Prepare for release (#138)

* Update version, fix errors on windows * News * rebuild website * Updated cran-comments * Post submission * Update * Update version because cran comments were wrong * Clarify * Update
cytomining · Mar 20, 2020 · 475eeb9 · 475eeb9
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -8,3 +8,4 @@
 ^docs$
 ^LICENSE.md$
 ^CONTRIBUTING.md$
+^CRAN-RELEASE$
diff --git a/CRAN-RELEASE b/CRAN-RELEASE
@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2020-03-20.
+Once it is accepted, delete this file and tag the release (commit 0bf3161347).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Encoding: UTF-8
 Package: cytominer
 Type: Package
 Title: Methods for Image-Based Cell Profiling
-Version: 0.1.0.9000
+Version: 0.2.1
 Authors@R: c(person("Tim", "Becker", email = "[email protected]", role = "aut"),
     person("Allen", "Goodman", email = "[email protected]", role = "aut"),
     person("Claire", "McQuin", email = "[email protected]", role = "aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,17 @@
+# cytominer 0.2.1
+
+This is a minor release but contains several new functions as well as a long-pending fix for incompatibility with the new (2018) tidyeval API.
+
+## New functions
+- `whiten()` (#103)
+- `extract_subpopulations()` (#107)
+- `sparse_random_projection()` (#117)
+- `svd_entropy()` (#123)
+- `covariance()` (#114)
+
+## Bug fixes
+- Fixed tidyeval incompatibilities reported in #131,#133,#134 (#135)
+
 # cytominer 0.1.0
 
 Hello world!

diff --git a/R/replicate_correlation.R b/R/replicate_correlation.R
@@ -88,6 +88,7 @@ replicate_correlation <-
       .strata <- rlang::syms(strata)
     }
 
+    result <-
     foreach::foreach(variable = variables, .combine = rbind) %dopar%
       {
         sample %>%
@@ -111,4 +112,8 @@ replicate_correlation <-
       tidyr::gather_(replicate_by, "pearson", setdiff(names(.), "variable")) %>%
       dplyr::group_by(variable) %>%
       dplyr::summarize_at("pearson", c("median", "min", "max"))
+
+    doParallel::stopImplicitCluster()
+
+    result
   }
diff --git a/R/svd_entropy.R b/R/svd_entropy.R
@@ -25,25 +25,6 @@ utils::globalVariables(c(".", "i"))
 svd_entropy <- function(variables, sample, cores = NULL) {
   doParallel::registerDoParallel(cores = cores)
 
-  singular_value_entropy <- function(A) {
-    singular_values <- svd(A, 0, 0)$d
-
-    # normalize
-    singular_values <- singular_values / sum(singular_values)
-
-    # entropy
-    -sum(singular_values * log10(singular_values))
-  }
-
-  entropy_score <- function(data) {
-
-    # calculate contribution of each features to the entropy by leaving that feature out
-    sv_entropy <-
-      foreach::foreach(i = 1:ncol(data), .combine = c) %dopar% singular_value_entropy(data[-i, -i])
-
-    singular_value_entropy(data) - sv_entropy
-  }
-
   sample %<>%
     dplyr::select(variables) %>%
     dplyr::collect()
@@ -56,8 +37,30 @@ svd_entropy <- function(variables, sample, cores = NULL) {
     crossprod(., .) %>%
     entropy_score()
 
+  doParallel::stopImplicitCluster()
+
   dplyr::tibble(
     variable = variables,
     svd_entropy = entropy_scores
   )
 }
+
+singular_value_entropy <- function(A) {
+  singular_values <- svd(A, 0, 0)$d
+
+  # normalize
+  singular_values <- singular_values / sum(singular_values)
+
+  # entropy
+  -sum(singular_values * log10(singular_values))
+}
+
+entropy_score <- function(data) {
+
+  # calculate contribution of each features to the entropy by leaving that feature out
+  sv_entropy <-
+    foreach::foreach(i = 1:ncol(data), .combine = c) %dopar% singular_value_entropy(data[-i, -i])
+
+  singular_value_entropy(data) - sv_entropy
+}
+
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,15 +1,22 @@
+## Note about two consecutive submissions
+I mistakenly submitted to CRAN without saving cran-comments.md. 
+I am thus resubmitting, but have bumped up the version because I get the message
+"The Server already contains a file with that name/version, please increase version number"
+
 ## Test environments
-* local OS X install, R 3.3.3
-* ubuntu 14.04.5 LTS (on travis-ci), R 3.4.1
-* win-builder
+* local OS X install, R 3.6.1 
+* Ubuntu 16.04.6 LTS (on travis-ci), R 3.6.2
+* win-builder (release and devel)
 
 ## R CMD check results
 There were no ERRORs or WARNINGs or NOTEs for OS X and ubuntu.
 
 There is 1 NOTE on winbuild:
 
-- *New submission*: This is my first submission!
-
+- *New submission*: Because package was archived on CRAN
+- *Misspelling*: Possibly mis-spelled words in DESCRIPTION: Caicedo (18:18, 19:27) -- I confirm no typo here
+- *CRAN repository db overrides*: X-CRAN-Comment: Archived on 2019-05-08 as check problems were not corrected in time -- Correct. I just recovered from the shock of being bumped off CRAN.
+
 ## Downstream dependencies
 
 There are currently no downstream dependencies for this package.

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