crancheck update

umccr · Nov 30, 2023 · 2d2dcce · 2d2dcce
1 parent fdc404b
commit 2d2dcce
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Showing 6 changed files with 12 additions and 7 deletions.
diff --git a/R/portal_meta.R b/R/portal_meta.R
@@ -493,7 +493,7 @@ meta_tso_ctdna_tumor_only <- function(pmeta, status = c("Succeeded")) {
 #' pmeta <- system.file("extdata/portal_meta_top4.csv", package = "dracarys")
 #' (m <- meta_star_alignment(pmeta))
 #' @testexamples
-#' expect_equal(all(c("s3_outdir_star", "LibraryID_tumor") %in% colnames(m)), TRUE)
+#' expect_equal(all(c("s3_outdir_star", "LibraryID") %in% colnames(m)), TRUE)
 #' @export
 meta_star_alignment <- function(pmeta, status = "Succeeded") {
   # retrieve workflow runs with the given type and status
@@ -710,7 +710,7 @@ meta_oncoanalyser_wgts_existing_both <- function(pmeta, status = "Succeeded") {
 #' pmeta <- system.file("extdata/portal_meta_top4.csv", package = "dracarys")
 #' (m <- meta_oncoanalyser_wts(pmeta))
 #' @testexamples
-#' expect_equal(all(c("s3_outdir_oncoanalyser", "LibraryID_tumor", "s3_bam_tumor") %in% colnames(m)), TRUE)
+#' expect_equal(all(c("s3_outdir_oncoanalyser", "LibraryID", "s3_bam") %in% colnames(m)), TRUE)
 #' @export
 meta_oncoanalyser_wts <- function(pmeta, status = "Succeeded") {
   # retrieve workflow runs with the given type and status

diff --git a/R/utils.R b/R/utils.R
@@ -50,6 +50,7 @@ session_info_tbls <- function(pkgs = NULL) {
 #' Output Format is Valid
 #'
 #' Checks that the specified output format is valid.
+#' @param x Output format.
 #' @export
 dr_output_format_valid <- function(x) {
   format_choices <- c("tsv", "parquet", "delta", "rds")

diff --git a/inst/rmd/umccr_portal/portal_summary.Rmd b/inst/rmd/umccr_portal/portal_summary.Rmd
@@ -116,8 +116,8 @@ get_sbj_url <- function(x, colour = NULL, account = "pro") {
 # Get metadata for workflows run within the date range
 # options(width = 150)
 fmt1 <- "%Y-%m-%dT%H:%M:%S"
-date_start <- as.POSIXct("2023-11-22T00:00:01", format = fmt1)
-date_end <- as.POSIXct("2023-11-23T23:59:59", format = fmt1)
+date_start <- as.POSIXct("2023-11-27T00:00:01", format = fmt1)
+date_end <- as.POSIXct("2023-11-28T23:59:59", format = fmt1)
 wf_order <- c(
   "bcl_convert",
   "tso_ctdna_tumor_only",
@@ -134,6 +134,7 @@ wf_order <- c(
   "sash"
 )
 
+invisible(capture.output(dracarys:::awsvault_profile("upro")))
 lims_rds <- here(glue("nogit/data_portal/lims/{as.Date(date_end)}.rds"))
 # lims_raw <- dracarys::glims_read()
 # saveRDS(lims_raw, file = lims_rds)

diff --git a/man/dr_output_format_valid.Rd b/man/dr_output_format_valid.Rd
diff --git a/tests/testthat/test-roxytest-testexamples-portal_meta.R b/tests/testthat/test-roxytest-testexamples-portal_meta.R
@@ -73,7 +73,7 @@ test_that("Function meta_star_alignment() @ L498", {
 
   pmeta <- system.file("extdata/portal_meta_top4.csv", package = "dracarys")
   (m <- meta_star_alignment(pmeta))
-  expect_equal(all(c("s3_outdir_star", "LibraryID_tumor") %in% colnames(m)), TRUE)
+  expect_equal(all(c("s3_outdir_star", "LibraryID") %in% colnames(m)), TRUE)
 })
 
 
@@ -105,6 +105,6 @@ test_that("Function meta_oncoanalyser_wts() @ L715", {
 
   pmeta <- system.file("extdata/portal_meta_top4.csv", package = "dracarys")
   (m <- meta_oncoanalyser_wts(pmeta))
-  expect_equal(all(c("s3_outdir_oncoanalyser", "LibraryID_tumor", "s3_bam_tumor") %in% colnames(m)), TRUE)
+  expect_equal(all(c("s3_outdir_oncoanalyser", "LibraryID", "s3_bam") %in% colnames(m)), TRUE)
 })
 
diff --git a/tests/testthat/test-roxytest-testexamples-regex.R b/tests/testthat/test-roxytest-testexamples-regex.R
@@ -2,7 +2,7 @@
 
 # File R/regex.R: @testexamples
 
-test_that("Function dr_func_eval() @ L89", {
+test_that("Function dr_func_eval() @ L91", {
 
   mean_1_to_10 <- dr_func_eval("mean", v = c("mean", "sd"))(1:10)
   x <- system.file("extdata/tso/sample705.fragment_length_hist.json.gz", package = "dracarys")