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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoGAPS_3.26.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CoGAPS.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.26.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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 ‘CoGAPS’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is 21.4Mb
  sub-directories of 1Mb or more:
    extdata  19.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* 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 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 ... NOTE
.patternMarkers_all: no visible global function definition for
  ‘setNames’
getPatternGeneSet,CogapsResult-list-character : <anonymous>: no visible
  binding for global variable ‘gene.set’
getPatternGeneSet,CogapsResult-list-character : <anonymous>: no visible
  binding for global variable ‘padj’
plotPatternGeneSet,list-numeric-numeric: no visible binding for global
  variable ‘neg.log.padj’
plotPatternGeneSet,list-numeric-numeric: no visible binding for global
  variable ‘gene.set’
show,CogapsParams: no visible binding for global variable
  ‘checkpointInFile’
Undefined global functions or variables:
  checkpointInFile gene.set neg.log.padj padj setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) getPatternGeneSet-methods.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{method}{enrichment or overrepresentation. Conducts a test for gene set enrichment using {fgsea::gsea} ranking features by pattern amplitude or a test for gene set overrepresentation in pattern markers using {fgsea::fora}, respectively.}
       |                                                                                               ^
checkRd: (-1) getPatternGeneSet-methods.Rd:28: Lost braces; missing escapes or markup?
    28 | \item{method}{enrichment or overrepresentation. Conducts a test for gene set enrichment using {fgsea::gsea} ranking features by pattern amplitude or a test for gene set overrepresentation in pattern markers using {fgsea::fora}, respectively.}
       |                                                                                                                                                                                                                      ^
checkRd: (-1) getPatternGeneSet-methods.Rd:30: Lost braces; missing escapes or markup?
    30 | \item{...}{additional parameters passed to {patternMarkers} if using overrepresentation method}
       |                                            ^
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'callInternalCoGAPS.Rd':
  ‘index’ ‘sets’ ‘geneNames’ ‘sampleNames’ ‘fixedMatrix’

Documented arguments not in \usage in Rd file 'sampleWithExplictSets.Rd':
  ‘total’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/libs/CoGAPS.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.