##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:GSVA.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings GSVA_1.52.3.tar.gz
###
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* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/GSVA.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'GSVA/DESCRIPTION' ... OK
* this is package 'GSVA' version '1.52.3'
* 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 'GSVA' can be installed ... OK
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* checking installed package size ... OK
* 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 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 ... 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 line endings in shell scripts ... 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-3.19-bioc/R/library/GSVA/libs/x64/GSVA.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  Running 'runTests.R'
  Running 'test_gsva_newapi.R'
  Comparing 'test_gsva_newapi.Rout' to 'test_gsva_newapi.Rout.save' ...16,21c16,21
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
<     as.data.frame, basename, cbind, colnames, dirname, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
<     union, unique, unsplit, which.max, which.min
---
>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
>     table, tapply, union, unique, unsplit, which.max, which.min
38,45c38
<     I, expand.grid, unname
< 
< 
< Attaching package: 'IRanges'
< 
< The following object is masked from 'package:grDevices':
< 
<     windows
---
>     expand.grid, I, unname
168c161
< KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.22920126 -0.264187722 -0.37401687  0.291350766  0.17081880 -0.45702585  0.5003620 -0.09626897 -0.47879766  0.2009603094  0.092846463  0.39386860 -0.10064875  0.25767347 -0.006960737 -0.323002689  0.54088138  0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429  0.206128783 -0.38394575 -0.26111852  0.11124358 -0.307607156 -0.23108674  0.118623744  0.40568230 -0.35928390 -0.2287986403  0.0674126870 -0.194909729  0.406279736
---
> KEGG_GLYCOLYSIS_GLUCONEOGENESIS                  0.22920126 -0.264187722 -0.37401687  0.291350766  0.17081880 -0.45702585  0.5003620 -0.09626897 -0.47879477  0.2009603094  0.092846463  0.39386860 -0.10064875  0.25767347 -0.006960737 -0.323002689  0.54088138  0.36740468 -0.230653742 -0.21517689 -0.39153412 -0.10416424 -0.0260882429  0.206128783 -0.38394575 -0.26111852  0.11124358 -0.307607156 -0.23108674  0.118623744  0.40568230 -0.35928390 -0.2287986403  0.0674126870 -0.194909729  0.406279736
170c163
< KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.39571823 -0.352221233 -0.14016244  0.358512977  0.16414025 -0.26589439  0.6674822  0.17953342 -0.55050994  0.0562838685  0.021675321  0.57648156  0.11371008  0.29864451  0.104942610 -0.504014044  0.57693561  0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598  0.1109189257  0.023878095 -0.34214747 -0.25852067  0.28121726 -0.435798801 -0.31480707 -0.007553482  0.26670234 -0.45518879 -0.4532774636  0.2948129840 -0.267281290  0.463433745
---
> KEGG_PENTOSE_PHOSPHATE_PATHWAY                   0.39571823 -0.352221233 -0.14016244  0.358512977  0.16414025 -0.26589439  0.6674822  0.17953342 -0.55049088  0.0562838685  0.021675321  0.57648156  0.11371008  0.29864451  0.104942610 -0.504014044  0.57693561  0.46862262 -0.257288782 -0.36529987 -0.33598186 -0.39358598  0.1109189257  0.023878095 -0.34214747 -0.25852067  0.28121726 -0.435798801 -0.31480707 -0.007553482  0.26670234 -0.45518879 -0.4532774636  0.2948129840 -0.267281290  0.463433745
173c166
< KEGG_GALACTOSE_METABOLISM                        0.06062020 -0.424855520 -0.03930301  0.349652791 -0.12188569 -0.46296074  0.5180153 -0.01789657 -0.35347309  0.2446797481  0.473003017  0.34499007  0.34112213  0.25024239  0.250381767 -0.453215048  0.57769569  0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855  0.056226416 -0.07839585  0.07879640  0.27290820 -0.414140702 -0.36050412 -0.191532611  0.39567826 -0.53298775 -0.4127888920  0.3440494486 -0.178365423  0.513262262
---
> KEGG_GALACTOSE_METABOLISM                        0.06062020 -0.424855520 -0.03930301  0.349652791 -0.12188569 -0.46296074  0.5180153 -0.01789657 -0.35356594  0.2446797481  0.473003017  0.34499007  0.34112213  0.25024239  0.250381767 -0.453215048  0.57769569  0.21561858 -0.337261669 -0.08753488 -0.42331301 -0.04093081 -0.2210103855  0.056226416 -0.07839585  0.07879640  0.27290820 -0.414140702 -0.36050412 -0.191532611  0.39567826 -0.53298775 -0.4127888920  0.3440494486 -0.178365423  0.513262262
180c173
< KEGG_PURINE_METABOLISM                           0.20191160 -0.108479208 -0.10596002  0.292297651 -0.05290036 -0.02776887  0.3629813  0.19221693 -0.19257010 -0.1570618328  0.049458419  0.10941378 -0.11575356  0.10624767  0.139611752 -0.104415107  0.24845743  0.18074380  0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986  0.14562604 -0.027395894  0.03493636  0.032161754 -0.01145234  0.00244119 -0.1717349277  0.1040248755 -0.158512548 -0.016876129
---
> KEGG_PURINE_METABOLISM                           0.20191160 -0.108479208 -0.10596002  0.292297651 -0.05290036 -0.02776887  0.3629813  0.19221693 -0.19257184 -0.1570618328  0.049458419  0.10941378 -0.11575356  0.10624767  0.139611752 -0.104415107  0.24845743  0.18074380  0.044016416 -0.21432408 -0.20002101 -0.17818482 -0.1294276990 -0.149379806 -0.20372875 -0.18695986  0.14562604 -0.027395894  0.03493636  0.032161754 -0.01145234  0.00244119 -0.1717349277  0.1040248755 -0.158512548 -0.016876129
  Running 'test_plage_newapi.R'
  Comparing 'test_plage_newapi.Rout' to 'test_plage_newapi.Rout.save' ...16,21c16,21
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
<     as.data.frame, basename, cbind, colnames, dirname, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
<     union, unique, unsplit, which.max, which.min
---
>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
>     table, tapply, union, unique, unsplit, which.max, which.min
38,45c38
<     I, expand.grid, unname
< 
< 
< Attaching package: 'IRanges'
< 
< The following object is masked from 'package:grDevices':
< 
<     windows
---
>     expand.grid, I, unname
  Running 'test_ssgsea_newapi.R'
  Comparing 'test_ssgsea_newapi.Rout' to 'test_ssgsea_newapi.Rout.save' ...16,21c16,21
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
<     as.data.frame, basename, cbind, colnames, dirname, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
<     union, unique, unsplit, which.max, which.min
---
>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
>     table, tapply, union, unique, unsplit, which.max, which.min
38,45c38
<     I, expand.grid, unname
< 
< 
< Attaching package: 'IRanges'
< 
< The following object is masked from 'package:grDevices':
< 
<     windows
---
>     expand.grid, I, unname
  Running 'test_zscore_newapi.R'
  Comparing 'test_zscore_newapi.Rout' to 'test_zscore_newapi.Rout.save' ...16,21c16,21
<     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
<     as.data.frame, basename, cbind, colnames, dirname, do.call,
<     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
<     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
<     pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
<     union, unique, unsplit, which.max, which.min
---
>     anyDuplicated, aperm, append, as.data.frame, basename, cbind,
>     colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
>     get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>     Position, rank, rbind, Reduce, rownames, sapply, setdiff, sort,
>     table, tapply, union, unique, unsplit, which.max, which.min
38,45c38
<     I, expand.grid, unname
< 
< 
< Attaching package: 'IRanges'
< 
< The following object is masked from 'package:grDevices':
< 
<     windows
---
>     expand.grid, I, unname
 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: 1 NOTE
See
  'F:/biocbuild/bbs-3.19-bioc/meat/GSVA.Rcheck/00check.log'
for details.