Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-06-11 15:41 -0400 (Tue, 11 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" 4679
palomino4Windows Server 2022 Datacenterx644.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" 4414
merida1macOS 12.7.4 Montereyx86_644.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" 4441
kjohnson1macOS 13.6.6 Venturaarm644.4.0 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

Package 396/2239HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 3.25.0  (landing page)
Elana J. Fertig
Snapshot Date: 2024-06-09 14:00 -0400 (Sun, 09 Jun 2024)
git_url: https://git.bioconductor.org/packages/CoGAPS
git_branch: devel
git_last_commit: 5e91cbe
git_last_commit_date: 2024-04-30 10:22:20 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for CoGAPS on merida1

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: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoGAPS_3.25.0.tar.gz
StartedAt: 2024-06-10 01:37:04 -0400 (Mon, 10 Jun 2024)
EndedAt: 2024-06-10 01:46:04 -0400 (Mon, 10 Jun 2024)
EllapsedTime: 540.0 seconds
RetCode: 0
Status:   OK  
CheckDir: CoGAPS.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CoGAPS_3.25.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/CoGAPS.Rcheck’
* using R version 4.4.0 Patched (2024-04-24 r86482)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.4
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CoGAPS’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is 21.4Mb
  sub-directories of 1Mb or more:
    extdata  19.9Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
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 is not available
File ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/libs/CoGAPS.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
  Found ‘_printf’, possibly from ‘printf’ (C)
  Found ‘_putchar’, possibly from ‘putchar’ (C)
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)

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

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

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


Installation output

CoGAPS.Rcheck/00install.out

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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoGAPS
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 clang++ -arch x86_64 -std=gnu++17 accepts -g... yes
checking for clang++ -arch x86_64 -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... clang++ -arch x86_64 -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether clang++ -arch x86_64 -std=gnu++17 accepts -g... (cached) yes
checking for clang++ -arch x86_64 -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: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c Cogaps.cpp -o Cogaps.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c GapsParameters.cpp -o GapsParameters.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c GapsResult.cpp -o GapsResult.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c GapsRunner.cpp -o GapsRunner.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c GapsStatistics.cpp -o GapsStatistics.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c test-runner.cpp -o test-runner.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c atomic/Atom.cpp -o atomic/Atom.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c data_structures/HashSets.cpp -o data_structures/HashSets.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c data_structures/Matrix.cpp -o data_structures/Matrix.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c data_structures/Vector.cpp -o data_structures/Vector.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c file_parser/FileParser.cpp -o file_parser/FileParser.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c math/Math.cpp -o math/Math.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c math/MatrixMath.cpp -o math/MatrixMath.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c math/Random.cpp -o math/Random.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/BH/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c math/VectorMath.cpp -o math/VectorMath.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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    worker 3 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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
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    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
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    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
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    worker 3 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
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    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
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    worker 2 is finished! Time: 00:00:00
    worker 3 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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.tsv (9 genes and 1363 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
    worker 1 is starting!
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    worker 1 is finished! Time: 00:00:00
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This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.tsv (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 3.25.0 
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
    worker 2 is starting!
    worker 1 is starting!
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    worker 2 is finished! Time: 00:00:00
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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 3.25.0 
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
    worker 2 is starting!
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    worker 2 is finished! Time: 00:00:00
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    worker 3 is finished! Time: 00:00:00
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    worker 1 is finished! Time: 00:00:00
    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 /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 5 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 4 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.25.0 
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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 5 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 2 is starting!
    worker 4 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
[ FAIL 0 | WARN 10 | 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 10 | SKIP 3 | PASS 68 ]
> 
> proc.time()
   user  system elapsed 
 71.899  10.965  74.401 

Example timings

CoGAPS.Rcheck/CoGAPS-Ex.timings

nameusersystemelapsed
CoGAPS0.5360.0180.620
CogapsParams0.0050.0010.006
GWCoGAPS0.0000.0010.001
binaryA-methods0.0360.0030.043
buildReport0.0000.0000.001
calcZ-methods0.0360.0030.046
checkpointsEnabled000
compiledWithOpenMPSupport0.0010.0000.001
getAmplitudeMatrix-methods0.0360.0030.041
getClusteredPatterns-methods0.0370.0030.053
getCorrelationToMeanPattern-methods0.0350.0020.046
getFeatureLoadings-methods0.0350.0030.043
getMeanChiSq-methods0.0350.0030.041
getOriginalParameters-methods0.0340.0020.042
getParam-methods0.0030.0010.004
getPatternGeneSet-methods3.6360.0364.273
getPatternMatrix-methods0.0360.0030.041
getRetinaSubset2.6520.6813.982
getSampleFactors-methods0.0360.0030.043
getSubsets-methods0.0340.0030.041
getUnmatchedPatterns-methods0.0360.0030.042
getVersion-methods0.0350.0030.047
patternMarkers-methods0.1620.0050.191
plotResiduals-methods0.0350.0040.044
reconstructGene-methods0.0350.0030.043
scCoGAPS0.0000.0010.001
setAnnotationWeights-methods0.0040.0010.004
setDistributedParams-methods0.0040.0000.005
setFixedPatterns-methods0.0380.0030.051
setParam-methods0.0040.0000.004