Elana J. Fertig
| Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022) |
| git_url: https://git.bioconductor.org/packages/CoGAPS |
| git_branch: master |
| git_last_commit: 79a489f |
| git_last_commit_date: 2022-03-15 18:11:04 -0400 (Tue, 15 Mar 2022) |
| Back to Multiple platform build/check report for BioC 3.15 |
|
This page was generated on 2022-03-18 11:07:14 -0400 (Fri, 18 Mar 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" | 4334 |
| riesling1 | Windows Server 2019 Standard | x64 | R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" | 4097 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" | 4083 |
| merida1 | macOS 10.14.6 Mojave | x86_64 | R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" | 4134 |
| 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 | ||||
|
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 367/2090 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CoGAPS 3.15.2 (landing page) Elana J. Fertig
| nebbiolo1 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| riesling1 | Windows Server 2019 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: CoGAPS |
| Version: 3.15.2 |
| Command: D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoGAPS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CoGAPS_3.15.2.tar.gz |
| StartedAt: 2022-03-17 18:46:30 -0400 (Thu, 17 Mar 2022) |
| EndedAt: 2022-03-17 18:53:12 -0400 (Thu, 17 Mar 2022) |
| EllapsedTime: 401.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: CoGAPS.Rcheck |
| Warnings: 2 |
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:CoGAPS.install-out.txt --library=D:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings CoGAPS_3.15.2.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.15-bioc/meat/CoGAPS.Rcheck'
* using R Under development (unstable) (2021-11-21 r81221)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'CoGAPS/DESCRIPTION' ... OK
* this is package 'CoGAPS' version '3.15.2'
* 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 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 'D:/biocbuild/bbs-3.15-bioc/meat/CoGAPS.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
installed size is 22.3Mb
sub-directories of 1Mb or more:
extdata 19.9Mb
libs 1.3Mb
* 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 for x64 is not available
File 'D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/libs/x64/CoGAPS.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (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
'D:/biocbuild/bbs-3.15-bioc/meat/CoGAPS.Rcheck/00check.log'
for details.
CoGAPS.Rcheck/00install.out
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###
### Running command:
###
### D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL CoGAPS
###
##############################################################################
##############################################################################
* installing to library 'D:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'CoGAPS' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c Cogaps.cpp -o Cogaps.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c GapsParameters.cpp -o GapsParameters.o
GapsParameters.cpp: In member function 'void GapsParameters::print() const':
GapsParameters.cpp:41:17: warning: format '%lu' expects argument of type 'long unsigned int', but argument 2 has type 'std::vector<unsigned int>::size_type' {aka 'long long unsigned int'} [-Wformat=]
gaps_printf("dataIndicesSubset.size(): %lu\n", dataIndicesSubset.size());
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c GapsResult.cpp -o GapsResult.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -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]
#pragma omp parallel for num_threads(nThreads)
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/algorithm/string/replace.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/date_facet.hpp:17,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian_io.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/gregorian/gregorian.hpp:31,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/posix_time/time_formatters.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/date_time/posix_time/posix_time.hpp:24,
from GapsRunner.cpp:27:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
D:/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]
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]
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]
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c GapsStatistics.cpp -o GapsStatistics.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c test-runner.cpp -o test-runner.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c atomic/Atom.cpp -o atomic/Atom.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c atomic/ConcurrentAtom.cpp -o atomic/ConcurrentAtom.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c atomic/ConcurrentAtomicDomain.cpp -o atomic/ConcurrentAtomicDomain.o
atomic/ConcurrentAtomicDomain.cpp:64: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
#pragma omp critical(AtomicInsertOrErase)
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o
atomic/ProposalQueue.cpp:101: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
#pragma omp atomic
atomic/ProposalQueue.cpp:107: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
#pragma omp atomic
atomic/ProposalQueue.cpp:113: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
#pragma omp atomic
atomic/ProposalQueue.cpp:119: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
#pragma omp atomic
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c data_structures/HashSets.cpp -o data_structures/HashSets.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o
data_structures/HybridVector.cpp:60: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
#pragma omp atomic
data_structures/HybridVector.cpp:65: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
#pragma omp atomic
data_structures/HybridVector.cpp:77: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
#pragma omp atomic
data_structures/HybridVector.cpp:82: warning: ignoring #pragma omp atomic [-Wunknown-pragmas]
#pragma omp atomic
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c data_structures/Matrix.cpp -o data_structures/Matrix.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c data_structures/Vector.cpp -o data_structures/Vector.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c file_parser/CharacterDelimitedParser.cpp -o file_parser/CharacterDelimitedParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c file_parser/FileParser.cpp -o file_parser/FileParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c file_parser/MatrixElement.cpp -o file_parser/MatrixElement.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c gibbs_sampler/DenseNormalModel.cpp -o gibbs_sampler/DenseNormalModel.o
gibbs_sampler/DenseNormalModel.cpp:26: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for num_threads(nThreads)
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c gibbs_sampler/SparseNormalModel.cpp -o gibbs_sampler/SparseNormalModel.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c math/Math.cpp -o math/Math.o
In file included from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
from D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/distributions/exponential.hpp:10,
from math/Math.cpp:4:
D:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
D:/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]
failed ************ (boost::mpl::not_<Pred>::************
^
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c math/MatrixMath.cpp -o math/MatrixMath.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c math/Random.cpp -o math/Random.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -DGAPS_DISABLE_CHECKPOINTS -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition -c math/VectorMath.cpp -o math/VectorMath.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CoGAPS.dll tmp.def 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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-CoGAPS/00new/CoGAPS/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'CoGAPS'
finding HTML links ... done
CoGAPS-package html
CoGAPS html
CogapsParams-class html
CogapsParams html
CogapsResult-class html
GIST.data_frame html
GIST.matrix html
GIST.result html
GIST.uncertainty html
GWCoGAPS html
binaryA-methods html
buildReport html
calcCoGAPSStat-methods html
calcGeneGSStat-methods html
calcZ-methods html
callInternalCoGAPS html
checkDataMatrix html
checkInputs html
checkpointsEnabled html
compiledWithOpenMPSupport html
computeGeneGSProb-methods html
convertDataToMatrix html
corcut html
corrToMeanPattern html
createCogapsResult html
createSets html
distributedCogaps html
findConsensusMatrix html
gapsCat html
getAmplitudeMatrix-methods html
getClusteredPatterns-methods html
getCorrelationToMeanPattern-methods html
getDimNames html
getFeatureLoadings-methods html
getGeneNames html
getMeanChiSq-methods html
getOriginalParameters-methods html
getParam-methods html
getPatternMatrix-methods html
getRetinaSubset html
getSampleFactors-methods html
getSampleNames html
getSubsets-methods html
getUnmatchedPatterns-methods html
getValueOrRds html
getVersion-methods html
initialize-CogapsParams-method html
initialize-CogapsResult-method html
isRdsFile html
ncolHelper html
nrowHelper html
parseExtraParams html
patternMarkers-methods html
patternMatch html
plotPatternMarkers-methods html
finding level-2 HTML links ... done
plotResiduals-methods html
reconstructGene-methods html
sampleUniformly html
sampleWithAnnotationWeights html
sampleWithExplictSets html
scCoGAPS html
setAnnotationWeights-methods html
setDistributedParams-methods html
setFixedPatterns-methods html
setParam-methods html
startupMessage html
stitchTogether html
supported html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CoGAPS)
Making 'packages.html' ... done
CoGAPS.Rcheck/tests/testthat.Rout
R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running genome-wide CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
worker 1 is starting!
worker 1 is finished! Time: 00:00:00
worker 2 is starting!
worker 2 is finished! Time: 00:00:00
worker 3 is starting!
worker 3 is finished! Time: 00:00:00
worker 4 is starting!
worker 4 is finished! Time: 00:00:00
worker 1 is starting!
worker 1 is finished! Time: 00:00:00
worker 2 is starting!
worker 2 is finished! Time: 00:00:00
worker 3 is starting!
worker 3 is finished! Time: 00:00:00
worker 4 is starting!
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.15.2
Running genome-wide CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
worker 1 is starting!
worker 1 is finished! Time: 00:00:00
worker 2 is starting!
worker 2 is finished! Time: 00:00:00
worker 3 is starting!
worker 3 is finished! Time: 00:00:00
worker 4 is starting!
worker 4 is finished! Time: 00:00:00
worker 1 is starting!
worker 1 is finished! Time: 00:00:00
worker 2 is starting!
worker 2 is finished! Time: 00:00:00
worker 3 is starting!
worker 3 is finished! Time: 00:00:00
worker 4 is starting!
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
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 3.15.2
Running genome-wide CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
worker 1 is starting!
worker 1 is finished! Time: 00:00:00
worker 2 is starting!
worker 2 is finished! Time: 00:00:00
worker 3 is starting!
worker 3 is finished! Time: 00:00:00
worker 4 is starting!
worker 4 is finished! Time: 00:00:00
worker 1 is starting!
worker 1 is finished! Time: 00:00:00
worker 2 is starting!
worker 2 is finished! Time: 00:00:00
worker 3 is starting!
worker 3 is finished! Time: 00:00:00
worker 4 is starting!
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.15.2
Running single-cell CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 1 is starting!
worker 1 is finished! Time: 00:00:00
worker 2 is starting!
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This is CoGAPS version 3.15.2
Running genome-wide CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
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worker 4 is starting!
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.15.2
Running single-cell CoGAPS on D:/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 4 is starting!
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.15.2
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.gct (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on testDataFrame (9 genes and 1363 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on testMatrix (9 genes and 1363 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (9 genes and 1363 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.tsv (9 genes and 1363 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.gct (9 genes and 1363 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on testDataFrame (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running genome-wide CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
worker 1 is starting!
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worker 4 is starting!
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.15.2
Running genome-wide CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.tsv (1363 genes and 9 samples)
worker 1 is starting!
worker 1 is finished! Time: 00:00:00
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worker 4 is starting!
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.15.2
Running single-cell CoGAPS on D:/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 2 is finished! Time: 00:00:00
worker 3 is starting!
worker 3 is finished! Time: 00:00:00
worker 4 is starting!
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.15.2
Running single-cell CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.mtx (9 genes and 1363 samples)
worker 1 is starting!
worker 1 is finished! Time: 00:00:00
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worker 3 is finished! Time: 00:00:00
worker 4 is starting!
worker 4 is finished! Time: 00:00:00
This is CoGAPS version 3.15.2
Running Standard CoGAPS on testMatrix (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running Standard CoGAPS on D:/biocbuild/bbs-3.15-bioc/R/library/CoGAPS/extdata/GIST.csv (1363 genes and 9 samples)
This is CoGAPS version 3.15.2
Running genome-wide CoGAPS on D:/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! (00:00:02)
worker 1 is starting!
-- Equilibration Phase --
-- Sampling Phase --
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worker 5 is finished! Time: 00:00:00
This is CoGAPS version 3.15.2
Running genome-wide CoGAPS on D:/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! (00:00:01)
worker 1 is starting!
-- Equilibration Phase --
-- Sampling Phase --
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[ FAIL 0 | WARN 19 | SKIP 3 | PASS 58 ]
== Skipped tests ===============================================================
* empty test (3)
[ FAIL 0 | WARN 19 | SKIP 3 | PASS 58 ]
>
> proc.time()
user system elapsed
141.95 102.32 244.32
CoGAPS.Rcheck/CoGAPS-Ex.timings
| name | user | system | elapsed | |
| CoGAPS | 1.39 | 1.12 | 2.52 | |
| CogapsParams | 0 | 0 | 0 | |
| GWCoGAPS | 0 | 0 | 0 | |
| binaryA-methods | 0.01 | 0.00 | 0.02 | |
| buildReport | 0 | 0 | 0 | |
| calcZ-methods | 0.02 | 0.02 | 0.03 | |
| checkpointsEnabled | 0 | 0 | 0 | |
| compiledWithOpenMPSupport | 0 | 0 | 0 | |
| getAmplitudeMatrix-methods | 0.02 | 0.00 | 0.02 | |
| getClusteredPatterns-methods | 0.01 | 0.00 | 0.01 | |
| getCorrelationToMeanPattern-methods | 0.01 | 0.00 | 0.01 | |
| getFeatureLoadings-methods | 0.02 | 0.00 | 0.02 | |
| getMeanChiSq-methods | 0.03 | 0.00 | 0.03 | |
| getOriginalParameters-methods | 0.02 | 0.00 | 0.02 | |
| getParam-methods | 0 | 0 | 0 | |
| getPatternMatrix-methods | 0.01 | 0.01 | 0.03 | |
| getRetinaSubset | 1.56 | 1.21 | 2.76 | |
| getSampleFactors-methods | 0.03 | 0.00 | 0.03 | |
| getSubsets-methods | 0.02 | 0.00 | 0.02 | |
| getUnmatchedPatterns-methods | 0.02 | 0.01 | 0.03 | |
| getVersion-methods | 0.03 | 0.00 | 0.03 | |
| patternMarkers-methods | 0.06 | 0.00 | 0.07 | |
| plotResiduals-methods | 0.02 | 0.02 | 0.03 | |
| reconstructGene-methods | 0.01 | 0.01 | 0.03 | |
| scCoGAPS | 0 | 0 | 0 | |
| setAnnotationWeights-methods | 0 | 0 | 0 | |
| setDistributedParams-methods | 0 | 0 | 0 | |
| setFixedPatterns-methods | 0.03 | 0.00 | 0.03 | |
| setParam-methods | 0 | 0 | 0 | |