Multiple platform build/check report for BioC 3.20 - CHECK results for CoGAPS on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.1 LTS)	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4744
palomino8	Windows Server 2022 Datacenter	x64	4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves"	4487
merida1	macOS 12.7.5 Monterey	x86_64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4515
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.2 (2024-10-31) -- "Pile of Leaves"	4467
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 nebbiolo2

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: 3.26.0

Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CoGAPS_3.26.0.tar.gz

StartedAt: 2024-12-19 21:47:32 -0500 (Thu, 19 Dec 2024)

EndedAt: 2024-12-19 21:55:31 -0500 (Thu, 19 Dec 2024)

EllapsedTime: 479.3 seconds

RetCode: 0

Status: OK

CheckDir: CoGAPS.Rcheck

Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings CoGAPS_3.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/CoGAPS.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
  installed size is 29.7Mb
  sub-directories of 1Mb or more:
    extdata  19.9Mb
    libs      9.0Mb
* 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 loading without being on the library search path ... 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 ‘/home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/libs/CoGAPS.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

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

Installation output

CoGAPS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL CoGAPS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘CoGAPS’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
./configure: line 3246: AX_COMPILER_VENDOR: command not found
./configure: line 3247: AX_COMPILER_VERSION: command not found
./configure: line 3259: AX_OPENMP: command not found
building on  compiler version 
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c Cogaps.cpp -o Cogaps.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c GapsParameters.cpp -o GapsParameters.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c GapsResult.cpp -o GapsResult.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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 /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/algorithm/string/replace.hpp:16,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/date_time/date_facet.hpp:17,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/date_time/gregorian/gregorian.hpp:31,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12,
                 from /home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include/boost/date_time/posix_time/posix_time.hpp:24,
                 from GapsRunner.cpp:28:
/home/biocbuild/bbs-3.20-bioc/R/site-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 |     );
      |     ~                
/home/biocbuild/bbs-3.20-bioc/R/site-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 |     );
      |     ~                
      |     -
/home/biocbuild/bbs-3.20-bioc/R/site-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 |     );
      |     ~                
/home/biocbuild/bbs-3.20-bioc/R/site-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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c GapsStatistics.cpp -o GapsStatistics.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c atomic/Atom.cpp -o atomic/Atom.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c data_structures/HashSets.cpp -o data_structures/HashSets.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c data_structures/Matrix.cpp -o data_structures/Matrix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c data_structures/Vector.cpp -o data_structures/Vector.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c file_parser/FileParser.cpp -o file_parser/FileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c math/Math.cpp -o math/Math.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c math/MatrixMath.cpp -o math/MatrixMath.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c math/Random.cpp -o math/Random.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c math/VectorMath.cpp -o math/VectorMath.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o CoGAPS.so 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 -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-CoGAPS/00new/CoGAPS/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** 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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 3.26.0 
Running Standard CoGAPS on data (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running single-cell CoGAPS on GIST.data_frame (1363 genes and 9 samples)
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This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running genome-wide CoGAPS on GIST.data_frame (1363 genes and 9 samples)
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This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.26.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
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 3.26.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.26.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
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    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.26.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
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    worker 1 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.26.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
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This is CoGAPS version 3.26.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.gct (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on testDataFrame (9 genes and 1363 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on testMatrix (9 genes and 1363 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.tsv (9 genes and 1363 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.gct (9 genes and 1363 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
    worker 1 is starting!
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This is CoGAPS version 3.26.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
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This is CoGAPS version 3.26.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
    worker 1 is starting!
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This is CoGAPS version 3.26.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
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This is CoGAPS version 3.26.0 
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.26.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-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! (00:00:00)
    worker 1 is starting!
    worker 3 is starting!
    worker 5 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 5 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.26.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.20-bioc/R/site-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! (00:00:00)
    worker 1 is starting!
    worker 3 is starting!
    worker 5 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 5 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
[ FAIL 0 | WARN 11 | SKIP 8 | PASS 99 ]

══ Skipped tests (8) ═══════════════════════════════════════════════════════════
• empty test (8): 'test_checkpoints.R:3:1', 'test_getPatternGeneSet.R:1:1',
  'test_getPatternGeneSet.R:12:1', 'test_parameters.R:3:1',
  'test_patternMarkers.R:2:1', 'test_patternMarkers.R:11:1',
  'test_patternMarkers.R:159:1', 'test_subset_data.R:53:1'

[ FAIL 0 | WARN 11 | SKIP 8 | PASS 99 ]
> 
> proc.time()
   user  system elapsed 
 46.035  11.076  45.813

Example timings

CoGAPS.Rcheck/CoGAPS-Ex.timings

name	user	system	elapsed
CoGAPS	0.234	0.002	0.235
CogapsParams	0.002	0.000	0.001
GWCoGAPS	0	0	0
binaryA-methods	0.023	0.000	0.024
buildReport	0.000	0.000	0.001
calcZ-methods	0.024	0.000	0.023
checkpointsEnabled	0	0	0
compiledWithOpenMPSupport	0	0	0
getAmplitudeMatrix-methods	0.022	0.000	0.023
getClusteredPatterns-methods	0.023	0.000	0.024
getCorrelationToMeanPattern-methods	0.024	0.001	0.023
getFeatureLoadings-methods	0.024	0.000	0.023
getMeanChiSq-methods	0.024	0.000	0.023
getOriginalParameters-methods	0.022	0.000	0.023
getParam-methods	0.001	0.000	0.001
getPatternGeneSet-methods	2.368	0.064	2.432
getPatternMatrix-methods	0.023	0.000	0.024
getRetinaSubset	1.839	0.623	2.469
getSampleFactors-methods	0.024	0.000	0.024
getSubsets-methods	0.024	0.000	0.024
getUnmatchedPatterns-methods	0.024	0.000	0.023
getVersion-methods	0.021	0.002	0.023
patternMarkers-methods	0.064	0.006	0.069
plotResiduals-methods	0.023	0.001	0.023
reconstructGene-methods	0.024	0.000	0.023
scCoGAPS	0.001	0.000	0.000
setAnnotationWeights-methods	0.001	0.000	0.002
setDistributedParams-methods	0.000	0.001	0.002
setFixedPatterns-methods	0.023	0.001	0.025
setParam-methods	0.001	0.000	0.002