CRAN submission

mayer79 · Dec 7, 2024 · ddec2b5 · ddec2b5
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 2.6.0
-Date: 2024-08-17 15:06:30 UTC
-SHA: b46552ad32230999d13182b3cad2c073213c84eb
+Version: 2.6.1
+Date: 2024-12-07 08:49:37 UTC
+SHA: 5e698341f51b1a7f899c28302a0b9082c950ab28
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,10 +1,8 @@
-# missRanger 2.6.0
+# missRanger 2.6.1
 
-Hello CRAN
+Dear CRAN team
 
-This update
-- fixes a major bug,
-- and brings a long awaited feature of out-of-sample application of the imputation models.
+This update introduces a workaround around an incompatibility issue with {formula.tools}.
 
 ## R CMD check (local)
 
@@ -16,5 +14,5 @@ Status: OK
 
 ## revdepcheck results
 
-OK: 7
+OK: 6
 BROKEN: 0
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,28 +1,36 @@
 # Platform
 
-|field    |value                                                    |
-|:--------|:--------------------------------------------------------|
-|version  |R version 4.4.1 (2024-06-14 ucrt)                        |
-|os       |Windows 11 x64 (build 22631)                             |
-|system   |x86_64, mingw32                                          |
-|ui       |RStudio                                                  |
-|language |(EN)                                                     |
-|collate  |German_Switzerland.utf8                                  |
-|ctype    |German_Switzerland.utf8                                  |
-|tz       |Europe/Zurich                                            |
-|date     |2024-08-15                                               |
-|rstudio  |2024.04.2+764 Chocolate Cosmos (desktop)                 |
-|pandoc   |3.1.6 @ C:\Users\Michael\AppData\Local\Pandoc\pandoc.exe |
+|field    |value                                    |
+|:--------|:----------------------------------------|
+|version  |R version 4.4.1 (2024-06-14 ucrt)        |
+|os       |Windows 11 x64 (build 22631)             |
+|system   |x86_64, mingw32                          |
+|ui       |RStudio                                  |
+|language |(EN)                                     |
+|collate  |English_Switzerland.utf8                 |
+|ctype    |English_Switzerland.utf8                 |
+|tz       |Europe/Zurich                            |
+|date     |2024-12-07                               |
+|rstudio  |2024.04.2+764 Chocolate Cosmos (desktop) |
+|pandoc   |NA                                       |
 
 # Dependencies
 
 |package    |old       |new       |Δ  |
 |:----------|:---------|:---------|:--|
-|missRanger |2.5.0     |2.6.0     |*  |
-|FNN        |1.1.4     |1.1.4     |   |
-|ranger     |0.16.0    |0.16.0    |   |
-|Rcpp       |1.0.13    |1.0.13    |   |
-|RcppEigen  |0.3.4.0.0 |0.3.4.0.0 |   |
+|missRanger |2.6.0     |2.6.1     |*  |
+|FNN        |1.1.4.1   |1.1.4.1   |   |
+|ranger     |0.17.0    |0.17.0    |   |
+|Rcpp       |1.0.13-1  |1.0.13-1  |   |
+|RcppEigen  |0.3.4.0.2 |0.3.4.0.2 |   |
 
 # Revdeps
 
+## Failed to check (3)
+
+|package         |version |error |warning |note |
+|:---------------|:-------|:-----|:-------|:----|
+|marginaleffects |?       |      |        |     |
+|outqrf          |1.0.0   |1     |        |     |
+|worcs           |?       |      |        |     |
+
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -1,7 +1,12 @@
 ## revdepcheck results
 
-We checked 7 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 6 reverse dependencies (4 from CRAN + 2 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
- * We failed to check 0 packages
+ * We failed to check 1 packages
 
+Issues with CRAN packages are summarised below.
+
+### Failed to check
+
+* outqrf (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
@@ -1 +1,245 @@
-*Wow, no problems at all. :)*
+# marginaleffects
+
+<details>
+
+* Version: 
+* GitHub: https://github.com/mayer79/missRanger
+* Source code: NA
+* Number of recursive dependencies: 0
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+
+  There are binary versions available but the source versions are later:
+                binary   source needs_compilation
+data.table      1.16.2   1.16.4              TRUE
+RcppArmadillo 14.2.0-1 14.2.2-1              TRUE
+textshaping      0.4.0    0.4.1              TRUE
+
+  Binaries will be installed
+package 'abind' successfully unpacked and MD5 sums checked
+package 'AER' successfully unpacked and MD5 sums checked
+...
+package 'hardhat' successfully unpacked and MD5 sums checked
+package 'haven' successfully unpacked and MD5 sums checked
+package 'here' successfully unpacked and MD5 sums checked
+package 'highr' successfully unpacked and MD5 sums checked
+package 'Hmisc' successfully unpacked and MD5 sums checked
+package 'hms' successfully unpacked and MD5 sums checked
+package 'htmlTable' successfully unpacked and MD5 sums checked
+package 'htmltools' successfully unpacked and MD5 sums checked
+package 'htmlwidgets' successfully unpacked and MD5 sums checked
+package 'httpuv' successfully unpacked and MD5 sums checked
+
+
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
+...
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES'
+
+
+```
+### CRAN
+
+```
+
+  There are binary versions available but the source versions are later:
+                binary   source needs_compilation
+data.table      1.16.2   1.16.4              TRUE
+RcppArmadillo 14.2.0-1 14.2.2-1              TRUE
+textshaping      0.4.0    0.4.1              TRUE
+
+  Binaries will be installed
+package 'abind' successfully unpacked and MD5 sums checked
+package 'AER' successfully unpacked and MD5 sums checked
+...
+package 'hardhat' successfully unpacked and MD5 sums checked
+package 'haven' successfully unpacked and MD5 sums checked
+package 'here' successfully unpacked and MD5 sums checked
+package 'highr' successfully unpacked and MD5 sums checked
+package 'Hmisc' successfully unpacked and MD5 sums checked
+package 'hms' successfully unpacked and MD5 sums checked
+package 'htmlTable' successfully unpacked and MD5 sums checked
+package 'htmltools' successfully unpacked and MD5 sums checked
+package 'htmlwidgets' successfully unpacked and MD5 sums checked
+package 'httpuv' successfully unpacked and MD5 sums checked
+
+
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
+...
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES'
+
+
+```
+# outqrf
+
+<details>
+
+* Version: 1.0.0
+* GitHub: https://github.com/flystar233/outqrf
+* Source code: https://github.com/cran/outqrf
+* Date/Publication: 2024-09-10 09:10:02 UTC
+* Number of recursive dependencies: 93
+
+Run `revdepcheck::revdep_details(, "outqrf")` for more info
+
+</details>
+
+## In both
+
+*   R CMD check timed out
+
+
+# worcs
+
+<details>
+
+* Version: 
+* GitHub: https://github.com/mayer79/missRanger
+* Source code: NA
+* Number of recursive dependencies: 0
+
+</details>
+
+## Error before installation
+
+### Devel
+
+```
+
+  There is a binary version available but the source version is later:
+           binary source needs_compilation
+data.table 1.16.2 1.16.4              TRUE
+
+  Binaries will be installed
+package 'abind' successfully unpacked and MD5 sums checked
+package 'askpass' successfully unpacked and MD5 sums checked
+package 'assertthat' successfully unpacked and MD5 sums checked
+package 'backports' successfully unpacked and MD5 sums checked
+...
+package 'RColorBrewer' successfully unpacked and MD5 sums checked
+package 'Rcpp' successfully unpacked and MD5 sums checked
+package 'RcppEigen' successfully unpacked and MD5 sums checked
+package 'RcppParallel' successfully unpacked and MD5 sums checked
+package 'remotes' successfully unpacked and MD5 sums checked
+package 'renv' successfully unpacked and MD5 sums checked
+package 'reshape2' successfully unpacked and MD5 sums checked
+package 'rlang' successfully unpacked and MD5 sums checked
+package 'rmarkdown' successfully unpacked and MD5 sums checked
+package 'rmdfiltr' successfully unpacked and MD5 sums checked
+
+
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
+...
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES'
+
+
+```
+### CRAN
+
+```
+
+  There is a binary version available but the source version is later:
+           binary source needs_compilation
+data.table 1.16.2 1.16.4              TRUE
+
+  Binaries will be installed
+package 'abind' successfully unpacked and MD5 sums checked
+package 'askpass' successfully unpacked and MD5 sums checked
+package 'assertthat' successfully unpacked and MD5 sums checked
+package 'backports' successfully unpacked and MD5 sums checked
+...
+package 'RColorBrewer' successfully unpacked and MD5 sums checked
+package 'Rcpp' successfully unpacked and MD5 sums checked
+package 'RcppEigen' successfully unpacked and MD5 sums checked
+package 'RcppParallel' successfully unpacked and MD5 sums checked
+package 'remotes' successfully unpacked and MD5 sums checked
+package 'renv' successfully unpacked and MD5 sums checked
+package 'reshape2' successfully unpacked and MD5 sums checked
+package 'rlang' successfully unpacked and MD5 sums checked
+package 'rmarkdown' successfully unpacked and MD5 sums checked
+package 'rmdfiltr' successfully unpacked and MD5 sums checked
+
+
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
+...
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/workflows/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES'
+Warning: unable to access index for repository https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4:
+  cannot open URL 'https://bioconductor.org/packages/3.18/books/bin/windows/contrib/4.4/PACKAGES'
+
+
+```