##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:singleCellTK.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings singleCellTK_2.16.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/singleCellTK.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘singleCellTK/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘singleCellTK’ version ‘2.16.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘singleCellTK’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R         1.0Mb
    extdata   1.6Mb
    shiny     3.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in Rd file 'importGeneSetsFromMSigDB.Rd':
  ‘[msigdbr]{msigdbr_show_species}’

See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘singleCellTK-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: importGeneSetsFromMSigDB
> ### Title: Imports gene sets from MSigDB
> ### Aliases: importGeneSetsFromMSigDB
> 
> ### ** Examples
> 
> data(scExample)
> sce <- importGeneSetsFromMSigDB(inSCE = sce,
+                                 categoryIDs = "H",
+                                 species = "Homo sapiens",
+                                 mapping = "gene_symbol",
+                                 by = "feature_name")
Warning: The `category` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `collection` argument instead.
ℹ The deprecated feature was likely used in the singleCellTK package.
  Please report the issue at
  <https://github.com/compbiomed/singleCellTK/issues>.
Warning: The `subcategory` argument of `msigdbr()` is deprecated as of msigdbr 10.0.0.
ℹ Please use the `subcollection` argument instead.
ℹ The deprecated feature was likely used in the singleCellTK package.
  Please report the issue at
  <https://github.com/compbiomed/singleCellTK/issues>.
Error in (function (cond)  : 
  error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': subcategory is not a character vector
Calls: importGeneSetsFromMSigDB -> as.data.frame -> <Anonymous> -> <Anonymous>
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘spelling.R’
  Running ‘testthat.R’
 ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  .Internal(C_tryCatchHelper(addr, 1L, cond)))(structure(list(message = "subcategory is not a character vector", 
      call = NULL), class = c("assertError", "simpleError", "error", 
  "condition")))`: error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': subcategory is not a character vector
  Backtrace:
      ▆
   1. ├─singleCellTK::importGeneSetsFromMSigDB(...) at test-misc.R:58:3
   2. │ ├─BiocGenerics::as.data.frame(...)
   3. │ └─msigdbr::msigdbr(species = species, category = category, subcategory = subcat)
   4. │   └─assertthat::assert_that(...)
   5. │     └─base::stop(assertError(attr(res, "msg")))
   6. └─base (local) `<fn>`(`<assrtErr>`)
  
  [ FAIL 2 | WARN 12 | SKIP 0 | PASS 222 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 ERRORs, 1 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/singleCellTK.Rcheck/00check.log’
for details.