Back to Multiple platform build/check report for BioC 3.15
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This page was generated on 2022-06-24 12:04:38 -0400 (Fri, 24 Jun 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4380
palomino3Windows Server 2022 Datacenterx644.2.0 (2022-04-22 ucrt) -- "Vigorous Calisthenics" 4156
merida1macOS 10.14.6 Mojavex86_644.2.0 (2022-04-22) -- "Vigorous Calisthenics" 4221
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for CoGAPS on nebbiolo1


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 377/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CoGAPS 3.16.0  (landing page)
Elana J. Fertig
Snapshot Date: 2022-06-23 13:55:15 -0400 (Thu, 23 Jun 2022)
git_url: https://git.bioconductor.org/packages/CoGAPS
git_branch: RELEASE_3_15
git_last_commit: 64e95af
git_last_commit_date: 2022-04-26 11:05:27 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: CoGAPS
Version: 3.16.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CoGAPS_3.16.0.tar.gz
StartedAt: 2022-06-23 19:21:15 -0400 (Thu, 23 Jun 2022)
EndedAt: 2022-06-23 19:24:16 -0400 (Thu, 23 Jun 2022)
EllapsedTime: 181.5 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: CoGAPS.Rcheck
Warnings: 2

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:CoGAPS.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings CoGAPS_3.16.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/CoGAPS.Rcheck’
* using R version 4.2.0 (2022-04-22)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CoGAPS/DESCRIPTION’ ... OK
* this is package ‘CoGAPS’ version ‘3.16.0’
* 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 ... WARNING
Found the following significant warnings:
  GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
See ‘/home/biocbuild/bbs-3.15-bioc/meat/CoGAPS.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 26.2Mb
  sub-directories of 1Mb or more:
    extdata  19.7Mb
    libs      5.8Mb
* 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 ... NOTE
plot.CogapsResult: no visible global function definition for ‘axis’
plot.CogapsResult: no visible global function definition for ‘text’
plot.CogapsResult: no visible global function definition for ‘par’
Undefined global functions or variables:
  axis par text
Consider adding
  importFrom("graphics", "axis", "par", "text")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'plotPatternMarkers':
plotPatternMarkers
  Code: function(object, data, patternMarkers, patternPalette,
                 sampleNames, samplePalette = NULL, heatmapCol =
                 bluered, colDendrogram = TRUE, scale = "row", ...)
  Docs: function(object, data, patternPalette, sampleNames,
                 samplePalette = NULL, heatmapCol = bluered,
                 colDenogram = TRUE, scale = "row", ...)
  Argument names in code not in docs:
    patternMarkers colDendrogram
  Argument names in docs not in code:
    colDenogram
  Mismatches in argument names (first 3):
    Position: 3 Code: patternMarkers Docs: patternPalette
    Position: 4 Code: patternPalette Docs: sampleNames
    Position: 5 Code: sampleNames Docs: samplePalette

* 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/bbs-3.15-bioc/R/library/CoGAPS/libs/CoGAPS.so’:
  Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
  Found ‘__printf_chk’, possibly from ‘printf’ (C)
  Found ‘putchar’, possibly from ‘putchar’ (C)
  Found ‘puts’, possibly from ‘printf’ (C), ‘puts’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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 WARNINGs, 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/CoGAPS.Rcheck/00check.log’
for details.



Installation output

CoGAPS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL CoGAPS
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/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 g++ -std=gnu++14 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++14 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++14 accepts -g... (cached) yes
./configure: line 2721: AX_COMPILER_VENDOR: command not found
./configure: line 2722: AX_COMPILER_VERSION: command not found
./configure: line 2733: AX_OPENMP: command not found
building on  compiler version 
Using AVX instructions if available
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c Cogaps.cpp -o Cogaps.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsParameters.cpp -o GapsParameters.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsResult.cpp -o GapsResult.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsRunner.cpp -o GapsRunner.o
In file included from GapsRunner.cpp:8:
gibbs_sampler/AsynchronousGibbsSampler.h:105: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  105 |         #pragma omp parallel for num_threads(nThreads)
      | 
In file included from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/replace.hpp:16,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/date_facet.hpp:17,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian.hpp:31,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time.hpp:24,
                 from GapsRunner.cpp:27:
/home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.15-bioc/R/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>::************
      |                     ^
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<SparseNormalModel>; DataType = Matrix]’:
GapsRunner.cpp:70:73:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = Matrix]’
GapsRunner.cpp:85:48:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
  430 |     switch (phase)
      |     ^~~~~~
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<SparseNormalModel>; DataType = Matrix]’:
GapsRunner.cpp:74:71:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = Matrix]’
GapsRunner.cpp:85:48:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<DenseNormalModel>; DataType = Matrix]’:
GapsRunner.cpp:70:73:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = Matrix]’
GapsRunner.cpp:88:43:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<DenseNormalModel>; DataType = Matrix]’:
GapsRunner.cpp:74:71:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = Matrix]’
GapsRunner.cpp:88:43:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = Matrix]’
GapsRunner.cpp:113:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<SparseNormalModel>; DataType = std::__cxx11::basic_string<char>]’:
GapsRunner.cpp:70:73:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:85:48:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<SparseNormalModel>; DataType = std::__cxx11::basic_string<char>]’:
GapsRunner.cpp:74:71:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = SparseNormalModel; DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:85:48:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = AsynchronousGibbsSampler<DenseNormalModel>; DataType = std::__cxx11::basic_string<char>]’:
GapsRunner.cpp:70:73:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:88:43:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
GapsRunner.cpp: In instantiation of ‘GapsResult runCoGAPSAlgorithm(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with Sampler = SingleThreadedGibbsSampler<DenseNormalModel>; DataType = std::__cxx11::basic_string<char>]’:
GapsRunner.cpp:74:71:   required from ‘GapsResult chooseSampler(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataModel = DenseNormalModel; DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:88:43:   required from ‘GapsResult chooseDataModel(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:104:27:   required from ‘GapsResult run_helper(const DataType&, GapsParameters&, const DataType&, GapsRandomState*) [with DataType = std::__cxx11::basic_string<char>]’
GapsRunner.cpp:119:59:   required from here
GapsRunner.cpp:430:5: warning: enumeration value ‘GAPS_ALL_PHASES’ not handled in switch [-Wswitch]
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c GapsStatistics.cpp -o GapsStatistics.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c test-runner.cpp -o test-runner.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/Atom.cpp -o atomic/Atom.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -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++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -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++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/HashSets.cpp -o data_structures/HashSets.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -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++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/Matrix.cpp -o data_structures/Matrix.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c data_structures/Vector.cpp -o data_structures/Vector.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/FileParser.cpp -o file_parser/FileParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -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++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/Math.cpp -o math/Math.o
In file included from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
                 from /home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/distributions/exponential.hpp:10,
                 from math/Math.cpp:4:
/home/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.15-bioc/R/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++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/MatrixMath.cpp -o math/MatrixMath.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/Random.cpp -o math/Random.o
g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -DGAPS_DISABLE_CHECKPOINTS -D__GAPS_R_BUILD__ -Iinclude -I'/home/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I/usr/local/include  -march=native  -fpic  -g -O2  -Wall -c math/VectorMath.cpp -o math/VectorMath.o
g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.15-bioc/R/lib -L/usr/local/lib -o CoGAPS.so Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/Atom.o atomic/ConcurrentAtom.o atomic/AtomicDomain.o atomic/ConcurrentAtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CharacterDelimitedParser.o file_parser/FileParser.o file_parser/MatrixElement.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseNormalModel.o gibbs_sampler/SparseNormalModel.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o -L/home/biocbuild/bbs-3.15-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CoGAPS/00new/CoGAPS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CoGAPS)

Tests output

CoGAPS.Rcheck/tests/testthat.Rout


R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 2 is finished! Time: 00:00:00
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    worker 1 is starting!
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    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 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.16.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 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 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    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 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
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 3.16.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 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 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 1 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 4 is starting!
    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 3.16.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/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 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    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 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.16.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 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
    worker 3 is finished! Time: 00:00:00
    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 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.16.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
    worker 4 is starting!
    worker 2 is starting!
    worker 3 is starting!
    worker 1 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 3 is finished! Time: 00:00:00
    worker 2 is finished! Time: 00:00:00
    worker 2 is starting!
    worker 1 is starting!
    worker 4 is starting!
    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 3.16.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.gct (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on testDataFrame (9 genes and 1363 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on testMatrix (9 genes and 1363 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.tsv (9 genes and 1363 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.gct (9 genes and 1363 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
    worker 1 is starting!
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This is CoGAPS version 3.16.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
    worker 1 is starting!
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This is CoGAPS version 3.16.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
    worker 1 is starting!
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    worker 1 is finished! Time: 00:00:00
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    worker 2 is finished! Time: 00:00:00
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    worker 1 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00

This is CoGAPS version 3.16.0 
Running single-cell CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
    worker 1 is starting!
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    worker 1 is finished! Time: 00:00:00
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    worker 4 is starting!
    worker 3 is finished! Time: 00:00:00
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This is CoGAPS version 3.16.0 
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running Standard CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)

This is CoGAPS version 3.16.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/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!
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    worker 3 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 4 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 5 is starting!
    worker 3 is finished! Time: 00:00:00
    worker 4 is finished! Time: 00:00:00
    worker 5 is finished! Time: 00:00:00

This is CoGAPS version 3.16.0 
Running genome-wide CoGAPS on /home/biocbuild/bbs-3.15-bioc/R/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 2 is starting!
    worker 3 is starting!
-- Equilibration Phase --
-- Sampling Phase --
    worker 1 is finished! Time: 00:00:00
    worker 5 is starting!
    worker 4 is starting!
    worker 2 is finished! Time: 00:00:00
    worker 5 is finished! Time: 00:00:00
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    worker 4 is finished! Time: 00:00:00
[ FAIL 0 | WARN 7 | SKIP 3 | PASS 58 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (3)

[ FAIL 0 | WARN 7 | SKIP 3 | PASS 58 ]
> 
> proc.time()
   user  system elapsed 
 51.117  22.156  32.045 

Example timings

CoGAPS.Rcheck/CoGAPS-Ex.timings

nameusersystemelapsed
CoGAPS0.2490.0150.268
CogapsParams0.0020.0000.002
GWCoGAPS000
binaryA-methods0.0210.0030.024
buildReport000
calcZ-methods0.0200.0040.024
checkpointsEnabled000
compiledWithOpenMPSupport0.0000.0010.000
getAmplitudeMatrix-methods0.0180.0060.024
getClusteredPatterns-methods0.0260.0010.026
getCorrelationToMeanPattern-methods0.0410.0000.041
getFeatureLoadings-methods0.0200.0030.024
getMeanChiSq-methods0.0250.0000.025
getOriginalParameters-methods0.0250.0000.025
getParam-methods0.0000.0000.001
getPatternMatrix-methods0.0240.0000.024
getRetinaSubset2.1280.5592.691
getSampleFactors-methods0.0250.0000.026
getSubsets-methods0.0170.0080.025
getUnmatchedPatterns-methods0.0280.0120.041
getVersion-methods0.0250.0000.025
patternMarkers-methods0.0510.0040.056
plotResiduals-methods0.0250.0000.025
reconstructGene-methods0.0240.0000.024
scCoGAPS000
setAnnotationWeights-methods0.0020.0000.001
setDistributedParams-methods0.0020.0000.001
setFixedPatterns-methods0.0260.0000.025
setParam-methods0.0010.0000.001