Prepare for CRAN release 25.1.1

igordot · igordot · commit 326de319db33 · 2025-07-21T22:54:53.000-04:00
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: msigdbr
 Title: MSigDB Gene Sets for Multiple Organisms in a Tidy Data Format
-Version: 25.1.0.9000
+Version: 25.1.1
 Authors@R:
     person("Igor", "Dolgalev", , "igor.dolgalev@nyumc.org", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-4451-126X"))
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# msigdbr 25.1.1
+
+* Updated tests and examples to comply with CRAN policies.
+
 # msigdbr 25.1.0
 
 * Included the MSigDB v2025.1 data.
diff --git a/cran-comments.md b/cran-comments.md
@@ -15,4 +15,4 @@
 We checked 12 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
- * We failed to check 4 packages
+ * We failed to check 1 packages
diff --git a/revdep/README.md b/revdep/README.md
@@ -10,16 +10,16 @@
 |collate  |en_US.UTF-8                                                                 |
 |ctype    |en_US.UTF-8                                                                 |
 |tz       |America/New_York                                                            |
-|date     |2025-07-03                                                                  |
+|date     |2025-07-21                                                                  |
 |rstudio  |2025.05.0+496 Mariposa Orchid (desktop)                                     |
-|pandoc   |3.6.4 @ /usr/local/bin/pandoc                                               |
+|pandoc   |3.6.4 @ /usr/local/bin/ (via rmarkdown)                                     |
 |quarto   |1.6.42 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/quarto |
 
 # Dependencies
 
 |package    |old    |new    |Δ  |
 |:----------|:------|:------|:--|
-|msigdbr    |24.1.0 |25.1.0 |*  |
+|msigdbr    |25.1.0 |25.1.1 |*  |
 |assertthat |0.2.1  |0.2.1  |   |
 |babelgene  |22.9   |22.9   |   |
 |cli        |3.6.5  |3.6.5  |   |
@@ -29,7 +29,7 @@
 |glue       |1.8.0  |1.8.0  |   |
 |lifecycle  |1.0.4  |1.0.4  |   |
 |magrittr   |2.0.3  |2.0.3  |   |
-|pillar     |1.10.2 |1.10.2 |   |
+|pillar     |1.11.0 |1.11.0 |   |
 |pkgconfig  |2.0.3  |2.0.3  |   |
 |R6         |2.6.1  |2.6.1  |   |
 |rlang      |1.1.6  |1.1.6  |   |
@@ -41,12 +41,9 @@
 
 # Revdeps
 
-## Failed to check (4)
+## Failed to check (1)
 
-|package   |version |error  |warning |note |
-|:---------|:-------|:------|:-------|:----|
-|pathfindR |2.5.0   |1      |        |     |
-|[Platypus](failures.md#platypus)|3.6.0   |__+1__ |        |1    |
-|RVA       |0.0.5   |1      |        |1    |
-|scITD     |1.0.4   |1      |        |     |
+|package   |version |error |warning |note |
+|:---------|:-------|:-----|:-------|:----|
+|pathfindR |2.5.1   |1     |        |     |
 
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -3,13 +3,10 @@
 We checked 12 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
- * We failed to check 4 packages
+ * We failed to check 1 packages
 
 Issues with CRAN packages are summarised below.
 
 ### Failed to check
 
 * pathfindR (NA)
-* Platypus  (NA)
-* RVA       (NA)
-* scITD     (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
@@ -2,10 +2,10 @@
 
 <details>
 
-* Version: 2.5.0
+* Version: 2.5.1
 * GitHub: https://github.com/egeulgen/pathfindR
 * Source code: https://github.com/cran/pathfindR
-* Date/Publication: 2025-06-15 00:00:02 UTC
+* Date/Publication: 2025-07-15 11:20:02 UTC
 * Number of recursive dependencies: 117
 
 Run `revdepcheck::revdep_details(, "pathfindR")` for more info
@@ -26,7 +26,7 @@ Run `revdepcheck::revdep_details(, "pathfindR")` for more info
 
 ```
 * installing *source* package ‘pathfindR’ ...
-** this is package ‘pathfindR’ version ‘2.5.0’
+** this is package ‘pathfindR’ version ‘2.5.1’
 ** package ‘pathfindR’ successfully unpacked and MD5 sums checked
 ** using staged installation
 ** R
@@ -53,7 +53,7 @@ ERROR: loading failed
 
 ```
 * installing *source* package ‘pathfindR’ ...
-** this is package ‘pathfindR’ version ‘2.5.0’
+** this is package ‘pathfindR’ version ‘2.5.1’
 ** package ‘pathfindR’ successfully unpacked and MD5 sums checked
 ** using staged installation
 ** R
@@ -76,76 +76,3 @@ ERROR: loading failed
 
 
 ```
-# Platypus
-
-<details>
-
-* Version: 3.6.0
-* GitHub: NA
-* Source code: https://github.com/cran/Platypus
-* Date/Publication: 2024-10-18 11:10:17 UTC
-* Number of recursive dependencies: 255
-
-Run `revdepcheck::revdep_details(, "Platypus")` for more info
-
-</details>
-
-## Newly broken
-
-*   R CMD check timed out
-    
-
-## In both
-
-*   checking DESCRIPTION meta-information ... NOTE
-    ```
-      Missing dependency on R >= 4.1.0 because package code uses the pipe
-      |> or function shorthand \(...) syntax added in R 4.1.0.
-      File(s) using such syntax:
-        ‘VDJ_build.R’
-    ```
-
-# RVA
-
-<details>
-
-* Version: 0.0.5
-* GitHub: https://github.com/THERMOSTATS/RVA
-* Source code: https://github.com/cran/RVA
-* Date/Publication: 2021-11-01 21:40:02 UTC
-* Number of recursive dependencies: 132
-
-Run `revdepcheck::revdep_details(, "RVA")` for more info
-
-</details>
-
-## In both
-
-*   R CMD check timed out
-    
-
-*   checking dependencies in R code ... NOTE
-    ```
-    Namespace in Imports field not imported from: ‘XML’
-      All declared Imports should be used.
-    ```
-
-# scITD
-
-<details>
-
-* Version: 1.0.4
-* GitHub: NA
-* Source code: https://github.com/cran/scITD
-* Date/Publication: 2023-09-08 16:00:02 UTC
-* Number of recursive dependencies: 248
-
-Run `revdepcheck::revdep_details(, "scITD")` for more info
-
-</details>
-
-## In both
-
-*   R CMD check timed out
-    
-
diff --git a/revdep/problems.md b/revdep/problems.md
@@ -1,29 +1 @@
-# Platypus
-
-<details>
-
-* Version: 3.6.0
-* GitHub: NA
-* Source code: https://github.com/cran/Platypus
-* Date/Publication: 2024-10-18 11:10:17 UTC
-* Number of recursive dependencies: 255
-
-Run `revdepcheck::revdep_details(, "Platypus")` for more info
-
-</details>
-
-## Newly broken
-
-*   R CMD check timed out
-    
-
-## In both
-
-*   checking DESCRIPTION meta-information ... NOTE
-    ```
-      Missing dependency on R >= 4.1.0 because package code uses the pipe
-      |> or function shorthand \(...) syntax added in R 4.1.0.
-      File(s) using such syntax:
-        ‘VDJ_build.R’
-    ```
-
+*Wow, no problems at all. :)*
