Elana J. Fertig
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/CoGAPS |
| git_branch: RELEASE_3_13 |
| git_last_commit: c297d7e |
| git_last_commit_date: 2021-05-19 11:45:58 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the CoGAPS package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 360/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CoGAPS 3.12.0 (landing page) Elana J. Fertig
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: CoGAPS |
| Version: 3.12.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoGAPS_3.12.0.tar.gz |
| StartedAt: 2021-10-14 17:39:08 -0400 (Thu, 14 Oct 2021) |
| EndedAt: 2021-10-14 17:42:59 -0400 (Thu, 14 Oct 2021) |
| EllapsedTime: 230.7 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CoGAPS.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings CoGAPS_3.12.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/CoGAPS.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.12.0’
* 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
* 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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking 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/4.1/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. 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 in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.13-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.
CoGAPS.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL CoGAPS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/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 we are using the GNU C++ compiler... yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... yes
checking how to run the C++ preprocessor... clang++ -mmacosx-version-min=10.13 -std=gnu++14 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether clang++ -mmacosx-version-min=10.13 -std=gnu++14 accepts -g... (cached) yes
./configure: line 2752: AX_COMPILER_VENDOR: command not found
./configure: line 2753: AX_COMPILER_VERSION: command not found
./configure: line 2764: AX_OPENMP: command not found
building on compiler version
Using AVX instructions if available
configure: creating ./config.status
config.status: creating src/Makevars
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c Cogaps.cpp -o Cogaps.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c GapsParameters.cpp -o GapsParameters.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c GapsResult.cpp -o GapsResult.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c GapsRunner.cpp -o GapsRunner.o
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
GapsRunner.cpp:430:13: warning: enumeration value 'GAPS_ALL_PHASES' not handled in switch [-Wswitch]
switch (phase)
^
GapsRunner.cpp:430:13: note: add missing switch cases
switch (phase)
^
9 warnings generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c GapsStatistics.cpp -o GapsStatistics.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c test-runner.cpp -o test-runner.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c atomic/Atom.cpp -o atomic/Atom.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/HashSets.cpp -o data_structures/HashSets.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/Matrix.cpp -o data_structures/Matrix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c data_structures/Vector.cpp -o data_structures/Vector.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c file_parser/FileParser.cpp -o file_parser/FileParser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c math/Math.cpp -o math/Math.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c math/MatrixMath.cpp -o math/MatrixMath.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c math/Random.cpp -o math/Random.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/BH/include' -I/usr/local/include -march=native -fPIC -Wall -g -O2 -c math/VectorMath.cpp -o math/VectorMath.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
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 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
worker 1 is starting!
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worker 2 is finished! Time: 00:00:00
worker 1 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 3.12.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
worker 2 is starting!
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worker 1 is starting!
worker 4 is finished! Time: 00:00:00
worker 2 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
worker 1 is finished! Time: 00:00:00
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
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 3.12.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
worker 3 is starting!
worker 1 is starting!
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worker 2 is starting!
worker 1 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
worker 4 is finished! Time: 00:00:00
worker 2 is finished! Time: 00:00:00
This is CoGAPS version 3.12.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 2 is starting!
worker 1 is starting!
worker 4 is starting!
worker 3 is starting!
worker 2 is finished! Time: 00:00:00
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worker 1 is starting!
worker 4 is finished! Time: 00:00:00
worker 2 is finished! Time: 00:00:00
worker 1 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
This is CoGAPS version 3.12.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
worker 1 is starting!
worker 2 is starting!
worker 4 is starting!
worker 3 is starting!
worker 1 is finished! Time: 00:00:00
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worker 1 is starting!
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worker 4 is starting!
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 3.12.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 1 is starting!
worker 2 is starting!
worker 3 is starting!
worker 4 is starting!
worker 1 is finished! Time: 00:00:00
worker 2 is finished! Time: 00:00:00
worker 4 is finished! Time: 00:00:00
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worker 4 is starting!
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worker 1 is starting!
worker 4 is finished! Time: 00:00:00
worker 2 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
worker 1 is finished! Time: 00:00:00
This is CoGAPS version 3.12.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.gct (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on testDataFrame (9 genes and 1363 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on testMatrix (9 genes and 1363 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.tsv (9 genes and 1363 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.gct (9 genes and 1363 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
worker 2 is starting!
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worker 2 is finished! Time: 00:00:00
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worker 3 is starting!
worker 2 is finished! Time: 00:00:00
worker 1 is finished! Time: 00:00:00
worker 4 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
This is CoGAPS version 3.12.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
worker 1 is starting!
worker 2 is starting!
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worker 1 is finished! Time: 00:00:00
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worker 1 is starting!
worker 2 is finished! Time: 00:00:00
worker 4 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
worker 1 is finished! Time: 00:00:00
This is CoGAPS version 3.12.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
worker 2 is starting!
worker 3 is starting!
worker 1 is starting!
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worker 2 is finished! Time: 00:00:00
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worker 2 is starting!
worker 1 is starting!
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worker 3 is starting!
worker 2 is finished! Time: 00:00:00
worker 4 is finished! Time: 00:00:00
worker 1 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
This is CoGAPS version 3.12.0
Running single-cell CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 2 is starting!
worker 1 is starting!
worker 3 is starting!
worker 4 is starting!
worker 2 is finished! Time: 00:00:00
worker 1 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
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worker 2 is starting!
worker 1 is starting!
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worker 3 is starting!
worker 2 is finished! Time: 00:00:00
worker 1 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 3.12.0
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running Standard CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/Resources/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.12.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/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 5 is starting!
worker 2 is starting!
worker 3 is starting!
worker 4 is starting!
-- Equilibration Phase --
-- Sampling Phase --
worker 1 is finished! Time: 00:00:00
worker 5 is finished! Time: 00:00:00
worker 2 is finished! Time: 00:00:00
worker 4 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
This is CoGAPS version 3.12.0
Running genome-wide CoGAPS on /Library/Frameworks/R.framework/Versions/4.1/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!
worker 2 is starting!
Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
worker 1 is starting!
worker 5 is starting!
worker 4 is starting!
worker 2 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 finished! Time: 00:00:00
-- Equilibration Phase --
-- Sampling Phase --
worker 1 is finished! Time: 00:00:00
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)
[ FAIL 0 | WARN 7 | SKIP 3 | PASS 58 ]
>
> proc.time()
user system elapsed
44.119 13.896 31.793
CoGAPS.Rcheck/CoGAPS-Ex.timings
| name | user | system | elapsed | |
| CoGAPS | 0.470 | 0.017 | 0.492 | |
| CogapsParams | 0.002 | 0.001 | 0.004 | |
| GWCoGAPS | 0.000 | 0.001 | 0.001 | |
| binaryA-methods | 0.032 | 0.002 | 0.034 | |
| buildReport | 0.000 | 0.000 | 0.001 | |
| calcZ-methods | 0.028 | 0.002 | 0.030 | |
| checkpointsEnabled | 0.001 | 0.001 | 0.001 | |
| compiledWithOpenMPSupport | 0 | 0 | 0 | |
| getAmplitudeMatrix-methods | 0.028 | 0.002 | 0.029 | |
| getClusteredPatterns-methods | 0.028 | 0.002 | 0.030 | |
| getCorrelationToMeanPattern-methods | 0.028 | 0.002 | 0.030 | |
| getFeatureLoadings-methods | 0.032 | 0.002 | 0.034 | |
| getMeanChiSq-methods | 0.031 | 0.002 | 0.034 | |
| getOriginalParameters-methods | 0.029 | 0.001 | 0.030 | |
| getParam-methods | 0.001 | 0.000 | 0.001 | |
| getPatternMatrix-methods | 0.030 | 0.003 | 0.032 | |
| getRetinaSubset | 1.915 | 0.353 | 2.273 | |
| getSampleFactors-methods | 0.029 | 0.002 | 0.030 | |
| getSubsets-methods | 0.033 | 0.002 | 0.035 | |
| getUnmatchedPatterns-methods | 0.025 | 0.001 | 0.026 | |
| getVersion-methods | 0.028 | 0.001 | 0.028 | |
| patternMarkers-methods | 0.102 | 0.004 | 0.105 | |
| plotResiduals-methods | 0.025 | 0.001 | 0.026 | |
| reconstructGene-methods | 0.032 | 0.002 | 0.034 | |
| scCoGAPS | 0.001 | 0.000 | 0.001 | |
| setAnnotationWeights-methods | 0.003 | 0.000 | 0.003 | |
| setDistributedParams-methods | 0.002 | 0.000 | 0.002 | |
| setFixedPatterns-methods | 0.033 | 0.002 | 0.035 | |
| setParam-methods | 0.003 | 0.001 | 0.003 | |