Elana J. Fertig
| Snapshot Date: 2023-11-01 14:05:06 -0400 (Wed, 01 Nov 2023) |
| git_url: https://git.bioconductor.org/packages/CoGAPS |
| git_branch: RELEASE_3_18 |
| git_last_commit: 4118fd6 |
| git_last_commit_date: 2023-10-24 09:44:27 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-02 11:40:33 -0400 (Thu, 02 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4729 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4463 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4478 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4464 |
| 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 400/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CoGAPS 3.22.0 (landing page) Elana J. Fertig
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: CoGAPS |
| Version: 3.22.0 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings CoGAPS_3.22.0.tar.gz |
| StartedAt: 2023-11-02 09:27:56 -0000 (Thu, 02 Nov 2023) |
| EndedAt: 2023-11-02 09:34:21 -0000 (Thu, 02 Nov 2023) |
| EllapsedTime: 385.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CoGAPS.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --no-vignettes --timings CoGAPS_3.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/CoGAPS.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.22.0’
* 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: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
installed size is 31.8Mb
sub-directories of 1Mb or more:
extdata 19.9Mb
libs 11.1Mb
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getPatternHallmarks,CogapsResult: no visible binding for global
variable ‘.’
getPatternHallmarks,CogapsResult: no visible binding for global
variable ‘MsigDB_Hallmark’
getPatternHallmarks,CogapsResult: no visible binding for global
variable ‘padj’
plotPatternHallmarks,CogapsResult-list-numeric: no visible binding for
global variable ‘overlapGenes’
plotPatternHallmarks,CogapsResult-list-numeric: no visible binding for
global variable ‘padj’
show,CogapsParams: no visible binding for global variable
‘checkpointInFile’
Undefined global functions or variables:
. MsigDB_Hallmark checkpointInFile overlapGenes padj
* 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 ‘/home/biocbuild/R/R-4.3.1/site-library/CoGAPS/libs/CoGAPS.so’:
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Found ‘printf’, possibly from ‘printf’ (C)
Found ‘putchar’, possibly from ‘putchar’ (C)
Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Found ‘stdout’, possibly from ‘stdout’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes 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: 3 NOTEs
See
‘/home/biocbuild/bbs-3.18-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.
CoGAPS.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL CoGAPS
###
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* installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’
* installing *source* package ‘CoGAPS’ ...
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C++... yes
checking whether g++ -std=gnu++17 accepts -g... yes
checking for g++ -std=gnu++17 option to enable C++11 features... none needed
checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
checking whether the compiler supports GNU C++... (cached) yes
checking whether g++ -std=gnu++17 accepts -g... (cached) yes
checking for g++ -std=gnu++17 option to enable C++11 features... (cached) none needed
./configure: line 3246: AX_COMPILER_VENDOR: command not found
./configure: line 3247: AX_COMPILER_VERSION: command not found
./configure: line 3259: AX_OPENMP: command not found
building on compiler version
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c Cogaps.cpp -o Cogaps.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c GapsParameters.cpp -o GapsParameters.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c GapsResult.cpp -o GapsResult.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsRunner.cpp:8:
gibbs_sampler/AsynchronousGibbsSampler.h:105: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
105 | #pragma omp parallel for num_threads(nThreads)
|
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/algorithm/string/replace.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/date_facet.hpp:17,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/gregorian/gregorian.hpp:31,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/date_time/posix_time/posix_time.hpp:24,
from GapsRunner.cpp:27:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c GapsStatistics.cpp -o GapsStatistics.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c atomic/Atom.cpp -o atomic/Atom.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
atomic/ConcurrentAtomicDomain.cpp:64: warning: ignoring ‘#pragma omp critical’ [-Wunknown-pragmas]
64 | #pragma omp critical(AtomicInsertOrErase)
|
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
atomic/ProposalQueue.cpp:101: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas]
101 | #pragma omp atomic
|
atomic/ProposalQueue.cpp:107: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas]
107 | #pragma omp atomic
|
atomic/ProposalQueue.cpp:113: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas]
113 | #pragma omp atomic
|
atomic/ProposalQueue.cpp:119: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas]
119 | #pragma omp atomic
|
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c data_structures/HashSets.cpp -o data_structures/HashSets.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
data_structures/HybridVector.cpp:60: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas]
60 | #pragma omp atomic
|
data_structures/HybridVector.cpp:65: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas]
65 | #pragma omp atomic
|
data_structures/HybridVector.cpp:77: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas]
77 | #pragma omp atomic
|
data_structures/HybridVector.cpp:82: warning: ignoring ‘#pragma omp atomic’ [-Wunknown-pragmas]
82 | #pragma omp atomic
|
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c data_structures/Matrix.cpp -o data_structures/Matrix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c data_structures/Vector.cpp -o data_structures/Vector.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c file_parser/FileParser.cpp -o file_parser/FileParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
gibbs_sampler/DenseNormalModel.cpp:26: warning: ignoring ‘#pragma omp parallel’ [-Wunknown-pragmas]
26 | #pragma omp parallel for num_threads(nThreads)
|
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c math/Math.cpp -o math/Math.o
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/arg.hpp:25,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/placeholders.hpp:24,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/range/iterator_range_core.hpp:27,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/lexical_cast.hpp:30,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/convert_from_string.hpp:15,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/constants/constants.hpp:14,
from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/distributions/exponential.hpp:10,
from math/Math.cpp:4:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
194 | failed ************ (Pred::************
| ^
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of ‘assert_not_arg’ [-Wparentheses]
199 | failed ************ (boost::mpl::not_<Pred>::************
| ^
In file included from /home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/distributions/gamma.hpp:14,
from math/Math.cpp:5:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp: In instantiation of ‘boost::math::detail::upper_incomplete_gamma_fract<T>::result_type boost::math::detail::upper_incomplete_gamma_fract<T>::operator()() [with T = double; boost::math::detail::upper_incomplete_gamma_fract<T>::result_type = std::pair<double, double>]’:
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:217:20: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&, uintmax_t&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double; uintmax_t = long unsigned int]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/tools/fraction.hpp:252:31: required from ‘typename boost::math::tools::detail::fraction_traits<Gen>::result_type boost::math::tools::continued_fraction_a(Gen&, const U&) [with Gen = boost::math::detail::upper_incomplete_gamma_fract<double>; U = double; typename boost::math::tools::detail::fraction_traits<Gen>::result_type = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:314:68: required from ‘T boost::math::detail::upper_gamma_fraction(T, T, T) [with T = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:1176:44: required from ‘T boost::math::detail::gamma_incomplete_imp(T, T, bool, bool, const Policy&, T*) [with T = double; Policy = boost::math::policies::policy<boost::math::policies::promote_float<false>, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:2128:35: required from ‘typename boost::math::tools::promote_args<RT1, RT2>::type boost::math::gamma_p(RT1, RT2, const Policy&) [with RT1 = double; RT2 = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>; typename boost::math::tools::promote_args<RT1, RT2>::type = double]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/distributions/gamma.hpp:194:33: required from ‘RealType boost::math::cdf(const boost::math::gamma_distribution<RealType, Policy>&, const RealType&) [with RealType = double; Policy = boost::math::policies::policy<boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy, boost::math::policies::default_policy>]’
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/distributions/detail/derived_accessors.hpp:123:14: required from ‘typename Distribution::value_type boost::math::cdf(const Distribution&, const RealType&) [with Distribution = boost::math::gamma_distribution<>; RealType = float; typename Distribution::value_type = double]’
math/Math.cpp:52:22: required from here
/home/biocbuild/R/R-4.3.1/site-library/BH/include/boost/math/special_functions/gamma.hpp:299:16: note: parameter passing for argument of type ‘std::pair<double, double>’ when C++17 is enabled changed to match C++14 in GCC 10.1
299 | result_type operator()()
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c math/MatrixMath.cpp -o math/MatrixMath.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c math/Random.cpp -o math/Random.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -c math/VectorMath.cpp -o math/VectorMath.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.3.1/lib -L/usr/local/lib -o CoGAPS.so Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/Atom.o atomic/ConcurrentAtom.o atomic/AtomicDomain.o atomic/ConcurrentAtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CharacterDelimitedParser.o file_parser/FileParser.o file_parser/MatrixElement.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseNormalModel.o gibbs_sampler/SparseNormalModel.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o -L/home/biocbuild/R/R-4.3.1/lib -lR
installing to /home/biocbuild/R/R-4.3.1/site-library/00LOCK-CoGAPS/00new/CoGAPS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CoGAPS)
CoGAPS.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running genome-wide CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.22.0
Running genome-wide CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
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 3.22.0
Running genome-wide CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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This is CoGAPS version 3.22.0
Running single-cell CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 1 is starting!
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This is CoGAPS version 3.22.0
Running genome-wide CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
worker 1 is starting!
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This is CoGAPS version 3.22.0
Running single-cell CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 1 is starting!
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This is CoGAPS version 3.22.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.gct (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on testDataFrame (9 genes and 1363 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on testMatrix (9 genes and 1363 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.tsv (9 genes and 1363 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.gct (9 genes and 1363 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running genome-wide CoGAPS on /home/biocbuild/R/R-4.3.1/site-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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worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.22.0
Running genome-wide CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
worker 1 is starting!
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This is CoGAPS version 3.22.0
Running single-cell CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
worker 1 is starting!
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worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.22.0
Running single-cell CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 1 is starting!
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worker 3 is starting!
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worker 1 is finished! Time: 00:00:00
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This is CoGAPS version 3.22.0
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running Standard CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.22.0
Running genome-wide CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples) with parameters:
-- Standard Parameters --
nPatterns 3
nIterations 175
seed 42
sparseOptimization TRUE
distributed genome-wide
-- Sparsity Parameters --
alpha 0.01
maxGibbsMass 100
-- Distributed CoGAPS Parameters --
nSets 5
cut 4
minNS 3
maxNS 8
Creating subsets...using provided indexed subsets
set sizes (min, mean, max): (200, 200, 200)
Running Final Stage...
Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
worker 1 is starting!
worker 3 is starting!
worker 5 is starting!
-- Equilibration Phase --
-- Sampling Phase --
worker 1 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
worker 5 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 3.22.0
Running genome-wide CoGAPS on /home/biocbuild/R/R-4.3.1/site-library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples) with parameters:
-- Standard Parameters --
nPatterns 3
nIterations 175
seed 42
sparseOptimization TRUE
distributed genome-wide
-- Sparsity Parameters --
alpha 0.01
maxGibbsMass 100
-- Distributed CoGAPS Parameters --
nSets 5
cut 4
minNS 3
maxNS 8
Creating subsets...using provided indexed subsets
set sizes (min, mean, max): (200, 200, 200)
Running Final Stage...
Data Model: Sparse, Normal
Sampler Type: Sequential
Loading Data...Done! (00:00:00)
worker 1 is starting!
worker 3 is starting!
worker 5 is starting!
-- Equilibration Phase --
-- Sampling Phase --
worker 1 is finished! Time: 00:00:00
worker 3 is finished! Time: 00:00:00
worker 5 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
[ FAIL 0 | WARN 9 | SKIP 3 | PASS 58 ]
══ 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 9 | SKIP 3 | PASS 58 ]
>
> proc.time()
user system elapsed
52.855 11.624 51.709
CoGAPS.Rcheck/CoGAPS-Ex.timings
| name | user | system | elapsed | |
| CoGAPS | 0.404 | 1.267 | 2.744 | |
| CogapsParams | 0.003 | 0.000 | 0.003 | |
| GWCoGAPS | 0.000 | 0.000 | 0.001 | |
| binaryA-methods | 0.023 | 0.001 | 0.028 | |
| buildReport | 0.001 | 0.000 | 0.000 | |
| calcZ-methods | 0.021 | 0.000 | 0.022 | |
| checkpointsEnabled | 0 | 0 | 0 | |
| compiledWithOpenMPSupport | 0 | 0 | 0 | |
| getAmplitudeMatrix-methods | 0.022 | 0.000 | 0.021 | |
| getClusteredPatterns-methods | 0.015 | 0.007 | 0.022 | |
| getCorrelationToMeanPattern-methods | 0.023 | 0.000 | 0.022 | |
| getFeatureLoadings-methods | 0.022 | 0.000 | 0.022 | |
| getMeanChiSq-methods | 0.021 | 0.001 | 0.022 | |
| getOriginalParameters-methods | 0.021 | 0.000 | 0.022 | |
| getParam-methods | 0.000 | 0.001 | 0.001 | |
| getPatternMatrix-methods | 0.019 | 0.002 | 0.021 | |
| getRetinaSubset | 3.451 | 0.450 | 3.933 | |
| getSampleFactors-methods | 0.022 | 0.000 | 0.022 | |
| getSubsets-methods | 0.022 | 0.000 | 0.022 | |
| getUnmatchedPatterns-methods | 0.021 | 0.000 | 0.022 | |
| getVersion-methods | 0.021 | 0.000 | 0.021 | |
| patternMarkers-methods | 0.079 | 0.004 | 0.083 | |
| plotResiduals-methods | 0.016 | 0.004 | 0.021 | |
| reconstructGene-methods | 0.021 | 0.000 | 0.021 | |
| scCoGAPS | 0 | 0 | 0 | |
| setAnnotationWeights-methods | 0.003 | 0.000 | 0.003 | |
| setDistributedParams-methods | 0.002 | 0.001 | 0.002 | |
| setFixedPatterns-methods | 0.023 | 0.000 | 0.024 | |
| setParam-methods | 0.003 | 0.000 | 0.002 | |