Multiple platform build/check report for BioC 3.20 - CHECK results for CoGAPS on palomino4

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup"	4679
palomino4	Windows Server 2022 Datacenter	x64	4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"	4414
merida1	macOS 12.7.4 Monterey	x86_64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4441
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"	4394
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for CoGAPS on palomino4

To the developers/maintainers of the CoGAPS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CoGAPS.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: CoGAPS

Version: 3.25.0

Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoGAPS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CoGAPS_3.25.0.tar.gz

StartedAt: 2024-06-10 01:09:06 -0400 (Mon, 10 Jun 2024)

EndedAt: 2024-06-10 01:24:56 -0400 (Mon, 10 Jun 2024)

EllapsedTime: 949.3 seconds

RetCode: 0

Status: OK

CheckDir: CoGAPS.Rcheck

Warnings: 0

Command output

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##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoGAPS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings CoGAPS_3.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/CoGAPS.Rcheck'
* using R version 4.4.0 RC (2024-04-16 r86468 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 'CoGAPS/DESCRIPTION' ... OK
* this is package 'CoGAPS' version '3.25.0'
* 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 'CoGAPS' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... NOTE
  installed size is 22.0Mb
  sub-directories of 1Mb or more:
    extdata  19.9Mb
    libs      1.4Mb
* 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
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'
plotPatternGeneSet,list-numeric-numeric: no visible binding for global
  variable 'padj'
show,CogapsParams: no visible binding for global variable
  'checkpointInFile'
Undefined global functions or variables:
  checkpointInFile gene.set neg.log.padj padj
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/libs/x64/CoGAPS.dll':
  Found '_exit', possibly from '_exit' (C)
  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
CoGAPS 4.09   1.97    6.07
* 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
  'F:/biocbuild/bbs-3.20-bioc/meat/CoGAPS.Rcheck/00check.log'
for details.

Installation output

CoGAPS.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL CoGAPS
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'CoGAPS' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Cogaps.cpp -o Cogaps.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GapsParameters.cpp -o GapsParameters.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GapsResult.cpp -o GapsResult.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsRunner.cpp:8:
gibbs_sampler/AsynchronousGibbsSampler.h:105: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  105 |         #pragma omp parallel for num_threads(nThreads)
      | 
In file included from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/algorithm/string/replace.hpp:16,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/date_time/date_facet.hpp:17,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian.hpp:31,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12,
                 from F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time.hpp:24,
                 from GapsRunner.cpp:27:
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: note: remove parentheses
  194 | failed ************ (Pred::************
      |                     ^~~~~~~~~~~~~~~~~~~
      |                     -
  195 |       assert_arg( void (*)(Pred), typename assert_arg_pred<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  196 |     );
      |     ~                
      |     -
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
F:/biocbuild/bbs-3.20-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: note: remove parentheses
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                     -
  200 |       assert_not_arg( void (*)(Pred), typename assert_arg_pred_not<Pred>::type )
      |       ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  201 |     );
      |     ~                
      |     -
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GapsStatistics.cpp -o GapsStatistics.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c atomic/Atom.cpp -o atomic/Atom.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
atomic/ConcurrentAtomicDomain.cpp:64: warning: ignoring '#pragma omp critical' [-Wunknown-pragmas]
   64 |     #pragma omp critical(AtomicInsertOrErase)
      | 
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
atomic/ProposalQueue.cpp:101: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
  101 |     #pragma omp atomic
      | 
atomic/ProposalQueue.cpp:107: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
  107 |     #pragma omp atomic
      | 
atomic/ProposalQueue.cpp:113: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
  113 |     #pragma omp atomic
      | 
atomic/ProposalQueue.cpp:119: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
  119 |     #pragma omp atomic
      | 
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c data_structures/HashSets.cpp -o data_structures/HashSets.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
data_structures/HybridVector.cpp:60: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
   60 |         #pragma omp atomic
      | 
data_structures/HybridVector.cpp:65: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
   65 |     #pragma omp atomic
      | 
data_structures/HybridVector.cpp:77: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
   77 |         #pragma omp atomic
      | 
data_structures/HybridVector.cpp:82: warning: ignoring '#pragma omp atomic' [-Wunknown-pragmas]
   82 |     #pragma omp atomic
      | 
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c data_structures/Matrix.cpp -o data_structures/Matrix.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c data_structures/Vector.cpp -o data_structures/Vector.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c file_parser/FileParser.cpp -o file_parser/FileParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
gibbs_sampler/DenseNormalModel.cpp:26: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   26 |     #pragma omp parallel for num_threads(nThreads)
      | 
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c math/Math.cpp -o math/Math.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c math/MatrixMath.cpp -o math/MatrixMath.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c math/Random.cpp -o math/Random.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c math/VectorMath.cpp -o math/VectorMath.o
g++ -std=gnu++17 -shared -s -static-libgcc -o CoGAPS.dll tmp.def Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/Atom.o atomic/ConcurrentAtom.o atomic/AtomicDomain.o atomic/ConcurrentAtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CharacterDelimitedParser.o file_parser/FileParser.o file_parser/MatrixElement.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseNormalModel.o gibbs_sampler/SparseNormalModel.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-CoGAPS/00new/CoGAPS/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CoGAPS)

Tests output

CoGAPS.Rcheck/tests/testthat.Rout


R version 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(CoGAPS)
> 
> test_check("CoGAPS")

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
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    worker 3 is finished! Time: 00:00:00
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    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
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    worker 3 is finished! Time: 00:00:00
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    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on GIST.matrix (1363 genes and 9 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
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    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running single-cell CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
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    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
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    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running single-cell CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
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    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.gct (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on testDataFrame (9 genes and 1363 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on testMatrix (9 genes and 1363 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.tsv (9 genes and 1363 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.gct (9 genes and 1363 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
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    worker 3 is finished! Time: 00:00:00
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    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
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    worker 2 is finished! Time: 00:00:00
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    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running single-cell CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
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    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running single-cell CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
    worker 1 is finished! Time: 00:00:00
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    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples) with parameters:

-- Standard Parameters --
nPatterns            3 
nIterations          175 
seed                 42 
sparseOptimization   TRUE 
distributed          genome-wide 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

-- Distributed CoGAPS Parameters -- 
nSets          5 
cut            4 
minNS          3 
maxNS          8 

Creating subsets...using provided indexed subsets
set sizes (min, mean, max): (200, 200, 200)
Running Final Stage...

Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:05)
    worker 1 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 5 is starting!
    worker 5 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on F:/biocbuild/bbs-3.20-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples) with parameters:

-- Standard Parameters --
nPatterns            3 
nIterations          175 
seed                 42 
sparseOptimization   TRUE 
distributed          genome-wide 

-- Sparsity Parameters --
alpha          0.01 
maxGibbsMass   100 

-- Distributed CoGAPS Parameters -- 
nSets          5 
cut            4 
minNS          3 
maxNS          8 

Creating subsets...using provided indexed subsets
set sizes (min, mean, max): (200, 200, 200)
Running Final Stage...

Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:05)
    worker 1 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 3 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 5 is starting!
    worker 5 is finished! Time: 00:00:00
[ FAIL 0 | WARN 20 | SKIP 3 | PASS 68 ]

══ Skipped tests (3) ═══════════════════════════════════════════════════════════
• empty test (3): 'test_checkpoints.R:3:1', 'test_parameters.R:3:1',
  'test_subset_data.R:53:1'

[ FAIL 0 | WARN 20 | SKIP 3 | PASS 68 ]
> 
> proc.time()
   user  system elapsed 
 430.73  217.93  649.43

Example timings

CoGAPS.Rcheck/CoGAPS-Ex.timings

name	user	system	elapsed
CoGAPS	4.09	1.97	6.07
CogapsParams	0	0	0
GWCoGAPS	0	0	0
binaryA-methods	0.02	0.02	0.03
buildReport	0	0	0
calcZ-methods	0.02	0.01	0.03
checkpointsEnabled	0	0	0
compiledWithOpenMPSupport	0	0	0
getAmplitudeMatrix-methods	0.03	0.00	0.03
getClusteredPatterns-methods	0.02	0.00	0.01
getCorrelationToMeanPattern-methods	0.03	0.00	0.04
getFeatureLoadings-methods	0.03	0.02	0.04
getMeanChiSq-methods	0.03	0.00	0.03
getOriginalParameters-methods	0.02	0.01	0.03
getParam-methods	0	0	0
getPatternGeneSet-methods	1.67	0.02	1.69
getPatternMatrix-methods	0.02	0.00	0.02
getRetinaSubset	2.03	0.59	2.64
getSampleFactors-methods	0.03	0.00	0.03
getSubsets-methods	0.01	0.02	0.03
getUnmatchedPatterns-methods	0.03	0.00	0.03
getVersion-methods	0.02	0.00	0.02
patternMarkers-methods	0.05	0.01	0.07
plotResiduals-methods	0.01	0.02	0.03
reconstructGene-methods	0.03	0.00	0.03
scCoGAPS	0	0	0
setAnnotationWeights-methods	0	0	0
setDistributedParams-methods	0	0	0
setFixedPatterns-methods	0.04	0.00	0.03
setParam-methods	0	0	0