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### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fgsea.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings fgsea_1.25.0.tar.gz
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* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/fgsea.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'fgsea/DESCRIPTION' ... OK
* this is package 'fgsea' version '1.25.0'
* 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 whether package 'fgsea' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
* checking installed package size ... NOTE
  installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.9Mb
    libs      1.1Mb
* 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 R 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
setUpBPPARAM: warning in MulticoreParam(workers = nproc, progress =
  TRUE): partial argument match of 'progress' to 'progressbar'
collapsePathways: no visible binding for global variable 'pathway'
collapsePathways: no visible binding for global variable 'ES'
collapsePathwaysGeseca: no visible binding for global variable
  'pvalCond'
collapsePathwaysGeseca: no visible binding for global variable
  'pathway'
collapsePathwaysGeseca: no visible binding for global variable
  'reciprocalPvalCond'
collapsePathwaysGeseca: no visible binding for global variable 'pScore'
collapsePathwaysGeseca: no visible binding for global variable 'pval'
fgseaMultilevel: no visible binding for global variable 'modeFraction'
fgseaMultilevel: no visible binding for global variable 'denomProb'
fora: no visible binding for global variable 'pval'
geseca: no visible binding for global variable 'gsScore'
geseca: no visible binding for global variable 'log2err'
geseca: no visible binding for global variable 'nGeScore'
geseca: no visible binding for global variable 'pctVar'
geseca: no visible binding for global variable 'size'
geseca: no visible binding for global variable 'pathway'
geseca: no visible global function definition for '.'
geseca: no visible binding for global variable 'pval'
geseca: no visible binding for global variable 'padj'
gesecaSimple: no visible binding for global variable 'pctVar'
gesecaSimple: no visible binding for global variable 'size'
gesecaSimple: no visible binding for global variable 'pval'
gesecaSimpleImpl: no visible binding for global variable 'pval'
gesecaSimpleImpl: no visible binding for global variable 'nGeScore'
gesecaSimpleImpl: no visible binding for global variable 'padj'
gesecaSimpleImpl: no visible binding for global variable 'size'
plotCoregulationProfile: no visible binding for global variable 'id'
plotCoregulationProfile: no visible binding for global variable 'gene'
plotCoregulationProfile: no visible binding for global variable
  'expressionValue'
plotCoregulationProfile: no visible binding for global variable 'x'
plotCoregulationProfile: no visible binding for global variable 'y'
plotCoregulationProfile: no visible binding for global variable
  'condition'
plotGesecaTable: no visible global function definition for 'modifyList'
plotGesecaTable: no visible binding for global variable 'pathway'
plotGesecaTable : <anonymous>: no visible binding for global variable
  'pathway'
plotGesecaTable : <anonymous>: no visible binding for global variable
  'value'
plotGseaTable: no visible global function definition for 'modifyList'
Undefined global functions or variables:
  . ES condition denomProb expressionValue gene gsScore id log2err
  modeFraction modifyList nGeScore pScore padj pathway pctVar pval
  pvalCond reciprocalPvalCond size value x y
Consider adding
  importFrom("utils", "modifyList")
to your NAMESPACE file.
* checking Rd files ... OK
* 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 ... 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.17-bioc/R/library/fgsea/libs/x64/fgsea.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
plotGseaTable    7.13   0.16   18.29
collapsePathways 4.39   0.07   12.38
mapIdsList       4.07   0.28   13.05
fgsea            1.17   0.07   11.26
fgseaMultilevel  1.02   0.06   10.96
fgseaSimple      0.73   0.08   16.04
geseca           0.51   0.06   13.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/fgsea.Rcheck/00check.log'
for details.