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: RELEASE_3_19 |
| git_last_commit: 5ecafd4 |
| git_last_commit_date: 2024-04-30 10:22:20 -0400 (Tue, 30 Apr 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-06-11 14:43 -0400 (Tue, 11 Jun 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4757 |
| palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4491 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4522 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4468 |
| 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 405/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CoGAPS 3.24.0 (landing page) Elana J. Fertig
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
|
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. |
| Package: CoGAPS |
| Version: 3.24.0 |
| 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_3.24.0.tar.gz |
| StartedAt: 2024-06-10 11:20:17 -0400 (Mon, 10 Jun 2024) |
| EndedAt: 2024-06-10 11:27:49 -0400 (Mon, 10 Jun 2024) |
| EllapsedTime: 451.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CoGAPS.Rcheck |
| Warnings: 0 |
##############################################################################
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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_3.24.0.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/CoGAPS.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-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 Ventura 13.6.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.24.0’
* 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 15.0.0 (clang-1500.1.0.2.5)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
installed size is 21.3Mb
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-arm64/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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getPatternGeneSet-methods 4.31 0.037 7.082
* 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-3.19-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.
CoGAPS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CoGAPS ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/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 arm64 -std=gnu++17 accepts -g... yes checking for clang++ -arch arm64 -std=gnu++17 option to enable C++11 features... none needed checking how to run the C++ preprocessor... clang++ -arch arm64 -std=gnu++17 -E checking whether the compiler supports GNU C++... (cached) yes checking whether clang++ -arch arm64 -std=gnu++17 accepts -g... (cached) yes checking for clang++ -arch arm64 -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 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Cogaps.cpp -o Cogaps.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GapsParameters.cpp -o GapsParameters.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GapsResult.cpp -o GapsResult.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GapsRunner.cpp -o GapsRunner.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GapsStatistics.cpp -o GapsStatistics.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c test-runner.cpp -o test-runner.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c atomic/Atom.cpp -o atomic/Atom.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/HashSets.cpp -o data_structures/HashSets.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/Matrix.cpp -o data_structures/Matrix.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c data_structures/Vector.cpp -o data_structures/Vector.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file_parser/FileParser.cpp -o file_parser/FileParser.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c math/Math.cpp -o math/Math.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c math/MatrixMath.cpp -o math/MatrixMath.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c math/Random.cpp -o math/Random.o clang++ -arch arm64 -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-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c math/VectorMath.cpp -o math/VectorMath.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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-arm64/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)
CoGAPS.Rcheck/tests/testthat.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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'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 3.24.0
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on GIST.data_frame (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.24.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
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 3.24.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.24.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
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This is CoGAPS version 3.24.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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worker 1 is finished! Time: 00:00:00
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worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.24.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
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This is CoGAPS version 3.24.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.gct (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on testDataFrame (9 genes and 1363 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on testMatrix (9 genes and 1363 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.tsv (9 genes and 1363 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.gct (9 genes and 1363 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
worker 2 is starting!
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This is CoGAPS version 3.24.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.tsv (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 3.24.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
worker 1 is starting!
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worker 2 is starting!
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worker 2 is finished! Time: 00:00:00
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.24.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 1 is starting!
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This is CoGAPS version 3.24.0
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.24.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/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...
worker 3 is starting!
Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
worker 1 is starting!
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worker 3 is finished! Time: 00:00:00
-- Equilibration Phase --
-- Sampling Phase --
worker 1 is finished! Time: 00:00:00
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worker 2 is starting!
worker 4 is starting!
worker 4 is finished! Time: 00:00:00
worker 2 is finished! Time: 00:00:00
This is CoGAPS version 3.24.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.4-arm64/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!
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-- Equilibration Phase --
-- Sampling Phase --
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[ 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
44.060 7.304 66.642
CoGAPS.Rcheck/CoGAPS-Ex.timings
| name | user | system | elapsed | |
| CoGAPS | 0.232 | 0.012 | 0.407 | |
| CogapsParams | 0.002 | 0.000 | 0.002 | |
| GWCoGAPS | 0 | 0 | 0 | |
| binaryA-methods | 0.022 | 0.002 | 0.037 | |
| buildReport | 0.001 | 0.000 | 0.000 | |
| calcZ-methods | 0.021 | 0.001 | 0.030 | |
| checkpointsEnabled | 0.001 | 0.000 | 0.000 | |
| compiledWithOpenMPSupport | 0.000 | 0.000 | 0.001 | |
| getAmplitudeMatrix-methods | 0.021 | 0.002 | 0.029 | |
| getClusteredPatterns-methods | 0.022 | 0.002 | 0.039 | |
| getCorrelationToMeanPattern-methods | 0.020 | 0.002 | 0.032 | |
| getFeatureLoadings-methods | 0.021 | 0.002 | 0.044 | |
| getMeanChiSq-methods | 0.021 | 0.002 | 0.044 | |
| getOriginalParameters-methods | 0.021 | 0.002 | 0.032 | |
| getParam-methods | 0.001 | 0.000 | 0.005 | |
| getPatternGeneSet-methods | 4.310 | 0.037 | 7.082 | |
| getPatternMatrix-methods | 0.022 | 0.002 | 0.039 | |
| getRetinaSubset | 2.607 | 0.290 | 4.631 | |
| getSampleFactors-methods | 0.021 | 0.002 | 0.027 | |
| getSubsets-methods | 0.021 | 0.002 | 0.035 | |
| getUnmatchedPatterns-methods | 0.020 | 0.002 | 0.034 | |
| getVersion-methods | 0.021 | 0.002 | 0.048 | |
| patternMarkers-methods | 0.058 | 0.003 | 0.121 | |
| plotResiduals-methods | 0.020 | 0.001 | 0.039 | |
| reconstructGene-methods | 0.020 | 0.002 | 0.033 | |
| scCoGAPS | 0 | 0 | 0 | |
| setAnnotationWeights-methods | 0.002 | 0.000 | 0.005 | |
| setDistributedParams-methods | 0.002 | 0.000 | 0.002 | |
| setFixedPatterns-methods | 0.021 | 0.002 | 0.027 | |
| setParam-methods | 0.001 | 0.000 | 0.002 | |