Re-run revdeps and update cran comments

tidyverse · Jan 27, 2023 · 199195d · 199195d
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diff --git a/cran-comments.md b/cran-comments.md
@@ -4,8 +4,17 @@
 
 ## revdepcheck results
 
-We checked 212 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 231 reverse dependencies (228 from CRAN + 3 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 saw 2 new problems:
 
+* epikit
+* stevemisc
+
+Both maintainers were notified on Jan 12 (~2 week ago) and supplied with patches.
+
+We failed to check 3 packages
+
+* genekitr     (NA)
+* OlinkAnalyze (NA)
+* SCpubr       (NA)
diff --git a/revdep/README.md b/revdep/README.md
@@ -11,12 +11,10 @@
 |SCpubr       |?       |      |        |     |
 |NA           |?       |      |        |     |
 
-## New problems (4)
+## New problems (2)
 
-|package      |version |error  |warning |note |
-|:------------|:-------|:------|:-------|:----|
-|[autostats](problems.md#autostats)|0.4.0   |__+1__ |__+1__  |     |
+|package   |version |error  |warning |note |
+|:---------|:-------|:------|:-------|:----|
 |[epikit](problems.md#epikit)|0.1.2   |__+1__ |        |1    |
-|[framecleaner](problems.md#framecleaner)|0.2.0   |__+1__ |        |     |
 |[stevemisc](problems.md#stevemisc)|1.4.1   |__+1__ |        |     |
 
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -1,25 +1,18 @@
 ## revdepcheck results
 
-We checked 220 reverse dependencies (217 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 231 reverse dependencies (228 from CRAN + 3 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 4 new problems
+ * We saw 2 new problems
  * We failed to check 3 packages
 
 Issues with CRAN packages are summarised below.
 
 ### New problems
 (This reports the first line of each new failure)
 
-* autostats
-  checking examples ... ERROR
-  checking re-building of vignette outputs ... WARNING
-
 * epikit
   checking tests ... ERROR
 
-* framecleaner
-  checking examples ... ERROR
-
 * stevemisc
   checking examples ... ERROR
 

diff --git a/revdep/failures.md b/revdep/failures.md
@@ -2,10 +2,10 @@
 
 <details>
 
-* Version: 1.0.8
+* Version: 1.1.0
 * GitHub: https://github.com/GangLiLab/genekitr
 * Source code: https://github.com/cran/genekitr
-* Date/Publication: 2022-11-23 11:30:02 UTC
+* Date/Publication: 2023-01-20 03:30:02 UTC
 * Number of recursive dependencies: 200
 
 Run `revdepcheck::cloud_details(, "genekitr")` for more info
@@ -24,7 +24,7 @@ Run `revdepcheck::cloud_details(, "genekitr")` for more info
 * using option ‘--no-manual’
 * checking for file ‘genekitr/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘genekitr’ version ‘1.0.8’
+* this is package ‘genekitr’ version ‘1.1.0’
 * package encoding: UTF-8
 * checking package namespace information ... OK
 * checking package dependencies ... ERROR
@@ -50,7 +50,7 @@ Status: 1 ERROR
 * using option ‘--no-manual’
 * checking for file ‘genekitr/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘genekitr’ version ‘1.0.8’
+* this is package ‘genekitr’ version ‘1.1.0’
 * package encoding: UTF-8
 * checking package namespace information ... OK
 * checking package dependencies ... ERROR
@@ -140,10 +140,10 @@ Run `revdepcheck::cloud_details(, "NA")` for more info
 
 <details>
 
-* Version: 3.2.2
+* Version: 3.3.0
 * GitHub: NA
 * Source code: https://github.com/cran/OlinkAnalyze
-* Date/Publication: 2022-11-16 00:30:05 UTC
+* Date/Publication: 2023-01-24 21:50:02 UTC
 * Number of recursive dependencies: 202
 
 Run `revdepcheck::cloud_details(, "OlinkAnalyze")` for more info
@@ -162,7 +162,7 @@ Run `revdepcheck::cloud_details(, "OlinkAnalyze")` for more info
 * using option ‘--no-manual’
 * checking for file ‘OlinkAnalyze/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘OlinkAnalyze’ version ‘3.2.2’
+* this is package ‘OlinkAnalyze’ version ‘3.3.0’
 * package encoding: UTF-8
 * checking package namespace information ... OK
 ...
@@ -192,7 +192,7 @@ Status: 1 NOTE
 * using option ‘--no-manual’
 * checking for file ‘OlinkAnalyze/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘OlinkAnalyze’ version ‘3.2.2’
+* this is package ‘OlinkAnalyze’ version ‘3.3.0’
 * package encoding: UTF-8
 * checking package namespace information ... OK
 ...
@@ -216,11 +216,11 @@ Status: 1 NOTE
 
 <details>
 
-* Version: 1.1.1
+* Version: 1.1.2
 * GitHub: https://github.com/enblacar/SCpubr
 * Source code: https://github.com/cran/SCpubr
-* Date/Publication: 2023-01-12 11:30:02 UTC
-* Number of recursive dependencies: 289
+* Date/Publication: 2023-01-18 12:20:02 UTC
+* Number of recursive dependencies: 290
 
 Run `revdepcheck::cloud_details(, "SCpubr")` for more info
 
@@ -238,20 +238,20 @@ Run `revdepcheck::cloud_details(, "SCpubr")` for more info
 * using option ‘--no-manual’
 * checking for file ‘SCpubr/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘SCpubr’ version ‘1.1.1’
+* this is package ‘SCpubr’ version ‘1.1.2’
 * package encoding: UTF-8
 * checking package namespace information ... OK
 ...
-  [ FAIL 1 | WARN 0 | SKIP 347 | PASS 320 ]
-  Error: Test failures
-  Execution halted
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+  Running ‘testthat.R’
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in ‘inst/doc’ ... OK
 * checking running R code from vignettes ... NONE
   ‘reference_manual.Rmd’ using ‘UTF-8’... OK
 * checking re-building of vignette outputs ... OK
 * DONE
-Status: 1 ERROR, 1 WARNING, 2 NOTEs
+Status: 1 WARNING, 2 NOTEs
 
 
 
@@ -268,20 +268,20 @@ Status: 1 ERROR, 1 WARNING, 2 NOTEs
 * using option ‘--no-manual’
 * checking for file ‘SCpubr/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘SCpubr’ version ‘1.1.1’
+* this is package ‘SCpubr’ version ‘1.1.2’
 * package encoding: UTF-8
 * checking package namespace information ... OK
 ...
-  [ FAIL 1 | WARN 0 | SKIP 347 | PASS 320 ]
-  Error: Test failures
-  Execution halted
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ... OK
+  Running ‘testthat.R’
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in ‘inst/doc’ ... OK
 * checking running R code from vignettes ... NONE
   ‘reference_manual.Rmd’ using ‘UTF-8’... OK
 * checking re-building of vignette outputs ... OK
 * DONE
-Status: 1 ERROR, 1 WARNING, 2 NOTEs
+Status: 1 WARNING, 2 NOTEs
 
 
 

diff --git a/revdep/problems.md b/revdep/problems.md
@@ -1,69 +1,3 @@
-# autostats
-
-<details>
-
-* Version: 0.4.0
-* GitHub: https://github.com/Harrison4192/autostats
-* Source code: https://github.com/cran/autostats
-* Date/Publication: 2022-11-07 10:20:06 UTC
-* Number of recursive dependencies: 233
-
-Run `revdepcheck::cloud_details(, "autostats")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘autostats-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: auto_anova
-    > ### Title: auto anova
-    > ### Aliases: auto_anova
-    > 
-    > ### ** Examples
-    > 
-    > 
-    ...
-     18. ├─framecleaner:::fct_or_prob(., ...)
-     19. │ └─... %>% ...
-     20. └─forcats::fct_lump(., n = max_levels, ties.method = "first")
-     21.   └─forcats::fct_lump_n(n = n)
-     22.     └─forcats:::check_number_whole(n)
-     23.       └─forcats:::.rlang_types_check_number(...)
-     24.         └─forcats (local) .stop(x, what, ...)
-     25.           └─forcats:::stop_input_type(...)
-     26.             └─rlang::abort(message, ..., call = call, arg = arg)
-    Execution halted
-    ```
-
-*   checking re-building of vignette outputs ... WARNING
-    ```
-    Error(s) in re-building vignettes:
-      ...
-    --- re-building ‘autostats.Rmd’ using rmarkdown
-    Quitting from lines 97-99 (autostats.Rmd) 
-    Error: processing vignette 'autostats.Rmd' failed with diagnostics:
-    Problem while computing `..1 = dplyr::across(...)`.
-    Caused by error in `across()`:
-    ! Problem while computing column `Species`.
-    Caused by error in `fct_lump_n()`:
-    ! `n` must be a whole number, not `Inf`.
-    ...
-    --- failed re-building ‘autostats.Rmd’
-    
-    --- re-building ‘tidyXgboost.Rmd’ using rmarkdown
-    --- finished re-building ‘tidyXgboost.Rmd’
-    
-    SUMMARY: processing the following file failed:
-      ‘autostats.Rmd’
-    
-    Error: Vignette re-building failed.
-    Execution halted
-    ```
-
 # epikit
 
 <details>
@@ -109,47 +43,6 @@ Run `revdepcheck::cloud_details(, "epikit")` for more info
       'LazyData' is specified without a 'data' directory
     ```
 
-# framecleaner
-
-<details>
-
-* Version: 0.2.0
-* GitHub: https://github.com/Harrison4192/framecleaner
-* Source code: https://github.com/cran/framecleaner
-* Date/Publication: 2021-11-17 05:40:02 UTC
-* Number of recursive dependencies: 105
-
-Run `revdepcheck::cloud_details(, "framecleaner")` for more info
-
-</details>
-
-## Newly broken
-
-*   checking examples ... ERROR
-    ```
-    Running examples in ‘framecleaner-Ex.R’ failed
-    The error most likely occurred in:
-    
-    > ### Name: set_fct
-    > ### Title: set factor
-    > ### Aliases: set_fct set_fct.data.frame set_fct.default
-    > 
-    > ### ** Examples
-    > 
-    > 
-    ...
-     16. ├─framecleaner:::fct_or_prob(., ...)
-     17. │ └─... %>% ...
-     18. └─forcats::fct_lump(., n = max_levels, ties.method = "first")
-     19.   └─forcats::fct_lump_n(n = n)
-     20.     └─forcats:::check_number_whole(n)
-     21.       └─forcats:::.rlang_types_check_number(...)
-     22.         └─forcats (local) .stop(x, what, ...)
-     23.           └─forcats:::stop_input_type(...)
-     24.             └─rlang::abort(message, ..., call = call, arg = arg)
-    Execution halted
-    ```
-
 # stevemisc
 
 <details>