## In both
-
-*   checking Rd files ... NOTE
-    ```
-    checkRd: (-1) shypEstFun.Rd:52: Escaped LaTeX specials: \$
-    checkRd: (-1) shypEstFun.Rd:54: Escaped LaTeX specials: \$
-    ```
-
-# squat
-
-<details>
-
-* Version: 0.3.0
-* GitHub: https://github.com/LMJL-Alea/squat
-* Source code: https://github.com/cran/squat
-* Date/Publication: 2024-01-10 15:40:02 UTC
-* Number of recursive dependencies: 133
-
-Run `revdep_details(, "squat")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘squat’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/squat/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/squat/new/squat.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 20.4Mb
-      sub-directories of 1Mb or more:
-        data   1.1Mb
-        help   1.1Mb
-        libs  18.0Mb
-    ```
-
-# ssdtools
-
-<details>
-
-* Version: 1.0.6
-* GitHub: https://github.com/bcgov/ssdtools
-* Source code: https://github.com/cran/ssdtools
-* Date/Publication: 2023-09-07 14:10:02 UTC
-* Number of recursive dependencies: 120
-
-Run `revdep_details(, "ssdtools")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 30.6Mb
-      sub-directories of 1Mb or more:
-        doc    1.2Mb
-        libs  28.1Mb
-    ```
-
-# StackImpute
-
-<details>
-
-* Version: 0.1.0
-* GitHub: NA
-* Source code: https://github.com/cran/StackImpute
-* Date/Publication: 2021-09-10 11:10:02 UTC
-* Number of recursive dependencies: 97
-
-Run `revdep_details(, "StackImpute")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘MASS’ ‘mice’ ‘sandwich’ ‘zoo’
-      All declared Imports should be used.
-    ```
-
-# stars
-
-<details>
-
-* Version: 0.6-4
-* GitHub: https://github.com/r-spatial/stars
-* Source code: https://github.com/cran/stars
-* Date/Publication: 2023-09-11 11:50:02 UTC
-* Number of recursive dependencies: 164
-
-Run `revdep_details(, "stars")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ...sh: line 1: 48234 Aborted                 (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R'
-    ```
-     ERROR
-    Running examples in ‘stars-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: mdim
-    > ### Title: Read or write data using GDAL's multidimensional array API
-    > ### Aliases: mdim read_mdim write_mdim
-    > 
-    > ### ** Examples
-    > 
-    ...
-                               dmalloc: no
-        Packages w/ extra debug output: none
-                           API tracing: no
-                  Using memory checker: no
-       Memory allocation sanity checks: no
-                Function stack tracing: no
-                      Use file locking: best-effort
-             Strict file format checks: no
-          Optimization instrumentation: no
-    Bye...
-    ```
-
-## Newly fixed
-
-*   checking examples ...sh: line 1: 48057 Aborted                 (core dumped) LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/software/c4/cbi/software/_centos7/R-4.3.2-gcc10/lib64/R/bin/R' --vanilla --encoding=UTF-8 > 'stars-Ex.Rout' 2>&1 < 'stars-Ex.R'
-    ```
-     ERROR
-    Running examples in ‘stars-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: mdim
-    > ### Title: Read or write data using GDAL's multidimensional array API
-    > ### Aliases: mdim read_mdim write_mdim
-    > 
-    > ### ** Examples
-    > 
-    ...
-                               dmalloc: no
-        Packages w/ extra debug output: none
-                           API tracing: no
-                  Using memory checker: no
-       Memory allocation sanity checks: no
-                Function stack tracing: no
-                      Use file locking: best-effort
-             Strict file format checks: no
-          Optimization instrumentation: no
-    Bye...
-    ```
-
-## In both
-
-*   checking tests ...
-    ```
-      Running ‘aggregate.R’
-      Comparing ‘aggregate.Rout’ to ‘aggregate.Rout.save’ ...4c4
-    < Linking to GEOS 3.11.2, GDAL 3.6.4, PROJ 8.2.1; sf_use_s2() is TRUE
-    ---
-    > Linking to GEOS 3.11.2, GDAL 3.6.2, PROJ 9.2.0; sf_use_s2() is TRUE
-      Running ‘align.R’
-      Comparing ‘align.Rout’ to ‘align.Rout.save’ ... OK
-      Running ‘area.R’
-      Comparing ‘area.Rout’ to ‘area.Rout.save’ ... OK
-      Running ‘crop.R’
-    ...
-                                 dmalloc: no
-          Packages w/ extra debug output: none
-                             API tracing: no
-                    Using memory checker: no
-         Memory allocation sanity checks: no
-                  Function stack tracing: no
-                        Use file locking: best-effort
-               Strict file format checks: no
-            Optimization instrumentation: no
-      Bye...
-    ```
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘starsdata’
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  6.1Mb
-      sub-directories of 1Mb or more:
-        doc   2.4Mb
-        nc    1.7Mb
-    ```
-
-# startR
-
-<details>
-
-* Version: 2.3.1
-* GitHub: NA
-* Source code: https://github.com/cran/startR
-* Date/Publication: 2023-12-21 16:20:02 UTC
-* Number of recursive dependencies: 60
-
-Run `revdep_details(, "startR")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘startR’ can be installed ... ERROR
-    ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/startR/new/startR.Rcheck/00install.out’ for details.
-    ```
-
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘startR’ ...
-** package ‘startR’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘startR’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/startR/new/startR.Rcheck/startR’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘startR’ ...
-** package ‘startR’ successfully unpacked and MD5 sums checked
-** using staged installation
-** R
-** inst
-** byte-compile and prepare package for lazy loading
-Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
-  there is no package called ‘ncdf4’
-Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: lazy loading failed for package ‘startR’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/startR/old/startR.Rcheck/startR’
-
-
-```
-# stppSim
-
-<details>
-
-* Version: 1.3.2
-* GitHub: https://github.com/Manalytics/stppSim
-* Source code: https://github.com/cran/stppSim
-* Date/Publication: 2023-10-29 21:20:02 UTC
-* Number of recursive dependencies: 133
-
-Run `revdep_details(, "stppSim")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘stppSim’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      Warning: no DISPLAY variable so Tk is not available
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/stppSim/new/stppSim.Rcheck/00install.out’ for details.
-    ```
-
-# superMICE
-
-<details>
-
-* Version: 1.1.1
-* GitHub: NA
-* Source code: https://github.com/cran/superMICE
-* Date/Publication: 2022-05-04 20:00:02 UTC
-* Number of recursive dependencies: 144
-
-Run `revdep_details(, "superMICE")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘extraTrees’
-    ```
-
-# survstan
-
-<details>
-
-* Version: 0.0.6.1
-* GitHub: https://github.com/fndemarqui/survstan
-* Source code: https://github.com/cran/survstan
-* Date/Publication: 2024-02-05 15:00:02 UTC
-* Number of recursive dependencies: 123
-
-Run `revdep_details(, "survstan")` for more info
-
-</details>
-
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 77.3Mb
-      sub-directories of 1Mb or more:
-        libs  76.8Mb
-    ```
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘RcppParallel’ ‘rstantools’
-      All declared Imports should be used.
-    ```
-
-*   checking for GNU extensions in Makefiles ... NOTE
-    ```
-    GNU make is a SystemRequirements.
-    ```
-
-# svars
-
-<details>
-
-* Version: 1.3.11
-* GitHub: NA
-* Source code: https://github.com/cran/svars
-* Date/Publication: 2023-02-06 10:00:02 UTC
-* Number of recursive dependencies: 91
-
-Run `revdep_details(, "svars")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘svars’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/svars/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/svars/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/svars/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/svars/new/svars.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 12.9Mb
-      sub-directories of 1Mb or more:
-        help   1.0Mb
-        libs  11.2Mb
-    ```
-
-# SynDI
-
-<details>
-
-* Version: 0.1.0
-* GitHub: https://github.com/umich-biostatistics/SynDI
-* Source code: https://github.com/cran/SynDI
-* Date/Publication: 2022-05-25 07:50:05 UTC
-* Number of recursive dependencies: 92
-
-Run `revdep_details(, "SynDI")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespaces in Imports field not imported from:
-      ‘MASS’ ‘StackImpute’ ‘arm’ ‘boot’ ‘broom’ ‘knitr’ ‘mvtnorm’
-      ‘randomForest’
-      All declared Imports should be used.
-    ```
-
-# synergyfinder
-
-<details>
-
-* Version: 3.10.3
-* GitHub: NA
-* Source code: https://github.com/cran/synergyfinder
-* Date/Publication: 2024-01-22
-* Number of recursive dependencies: 202
-
-Run `revdep_details(, "synergyfinder")` for more info
-
-</details>
-
-## In both
-
-*   checking dependencies in R code ... WARNING
-    ```
-    '::' or ':::' import not declared from: ‘scales’
-    Namespaces in Imports field not imported from:
-      ‘future’ ‘gstat’ ‘nleqslv’ ‘sp’ ‘tidyverse’
-      All declared Imports should be used.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  6.0Mb
-      sub-directories of 1Mb or more:
-        doc   5.7Mb
-    ```
-
-*   checking R code for possible problems ... NOTE
-    ```
-    .Extract2DrugPlotData: no visible binding for global variable
-      ‘input_type’
-    .Extract2DrugPlotData: no visible binding for global variable
-      ‘block_id’
-    .Extract2DrugPlotData: no visible binding for global variable ‘value’
-    .Extract2DrugPlotData: no visible binding for global variable ‘left’
-    .Extract2DrugPlotData: no visible binding for global variable ‘right’
-    .Extract2DrugPlotData: no visible binding for global variable ‘conc1’
-    .Extract2DrugPlotData: no visible binding for global variable ‘conc2’
-    .Extract2DrugPlotData: no visible binding for global variable ‘text’
-    ...
-      response_CI95 response_mean response_origin response_origin_CI95
-      response_origin_mean response_origin_sd response_origin_sem
-      response_sd response_sem right start synergy t.test text theta value
-      x y
-    Consider adding
-      importFrom("grDevices", "dev.list", "dev.off")
-      importFrom("graphics", "text")
-      importFrom("stats", "end", "predict", "start", "t.test")
-      importFrom("utils", "data", "head")
-    to your NAMESPACE file.
-    ```
-
-*   checking Rd files ... NOTE
-    ```
-    checkRd: (-1) FitDoseResponse.Rd:55: Escaped LaTeX specials: \&
-    ```
-
-# tableschema.r
-
-<details>
-
-* Version: 1.1.2
-* GitHub: https://github.com/frictionlessdata/tableschema-r
-* Source code: https://github.com/cran/tableschema.r
-* Date/Publication: 2022-09-29 20:00:03 UTC
-* Number of recursive dependencies: 66
-
-Run `revdep_details(, "tableschema.r")` for more info
-
-</details>
-
-## In both
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: ‘parsedate’
-    ```
-
-# targeted
-
-<details>
-
-* Version: 0.4
-* GitHub: https://github.com/kkholst/targeted
-* Source code: https://github.com/cran/targeted
-* Date/Publication: 2023-12-19 22:50:02 UTC
-* Number of recursive dependencies: 100
-
-Run `revdep_details(, "targeted")` for more info
-
-</details>
-
-## In both
-
-*   checking whether package ‘targeted’ can be installed ... WARNING
-    ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/targeted/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/targeted/new/targeted.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is 22.4Mb
-      sub-directories of 1Mb or more:
-        doc    1.1Mb
-        libs  20.9Mb
-    ```
-
-# targets
-
-<details>
-
-* Version: 1.4.1
-* GitHub: https://github.com/ropensci/targets
-* Source code: https://github.com/cran/targets
-* Date/Publication: 2024-01-09 09:30:02 UTC
-* Number of recursive dependencies: 166
-
-Run `revdep_details(, "targets")` for more info
-
-</details>
-
-## In both
-
-*   checking package dependencies ... NOTE
-    ```
-    Package suggested but not available for checking: ‘clustermq’
-    ```
-
-# TDApplied
-
-<details>
-
-* Version: 3.0.2
-* GitHub: https://github.com/shaelebrown/TDApplied
-* Source code: https://github.com/cran/TDApplied
-* Date/Publication: 2024-01-21 15:42:50 UTC
-* Number of recursive dependencies: 84
+* Version: 0.5-0
+* GitHub: https://github.com/drizopoulos/JMbayes2
+* Source code: https://github.com/cran/JMbayes2
+* Date/Publication: 2024-05-30 07:30:03 UTC
+* Number of recursive dependencies: 76
 
-Run `revdep_details(, "TDApplied")` for more info
+Run `revdepcheck::revdep_details(, "JMbayes2")` for more info
 
 </details>
 
@@ -7490,240 +308,209 @@ Run `revdep_details(, "TDApplied")` for more info
 
 *   checking installed package size ... NOTE
     ```
-      installed size is 12.5Mb
+      installed size is 12.6Mb
       sub-directories of 1Mb or more:
-        doc    8.0Mb
-        libs   4.2Mb
+        libs  11.8Mb
     ```
 
-# text
+# mappp
 
 <details>
 
-* Version: 1.2.0
-* GitHub: https://github.com/OscarKjell/text
-* Source code: https://github.com/cran/text
-* Date/Publication: 2024-02-13 20:51:36 UTC
-* Number of recursive dependencies: 160
+* Version: 1.0.0
+* GitHub: https://github.com/cole-brokamp/mappp
+* Source code: https://github.com/cran/mappp
+* Date/Publication: 2022-01-25 09:22:42 UTC
+* Number of recursive dependencies: 40
 
-Run `revdep_details(, "text")` for more info
+Run `revdepcheck::revdep_details(, "mappp")` for more info
 
 </details>
 
 ## In both
 
-*   checking data for non-ASCII characters ... NOTE
+*   checking dependencies in R code ... NOTE
     ```
-      Note: found 3 marked UTF-8 strings
+    Namespace in Imports field not imported from: ‘pbmcapply’
+      All declared Imports should be used.
     ```
 
-# tglkmeans
+# mice
 
 <details>
 
-* Version: 0.5.4
-* GitHub: https://github.com/tanaylab/tglkmeans
-* Source code: https://github.com/cran/tglkmeans
-* Date/Publication: 2024-01-09 14:10:02 UTC
-* Number of recursive dependencies: 91
+* Version: 3.16.0
+* GitHub: https://github.com/amices/mice
+* Source code: https://github.com/cran/mice
+* Date/Publication: 2023-06-05 14:40:02 UTC
+* Number of recursive dependencies: 131
 
-Run `revdep_details(, "tglkmeans")` for more info
+Run `revdepcheck::revdep_details(, "mice")` for more info
 
 </details>
 
-## In both
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  5.2Mb
-      sub-directories of 1Mb or more:
-        libs   5.0Mb
-    ```
+## Newly fixed
 
-*   checking for GNU extensions in Makefiles ... NOTE
+*   checking tests ...
     ```
-    GNU make is a SystemRequirements.
+      Running ‘testthat.R’
+     ERROR
+    Running the tests in ‘tests/testthat.R’ failed.
+    Last 50 lines of output:
+       1. ├─testthat::expect_warning(A <- parlmice(nhanes, m = 2, seed = 123)) at test-parlmice.R:5:3
+       2. │ └─testthat:::quasi_capture(...)
+       3. │   ├─testthat (local) .capture(...)
+       4. │   │ └─base::withCallingHandlers(...)
+       5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
+       6. └─mice::parlmice(nhanes, m = 2, seed = 123)
+    ...
+       4. │   │ └─base::withCallingHandlers(...)
+       5. │   └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
+       6. └─mice::parlmice(nhanes, n.core = 2, m = 7)
+       7.   └─parallel::makeCluster(n.core, type = cl.type)
+       8.     └─parallel::makePSOCKcluster(names = spec, ...)
+       9.       └─base::serverSocket(port = port)
+      
+      [ FAIL 4 | WARN 0 | SKIP 0 | PASS 357 ]
+      Error: Test failures
+      Execution halted
     ```
 
-# this.path
-
-<details>
-
-* Version: 2.3.1
-* GitHub: https://github.com/ArcadeAntics/this.path
-* Source code: https://github.com/cran/this.path
-* Date/Publication: 2023-12-11 08:20:02 UTC
-* Number of recursive dependencies: 1
-
-Run `revdep_details(, "this.path")` for more info
-
-</details>
-
 ## In both
 
 *   checking package dependencies ... NOTE
     ```
-    Packages which this enhances but not available for checking:
-      'box', 'IRkernel', 'jsonlite', 'knitr', 'plumber', 'rprojroot',
-      'rstudioapi', 'shiny', 'targets', 'testthat'
+    Package suggested but not available for checking: ‘miceadds’
     ```
 
-*   checking Rd cross-references ... NOTE
+*   checking Rd files ... NOTE
     ```
-    Packages unavailable to check Rd xrefs: ‘knitr’, ‘box’, ‘plumber’, ‘shiny’, ‘testthat’
+    checkRd: (-1) ampute.Rd:143: Lost braces
+       143 | we refer to \doi{10.1177/0049124118799376}{Schouten and Vink, 2018}.
+           |                                           ^
+    checkRd: (-1) ampute.Rd:188: Lost braces
+       188 | \doi{10.1080/00949655.2018.1491577}{Schouten, Lugtig and Vink, 2018}.
+           |                                    ^
+    checkRd: (-1) ampute.Rd:223: Lost braces
+       223 | Schouten, R.M. and Vink, G. (2018){The Dance of the Mechanisms: How Observed Information Influences the Validity of Missingness Assumptions}.
+           |                                   ^
+    checkRd: (-1) mice.Rd:348: Lost braces; missing escapes or markup?
+       348 | The \pkg{mice} software was published in the {Journal of Statistical Software} (Van Buuren and Groothuis-Oudshoorn, 2011). \doi{10.18637/jss.v045.i03}
+           |                                              ^
+    checkRd: (-1) mice.impute.pmm.Rd:87: Lost braces; missing escapes or markup?
+        87 | \item{Construct \eqn{n_0} sets \eqn{Z_j}, each containing \eqn{d} candidate donors, from Y_{obs} such that \eqn{\sum_d\dot\eta(i,j)} is minimum for all \eqn{j=1,\dots,n_0}. Break ties randomly.}
+           |                                                                                            ^
     ```
 
-# timetk
-
-<details>
-
-* Version: 2.9.0
-* GitHub: https://github.com/business-science/timetk
-* Source code: https://github.com/cran/timetk
-* Date/Publication: 2023-10-31 22:30:02 UTC
-* Number of recursive dependencies: 221
-
-Run `revdep_details(, "timetk")` for more info
-
-</details>
-
-## In both
-
-*   checking data for non-ASCII characters ... NOTE
+*   checking Rd cross-references ... NOTE
     ```
-      Note: found 2750 marked UTF-8 strings
+    Package unavailable to check Rd xrefs: ‘miceadds’
     ```
 
-# trawl
+# mmrm
 
 <details>
 
-* Version: 0.2.2
-* GitHub: NA
-* Source code: https://github.com/cran/trawl
-* Date/Publication: 2021-02-22 17:30:02 UTC
-* Number of recursive dependencies: 113
+* Version: 0.3.12
+* GitHub: https://github.com/openpharma/mmrm
+* Source code: https://github.com/cran/mmrm
+* Date/Publication: 2024-06-26 15:00:09 UTC
+* Number of recursive dependencies: 162
 
-Run `revdep_details(, "trawl")` for more info
+Run `revdepcheck::revdep_details(, "mmrm")` for more info
 
 </details>
 
 ## In both
 
-*   checking LazyData ... NOTE
+*   checking re-building of vignette outputs ... ERROR
     ```
-      'LazyData' is specified without a 'data' directory
+    Error(s) in re-building vignettes:
+    --- re-building ‘algorithm.Rmd’ using rmarkdown
+    --- finished re-building ‘algorithm.Rmd’
+    
+    --- re-building ‘between_within.Rmd’ using rmarkdown
+    --- finished re-building ‘between_within.Rmd’
+    
+    --- re-building ‘coef_vcov.Rmd’ using rmarkdown
+    --- finished re-building ‘coef_vcov.Rmd’
+    
+    ...
+    --- finished re-building ‘predict.Rmd’
+    
+    --- re-building ‘satterthwaite.Rmd’ using rmarkdown
+    --- finished re-building ‘satterthwaite.Rmd’
+    
+    SUMMARY: processing the following file failed:
+      ‘introduction.Rmd’
+    
+    Error: Vignette re-building failed.
+    Execution halted
     ```
 
-# TreeSearch
-
-<details>
-
-* Version: 1.4.0
-* GitHub: https://github.com/ms609/TreeSearch
-* Source code: https://github.com/cran/TreeSearch
-* Date/Publication: 2023-08-26 04:50:02 UTC
-* Number of recursive dependencies: 128
-
-Run `revdep_details(, "TreeSearch")` for more info
-
-</details>
-
-## In both
-
 *   checking installed package size ... NOTE
     ```
-      installed size is  6.9Mb
+      installed size is 188.8Mb
       sub-directories of 1Mb or more:
-        datasets   1.6Mb
-        doc        1.2Mb
-        libs       2.5Mb
+        libs  186.9Mb
     ```
 
-# TriDimRegression
+# modeltime
 
 <details>
 
-* Version: 1.0.2
-* GitHub: https://github.com/alexander-pastukhov/tridim-regression
-* Source code: https://github.com/cran/TriDimRegression
-* Date/Publication: 2023-09-13 14:10:03 UTC
-* Number of recursive dependencies: 100
+* Version: 1.2.8
+* GitHub: https://github.com/business-science/modeltime
+* Source code: https://github.com/cran/modeltime
+* Date/Publication: 2023-09-02 15:10:02 UTC
+* Number of recursive dependencies: 252
 
-Run `revdep_details(, "TriDimRegression")` for more info
+Run `revdepcheck::revdep_details(, "modeltime")` for more info
 
 </details>
 
 ## In both
 
-*   checking whether package ‘TriDimRegression’ can be installed ... ERROR
+*   checking dependencies in R code ... NOTE
     ```
-    Installation failed.
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/00install.out’ for details.
+    Namespaces in Imports field not imported from:
+      ‘tidymodels’ ‘tidyverse’
+      All declared Imports should be used.
     ```
 
-## Installation
-
-### Devel
-
-```
-* installing *source* package ‘TriDimRegression’ ...
-** package ‘TriDimRegression’ successfully unpacked and MD5 sums checked
-** using staged installation
-Error in loadNamespace(x) : there is no package called ‘rstantools’
-Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: configuration failed for package ‘TriDimRegression’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/TriDimRegression/new/TriDimRegression.Rcheck/TriDimRegression’
-
-
-```
-### CRAN
-
-```
-* installing *source* package ‘TriDimRegression’ ...
-** package ‘TriDimRegression’ successfully unpacked and MD5 sums checked
-** using staged installation
-Error in loadNamespace(x) : there is no package called ‘rstantools’
-Calls: loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
-Execution halted
-ERROR: configuration failed for package ‘TriDimRegression’
-* removing ‘/c4/home/henrik/repositories/parallelly/revdep/checks/TriDimRegression/old/TriDimRegression.Rcheck/TriDimRegression’
-
-
-```
-# txshift
+# NCC
 
 <details>
 
-* Version: 0.3.8
-* GitHub: https://github.com/nhejazi/txshift
-* Source code: https://github.com/cran/txshift
-* Date/Publication: 2022-02-09 22:30:02 UTC
+* Version: 1.0
+* GitHub: https://github.com/pavlakrotka/NCC
+* Source code: https://github.com/cran/NCC
+* Date/Publication: 2023-03-03 09:10:10 UTC
 * Number of recursive dependencies: 113
 
-Run `revdep_details(, "txshift")` for more info
+Run `revdepcheck::revdep_details(, "NCC")` for more info
 
 </details>
 
 ## In both
 
-*   checking package dependencies ... NOTE
+*   checking dependencies in R code ... NOTE
     ```
-    Package which this enhances but not available for checking: ‘sl3’
+    Namespace in Imports field not imported from: ‘magick’
+      All declared Imports should be used.
     ```
 
-# UCSCXenaShiny
+# nebula
 
 <details>
 
-* Version: 1.1.10
-* GitHub: https://github.com/openbiox/UCSCXenaShiny
-* Source code: https://github.com/cran/UCSCXenaShiny
-* Date/Publication: 2023-02-28 15:32:34 UTC
-* Number of recursive dependencies: 193
+* Version: 1.5.3
+* GitHub: https://github.com/lhe17/nebula
+* Source code: https://github.com/cran/nebula
+* Date/Publication: 2024-02-15 23:00:02 UTC
+* Number of recursive dependencies: 173
 
-Run `revdep_details(, "UCSCXenaShiny")` for more info
+Run `revdepcheck::revdep_details(, "nebula")` for more info
 
 </details>
 
@@ -7731,108 +518,141 @@ Run `revdep_details(, "UCSCXenaShiny")` for more info
 
 *   checking installed package size ... NOTE
     ```
-      installed size is  6.6Mb
+      installed size is 35.4Mb
       sub-directories of 1Mb or more:
-        doc        1.4Mb
-        shinyapp   3.3Mb
+        libs  33.7Mb
     ```
 
-# updog
+# outliers.ts.oga
 
 <details>
 
-* Version: 2.1.5
-* GitHub: https://github.com/dcgerard/updog
-* Source code: https://github.com/cran/updog
-* Date/Publication: 2023-11-29 15:50:02 UTC
-* Number of recursive dependencies: 151
+* Version: 0.0.1
+* GitHub: NA
+* Source code: https://github.com/cran/outliers.ts.oga
+* Date/Publication: 2024-05-28 17:00:02 UTC
+* Number of recursive dependencies: 155
 
-Run `revdep_details(, "updog")` for more info
+Run `revdepcheck::revdep_details(, "outliers.ts.oga")` for more info
 
 </details>
 
 ## In both
 
-*   checking whether package ‘updog’ can be installed ... WARNING
+*   checking whether package ‘outliers.ts.oga’ can be installed ... WARNING
     ```
     Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/updog/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/updog/new/updog.Rcheck/00install.out’ for details.
-    ```
-
-*   checking installed package size ... NOTE
-    ```
-      installed size is  8.0Mb
-      sub-directories of 1Mb or more:
-        libs   7.3Mb
+      Warning: no DISPLAY variable so Tk is not available
+    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/outliers.ts.oga/new/outliers.ts.oga.Rcheck/00install.out’ for details.
     ```
 
-# vip
+# pgxRpi
 
 <details>
 
-* Version: 0.4.1
-* GitHub: https://github.com/koalaverse/vip
-* Source code: https://github.com/cran/vip
-* Date/Publication: 2023-08-21 09:20:02 UTC
-* Number of recursive dependencies: 105
+* Version: 1.0.3
+* GitHub: https://github.com/progenetix/pgxRpi
+* Source code: https://github.com/cran/pgxRpi
+* Date/Publication: 2024-06-26
+* Number of recursive dependencies: 151
 
-Run `revdep_details(, "vip")` for more info
+Run `revdepcheck::revdep_details(, "pgxRpi")` for more info
 
 </details>
 
 ## In both
 
-*   checking package dependencies ... NOTE
+*   checking examples ... ERROR
     ```
-    Packages which this enhances but not available for checking:
-      'C50', 'caret', 'Cubist', 'earth', 'gbm', 'glmnet', 'h2o',
-      'lightgbm', 'mixOmics', 'mlr', 'mlr3', 'neuralnet', 'parsnip',
-      'partykit', 'pls', 'randomForest', 'ranger', 'rpart', 'RSNNS',
-      'sparklyr', 'tidymodels', 'workflows', 'xgboost'
+    Running examples in ‘pgxRpi-Ex.R’ failed
+    The error most likely occurred in:
+    
+    > ### Name: pgxLoader
+    > ### Title: Load data from Progenetix database
+    > ### Aliases: pgxLoader
+    > 
+    > ### ** Examples
+    > 
+    > ## query metadata
+    > biosamples <- pgxLoader(type="biosample", filters = "NCIT:C3512")
+    > ## query segment variants
+    > seg <- pgxLoader(type="variant", output = "pgxseg", biosample_id = "pgxbs-kftvgx4y")
+    Error in `[.data.frame`(result, , col) : undefined columns selected
+    Calls: pgxLoader ... <Anonymous> -> lapply -> FUN -> read_variant_pgxseg
+    Execution halted
     ```
 
-*   checking Rd cross-references ... NOTE
+*   checking re-building of vignette outputs ... ERROR
+    ```
+    Error(s) in re-building vignettes:
+    --- re-building ‘Introduction_1_loadmetadata.Rmd’ using rmarkdown
+    The magick package is required to crop "/c4/home/henrik/repositories/parallelly/revdep/checks/pgxRpi/new/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_1_loadmetadata_files/figure-html/unnamed-chunk-12-1.png" but not available.
+    --- finished re-building ‘Introduction_1_loadmetadata.Rmd’
+    
+    --- re-building ‘Introduction_2_loadvariants.Rmd’ using rmarkdown
+    
+    Quitting from lines 189-191 [unnamed-chunk-13] (Introduction_2_loadvariants.Rmd)
+    Error: processing vignette 'Introduction_2_loadvariants.Rmd' failed with diagnostics:
+    undefined columns selected
+    ...
+    The magick package is required to crop "/c4/home/henrik/repositories/parallelly/revdep/checks/pgxRpi/new/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-14-1.png" but not available.
+    The magick package is required to crop "/c4/home/henrik/repositories/parallelly/revdep/checks/pgxRpi/new/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-15-1.png" but not available.
+    The magick package is required to crop "/c4/home/henrik/repositories/parallelly/revdep/checks/pgxRpi/new/pgxRpi.Rcheck/vign_test/pgxRpi/vignettes/Introduction_4_process_pgxseg_files/figure-html/unnamed-chunk-16-1.png" but not available.
+    --- finished re-building ‘Introduction_4_process_pgxseg.Rmd’
+    
+    SUMMARY: processing the following files failed:
+      ‘Introduction_2_loadvariants.Rmd’ ‘Introduction_3_loadfrequency.Rmd’
+    
+    Error: Vignette re-building failed.
+    Execution halted
+    ```
+
+*   checking installed package size ... NOTE
     ```
-    Packages unavailable to check Rd xrefs: ‘randomForest’, ‘glmnet’, ‘C50’, ‘Cubist’, ‘caret’, ‘partykit’, ‘earth’, ‘gbm’, ‘h2o’, ‘sparklyr’, ‘ranger’, ‘rpart’, ‘xgboost’, ‘lightgbm’
+      installed size is  6.2Mb
+      sub-directories of 1Mb or more:
+        doc   5.9Mb
     ```
 
-# vmeasur
+# pmartR
 
 <details>
 
-* Version: 0.1.4
-* GitHub: NA
-* Source code: https://github.com/cran/vmeasur
-* Date/Publication: 2021-11-11 19:00:02 UTC
-* Number of recursive dependencies: 119
+* Version: 2.4.5
+* GitHub: https://github.com/pmartR/pmartR
+* Source code: https://github.com/cran/pmartR
+* Date/Publication: 2024-05-21 15:50:02 UTC
+* Number of recursive dependencies: 148
 
-Run `revdep_details(, "vmeasur")` for more info
+Run `revdepcheck::revdep_details(, "pmartR")` for more info
 
 </details>
 
 ## In both
 
-*   checking whether package ‘vmeasur’ can be installed ... WARNING
+*   checking package dependencies ... NOTE
     ```
-    Found the following significant warnings:
-      Warning: no DISPLAY variable so Tk is not available
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/vmeasur/new/vmeasur.Rcheck/00install.out’ for details.
+    Package suggested but not available for checking: ‘pmartRdata’
+    ```
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is 10.5Mb
+      sub-directories of 1Mb or more:
+        libs   8.1Mb
     ```
 
-# WeightedCluster
+# QDNAseq
 
 <details>
 
-* Version: 1.6-4
-* GitHub: NA
-* Source code: https://github.com/cran/WeightedCluster
-* Date/Publication: 2023-07-07 07:50:02 UTC
-* Number of recursive dependencies: 43
+* Version: 1.40.0
+* GitHub: https://github.com/ccagc/QDNAseq
+* Source code: https://github.com/cran/QDNAseq
+* Date/Publication: 2024-04-30
+* Number of recursive dependencies: 94
 
-Run `revdep_details(, "WeightedCluster")` for more info
+Run `revdepcheck::revdep_details(, "QDNAseq")` for more info
 
 </details>
 
@@ -7841,147 +661,204 @@ Run `revdep_details(, "WeightedCluster")` for more info
 *   checking re-building of vignette outputs ... WARNING
     ```
     Error(s) in re-building vignettes:
-    --- re-building ‘WeightedCluster.Rnw’ using knitr
-    --- finished re-building ‘WeightedCluster.Rnw’
-    
-    --- re-building ‘WeightedClusterFR.Rnw’ using knitr
-    --- finished re-building ‘WeightedClusterFR.Rnw’
+    --- re-building ‘QDNAseq.Rnw’ using Sweave
+    EM algorithm started ... 
     
-    --- re-building ‘WeightedClusterPreview.Rnw’ using knitr
-    Error: processing vignette 'WeightedClusterPreview.Rnw' failed with diagnostics:
-    Running 'texi2dvi' on 'WeightedClusterPreview.tex' failed.
+    Warning in allprior/tot :
+      Recycling array of length 1 in vector-array arithmetic is deprecated.
+      Use c() or as.vector() instead.
+    Warning in allprior/tot :
+      Recycling array of length 1 in vector-array arithmetic is deprecated.
+      Use c() or as.vector() instead.
     ...
-    l.85 \usepackage
-                    {tikz}^^M
+    l.197 \RequirePackage
+                         {parnotes}^^M
     !  ==> Fatal error occurred, no output PDF file produced!
-    --- failed re-building ‘WeightedClusterPreview.Rnw’
+    --- failed re-building ‘QDNAseq.Rnw’
     
     SUMMARY: processing the following file failed:
-      ‘WeightedClusterPreview.Rnw’
+      ‘QDNAseq.Rnw’
     
     Error: Vignette re-building failed.
     Execution halted
     ```
 
-# weights
+*   checking Rd files ... NOTE
+    ```
+    checkRd: (-1) exportBins.Rd:41: Lost braces
+        41 |         \code{"bed"}.  This argument is ignored if code{type = "calls"}.}
+           |                                                        ^
+    ```
+
+# qtl2pleio
 
 <details>
 
-* Version: 1.0.4
-* GitHub: NA
-* Source code: https://github.com/cran/weights
-* Date/Publication: 2021-06-10 21:50:02 UTC
-* Number of recursive dependencies: 119
+* Version: 1.4.3
+* GitHub: https://github.com/fboehm/qtl2pleio
+* Source code: https://github.com/cran/qtl2pleio
+* Date/Publication: 2020-12-02 22:50:02 UTC
+* Number of recursive dependencies: 130
 
-Run `revdep_details(, "weights")` for more info
+Run `revdepcheck::revdep_details(, "qtl2pleio")` for more info
 
 </details>
 
 ## In both
 
-*   checking Rd cross-references ... WARNING
+*   checking installed package size ... NOTE
     ```
-    Missing link or links in documentation object 'plotwtdinteraction.Rd':
-      ‘gam’ ‘bam’
-    
-    See section 'Cross-references' in the 'Writing R Extensions' manual.
+      installed size is 36.9Mb
+      sub-directories of 1Mb or more:
+        libs  36.6Mb
+    ```
+
+*   checking LazyData ... NOTE
+    ```
+      'LazyData' is specified without a 'data' directory
     ```
 
-# wru
+# scruff
 
 <details>
 
-* Version: 1.0.1
-* GitHub: https://github.com/kosukeimai/wru
-* Source code: https://github.com/cran/wru
-* Date/Publication: 2022-10-21 17:30:02 UTC
-* Number of recursive dependencies: 89
+* Version: 1.22.0
+* GitHub: https://github.com/campbio/scruff
+* Source code: https://github.com/cran/scruff
+* Date/Publication: 2024-04-30
+* Number of recursive dependencies: 189
 
-Run `revdep_details(, "wru")` for more info
+Run `revdepcheck::revdep_details(, "scruff")` for more info
 
 </details>
 
 ## In both
 
-*   checking whether package ‘wru’ can be installed ... WARNING
+*   checking installed package size ... NOTE
     ```
-    Found the following significant warnings:
-      /c4/home/henrik/repositories/parallelly/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:63:13: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:65:7: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-      /c4/home/henrik/repositories/parallelly/revdep/library/wru/RcppArmadillo/include/armadillo_bits/fn_reshape.hpp:74:9: warning: ‘arma::Mat<typename T1::elem_type> arma::reshape(const arma::Base<typename T1::elem_type, T1>&, arma::uword, arma::uword, arma::uword)’ is deprecated: don't use this form: it will be removed [-Wdeprecated-declarations]
-    See ‘/c4/home/henrik/repositories/parallelly/revdep/checks/wru/new/wru.Rcheck/00install.out’ for details.
+      installed size is  5.0Mb
+      sub-directories of 1Mb or more:
+        data   2.4Mb
+        doc    1.6Mb
     ```
 
-*   checking C++ specification ... NOTE
+*   checking DESCRIPTION meta-information ... NOTE
     ```
-      Specified C++11: please drop specification unless essential
+    License stub is invalid DCF.
     ```
 
-*   checking installed package size ... NOTE
+*   checking dependencies in R code ... NOTE
     ```
-      installed size is  5.5Mb
-      sub-directories of 1Mb or more:
-        data   3.4Mb
-        libs   1.9Mb
+    Unexported object imported by a ':::' call: 'ShortRead:::.set_omp_threads'
+      See the note in ?`:::` about the use of this operator.
     ```
 
-*   checking dependencies in R code ... NOTE
+*   checking foreign function calls ... NOTE
     ```
-    Namespace in Imports field not imported from: ‘future’
-      All declared Imports should be used.
+    Foreign function call to a different package:
+      .Call(ShortRead:::.set_omp_threads, ...)
+    See chapter ‘System and foreign language interfaces’ in the ‘Writing R
+    Extensions’ manual.
+    ```
+
+*   checking R code for possible problems ... NOTE
+    ```
+    .plotFracProteinCodingGenes: no visible binding for global variable
+      'genes'
+    .plotGenes: no visible binding for global variable 'genes'
+    .plotGenesPerMillionReads: no visible binding for global variable
+      'genes'
+    Undefined global functions or variables:
+      genes
     ```
 
-# XNAString
+# streetscape
 
 <details>
 
-* Version: 1.10.0
+* Version: 1.0.2
 * GitHub: NA
-* Source code: https://github.com/cran/XNAString
-* Date/Publication: 2023-10-24
-* Number of recursive dependencies: 106
+* Source code: https://github.com/cran/streetscape
+* Date/Publication: 2024-06-07 20:00:02 UTC
+* Number of recursive dependencies: 140
 
-Run `revdep_details(, "XNAString")` for more info
+Run `revdepcheck::revdep_details(, "streetscape")` for more info
 
 </details>
 
 ## In both
 
-*   checking compiled code ... WARNING
+*   checking data for ASCII and uncompressed saves ... WARNING
     ```
-    File ‘XNAString/libs/XNAString.so’:
-      Found ‘rand’, possibly from ‘rand’ (C)
-        Object: ‘./ViennaRNA/utils/utils.o’
-      Found ‘sprintf’, possibly from ‘sprintf’ (C)
-        Objects: ‘./ViennaRNA/part_func_up.o’, ‘./ViennaRNA/RNAstruct.o’,
-          ‘./ViennaRNA/model.o’
-      Found ‘srand’, possibly from ‘srand’ (C)
-        Object: ‘./ViennaRNA/utils/utils.o’
-    
-    Compiled code should not call entry points which might terminate R nor
-    write to stdout/stderr instead of to the console, nor use Fortran I/O
-    nor system RNGs nor [v]sprintf.
-    
-    See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
+      code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    ...
+      code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpatVectorProxy” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpPolyPart” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpPolyPart” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpPolygons” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+      code for methods in class “Rcpp_SpPolygons” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
     ```
 
-*   checking C++ specification ... NOTE
+*   checking whether startup messages can be suppressed ... NOTE
     ```
-      Specified C++11: please drop specification unless essential
+    code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpatCategories” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpatDataFrame” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpatExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpatFactor” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpatGraph” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    ...
+    code for methods in class “Rcpp_SpExtent” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpPoly” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpPolyPart” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpPolyPart” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpPolygons” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    code for methods in class “Rcpp_SpPolygons” was not checked for suspicious field assignments (recommended package ‘codetools’ not available?)
+    
+    It looks like this package (or a package it requires) has a startup
+    message which cannot be suppressed: see ?packageStartupMessage.
     ```
 
+# TDApplied
+
+<details>
+
+* Version: 3.0.3
+* GitHub: https://github.com/shaelebrown/TDApplied
+* Source code: https://github.com/cran/TDApplied
+* Date/Publication: 2024-03-12 23:00:02 UTC
+* Number of recursive dependencies: 81
+
+Run `revdepcheck::revdep_details(, "TDApplied")` for more info
+
+</details>
+
+## In both
+
 *   checking installed package size ... NOTE
     ```
-      installed size is 11.2Mb
+      installed size is 13.3Mb
       sub-directories of 1Mb or more:
-        doc    1.0Mb
-        libs   9.5Mb
-    ```
-
-*   checking top-level files ... NOTE
-    ```
-    File
-      LICENSE
-    is not mentioned in the DESCRIPTION file.
+        doc    8.6Mb
+        libs   4.4Mb
     ```
 
diff --git a/src/000.api.h b/src/000.api.h
index 3291c8c5..c31d325e 100644
--- a/src/000.api.h
+++ b/src/000.api.h
@@ -1,2 +1,3 @@
 /* C-level API that is called from R */
 SEXP R_test_tcp_port(SEXP port);
+SEXP R_calc_serialized_size(SEXP robj);
diff --git a/src/000.init.c b/src/000.init.c
index ddaffe8f..ab189b0c 100644
--- a/src/000.init.c
+++ b/src/000.init.c
@@ -6,6 +6,7 @@
 
 static R_CallMethodDef callMethods[]  = {
   CALLDEF(R_test_tcp_port, 1),
+  CALLDEF(R_calc_serialized_size, 1),
   {NULL, NULL, 0}
 };
 
diff --git a/src/calc-serialized-size.c b/src/calc-serialized-size.c
new file mode 100644
index 00000000..21083545
--- /dev/null
+++ b/src/calc-serialized-size.c
@@ -0,0 +1,79 @@
+// Adopted from https://github.com/coolbutuseless/serializer
+// which is released under the MIT license
+
+#include <R.h>
+#include <Rinternals.h>
+#include <Rdefines.h>
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <unistd.h>
+
+#ifndef R_INT_MAX
+#define R_INT_MAX  INT_MAX
+#endif
+
+
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+// Write a byte into the buffer at the current location.
+// The actual buffer is encapsulated as part of the stream structure, so you
+// have to extract it first
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+void count_byte(R_outpstream_t stream, int c) {
+  error("count_byte(): This function is never called for binary serialization");
+}
+
+
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+// Write multiple bytes into the buffer at the current location.
+// The actual buffer is encapsulated as part of the stream structure, so you
+// have to extract it first
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+void count_bytes(R_outpstream_t stream, void *src, int length) {
+  R_xlen_t *count = (R_xlen_t *)stream->data;
+  *count += length;
+}
+
+
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+// Serialize an R object, but only count the bytes.  
+// This function is only visible to C code
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+R_xlen_t calc_serialized_size(SEXP robj) {
+  // Initialise the count
+  R_xlen_t count = 0;
+
+  // Create the output stream structure
+  struct R_outpstream_st output_stream;
+
+  // Initialise the output stream structure
+  R_InitOutPStream(
+    &output_stream,            // The stream object which wraps everything
+    (R_pstream_data_t) &count, // user data that persists within the process
+    R_pstream_binary_format,   // Store as binary
+    3,                         // Version = 3 for R >3.5.0 See `?base::serialize`
+    count_byte,                // Function to write single byte to buffer
+    count_bytes,               // Function for writing multiple bytes to buffer
+    NULL,                      // Func for special handling of reference data.
+    R_NilValue                 // Data related to reference data handling
+  );
+
+  // Serialize the object into the output_stream
+  R_Serialize(robj, &output_stream);
+
+  return count;
+}
+
+
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+// Serialize an R object, but only count the bytes. 
+// This function is callable from R
+//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+SEXP R_calc_serialized_size(SEXP robj) {
+  R_xlen_t count = calc_serialized_size(robj);
+  if (count > R_INT_MAX) {
+    return(ScalarReal((double) count));
+  } else {
+    return(ScalarInteger(count));
+  }
+}
diff --git a/src/calc-serialized-size.h b/src/calc-serialized-size.h
new file mode 100644
index 00000000..22e86c3c
--- /dev/null
+++ b/src/calc-serialized-size.h
@@ -0,0 +1,2 @@
+R_xlen_t R_calc_serialized_size(SEXP robj);
+
diff --git a/tests/makeClusterSequential.R b/tests/makeClusterSequential.R
new file mode 100644
index 00000000..668fa7be
--- /dev/null
+++ b/tests/makeClusterSequential.R
@@ -0,0 +1,32 @@
+if (getRversion() >= "4.4.0") {
+
+  library(parallelly)
+  library(parallel)
+  
+  cl <- makeClusterSequential()
+  print(cl)
+
+  y_truth <- lapply(X = 1:3, FUN = sqrt)
+  y <- parLapply(cl, X = 1:3, fun = sqrt)
+  str(y)
+  stopifnot(identical(y, y_truth))
+  
+  pid <- Sys.getpid()
+  print(pid)
+  y <- clusterEvalQ(cl, Sys.getpid())
+  str(y)
+  stopifnot(identical(y[[1]], pid))
+  
+  y <- clusterEvalQ(cl, { abc <- 42; abc })
+  str(y)
+  stopifnot(!exists("abc", inherits = FALSE))
+
+  stopCluster(cl)
+  print(cl)
+
+  res <- tryCatch({
+    y <- clusterEvalQ(cl, { 42 })
+  }, error = identity)
+  print(res)
+  stopifnot(inherits(res, "error"))
+} ## if (getRversion() >= "4.4.0")