Elana J. Fertig
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/CoGAPS |
| Branch: RELEASE_3_7 |
| Last Commit: 9d82c1f |
| Last Changed Date: 2018-07-26 15:59:34 -0400 (Thu, 26 Jul 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:34:51 -0400 (Wed, 17 Oct 2018).
| Package 287/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CoGAPS 3.0.2 Elana J. Fertig
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CoGAPS |
| Version: 3.0.2 |
| Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoGAPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CoGAPS_3.0.2.tar.gz |
| StartedAt: 2018-10-17 01:16:25 -0400 (Wed, 17 Oct 2018) |
| EndedAt: 2018-10-17 01:21:31 -0400 (Wed, 17 Oct 2018) |
| EllapsedTime: 306.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: CoGAPS.Rcheck |
| Warnings: 0 |
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### Running command:
###
### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:CoGAPS.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings CoGAPS_3.0.2.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/CoGAPS.Rcheck'
* using R version 3.5.1 Patched (2018-07-24 r75005)
* 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 '3.0.2'
* 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 ... OK
* checking installed package size ... OK
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
GWCoGapsFromCheckpoint: no visible binding for global variable 'i'
GWCoGapsFromCheckpoint: no visible binding for global variable
'sampleS'
cellMatchR: no visible binding for global variable 'cluster.method'
patternMatcher : <anonymous>: no visible binding for global variable
'Samples'
patternMatcher : <anonymous>: no visible binding for global variable
'value'
patternMatcher : <anonymous>: no visible binding for global variable
'BySet'
runFinalPhase: no visible binding for global variable 'i'
runFinalPhase: no visible binding for global variable 'sampleS'
runInitialPhase: no visible binding for global variable 'i'
runInitialPhase: no visible binding for global variable 'sampleS'
scCoGapsFromCheckpoint: no visible binding for global variable 'i'
scCoGapsFromCheckpoint: no visible binding for global variable
'sampleS'
sc_runFinalPhase: no visible binding for global variable 'i'
sc_runFinalPhase: no visible binding for global variable 'sampleS'
sc_runInitialPhase: no visible binding for global variable 'i'
sc_runInitialPhase: no visible binding for global variable 'sampleS'
Undefined global functions or variables:
BySet Samples cluster.method i sampleS value
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/CoGAPS/libs/i386/CoGAPS.dll':
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Found 'printf', possibly from 'printf' (C)
Found 'rand', possibly from 'rand' (C)
Found 'srand', possibly from 'srand' (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 ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotDiag 104.75 5.97 110.78
GWCoGapsFromCheckpoint 0.08 0.03 6.07
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotDiag 91.80 5.86 97.67
GWCoGapsFromCheckpoint 0.08 0.00 5.76
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R'
OK
** running tests for arch 'x64' ...
Running 'testthat.R'
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
'C:/Users/biocbuild/bbs-3.7-bioc/meat/CoGAPS.Rcheck/00check.log'
for details.
CoGAPS.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/CoGAPS_3.0.2.tar.gz && rm -rf CoGAPS.buildbin-libdir && mkdir CoGAPS.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CoGAPS.buildbin-libdir CoGAPS_3.0.2.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL CoGAPS_3.0.2.zip && rm CoGAPS_3.0.2.tar.gz CoGAPS_3.0.2.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 1176k 100 1176k 0 0 17.4M 0 --:--:-- --:--:-- --:--:-- 19.4M
install for i386
* installing *source* package 'CoGAPS' ...
** libs
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Algorithms.cpp -o Algorithms.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c AtomicSupport.cpp -o AtomicSupport.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Cogaps.cpp -o Cogaps.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GibbsSampler.cpp -o GibbsSampler.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Matrix.cpp -o Matrix.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Random.cpp -o Random.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testAlgorithms.cpp -o cpp_tests/testAlgorithms.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testAtomicSupport.cpp -o cpp_tests/testAtomicSupport.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testGibbsSampler.cpp -o cpp_tests/testGibbsSampler.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testMatrix.cpp -o cpp_tests/testMatrix.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testRandom.cpp -o cpp_tests/testRandom.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testSerialization.cpp -o cpp_tests/testSerialization.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def Algorithms.o AtomicSupport.o Cogaps.o GibbsSampler.o Matrix.o Random.o RcppExports.o test-runner.o cpp_tests/testAlgorithms.o cpp_tests/testAtomicSupport.o cpp_tests/testGibbsSampler.o cpp_tests/testMatrix.o cpp_tests/testRandom.o cpp_tests/testSerialization.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/i386
** 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
CoGapsFromCheckpoint html
GIST.D html
GIST.S html
GSets html
GWCoGAPS html
GWCoGapsFromCheckpoint html
SimpSim.A html
SimpSim.D html
SimpSim.P html
SimpSim.S html
SimpSim.result html
binaryA html
calcCoGAPSStat html
calcGeneGSStat html
calcZ html
cellMatchR html
computeGeneGSProb html
createGWCoGAPSSets html
createscCoGAPSSets html
displayBuildReport html
gapsMapRun html
gapsRun html
generateSeeds html
patternMarkers html
patternMatch4Parallel html
patternMatcher html
plotAtoms html
plotDiag html
plotGAPS html
plotP html
plotPatternMarkers html
finding level-2 HTML links ... done
plotSmoothPatterns html
postFixed4Parallel html
postFixed4SC html
reOrderBySet html
reconstructGene html
reorderByPatternMatch html
residuals html
scCoGAPS html
scCoGapsFromCheckpoint html
tf2ugFC html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'CoGAPS' ...
** libs
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Algorithms.cpp -o Algorithms.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c AtomicSupport.cpp -o AtomicSupport.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Cogaps.cpp -o Cogaps.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c GibbsSampler.cpp -o GibbsSampler.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Matrix.cpp -o Matrix.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c Random.cpp -o Random.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c test-runner.cpp -o test-runner.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testAlgorithms.cpp -o cpp_tests/testAlgorithms.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testAtomicSupport.cpp -o cpp_tests/testAtomicSupport.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testGibbsSampler.cpp -o cpp_tests/testGibbsSampler.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testMatrix.cpp -o cpp_tests/testMatrix.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testRandom.cpp -o cpp_tests/testRandom.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/BH/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c cpp_tests/testSerialization.cpp -o cpp_tests/testSerialization.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o CoGAPS.dll tmp.def Algorithms.o AtomicSupport.o Cogaps.o GibbsSampler.o Matrix.o Random.o RcppExports.o test-runner.o cpp_tests/testAlgorithms.o cpp_tests/testAtomicSupport.o cpp_tests/testGibbsSampler.o cpp_tests/testMatrix.o cpp_tests/testRandom.o cpp_tests/testSerialization.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/CoGAPS.buildbin-libdir/CoGAPS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'CoGAPS' as CoGAPS_3.0.2.zip
* DONE (CoGAPS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'CoGAPS' successfully unpacked and MD5 sums checked
In R CMD INSTALL
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CoGAPS.Rcheck/tests_i386/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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)
Loading required package: Rcpp
Attaching package: 'CoGAPS'
The following object is masked from 'package:stats':
residuals
>
> test_check("CoGAPS")
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
is a Catch v1.10.0 host application.
Run with -? for options
-------------------------------------------------------------------------------
Test Archive.h
Random Generator Serialization
-------------------------------------------------------------------------------
cpp_tests/testSerialization.cpp:162
...............................................................................
cpp_tests/testSerialization.cpp:195: FAILED:
REQUIRE( gaps::random::normal(0.0, 2.0) == randSequence[i++] )
with expansion:
1.60336f == 1.60336f
-------------------------------------------------------------------------------
Test GibbsSampler.h
GibbsSampler Statistics
-------------------------------------------------------------------------------
cpp_tests/testGibbsSampler.cpp:57
...............................................................................
cpp_tests/testGibbsSampler.cpp:105: FAILED:
REQUIRE( sampler.meanChiSq() == Approx(8371.568).epsilon(0.001) )
with expansion:
11813.09766f == Approx( 8371.568 )
-------------------------------------------------------------------------------
Test Algorithms.h
mean
-------------------------------------------------------------------------------
cpp_tests/testAlgorithms.cpp:43
...............................................................................
cpp_tests/testAlgorithms.cpp:45: FAILED:
REQUIRE( gaps::algo::mean(D) == Dsum / (nrow * ncol) )
with expansion:
2.15f == 2.15f
===============================================================================
test cases: 7 | 4 passed | 3 failed
assertions: 93508 | 93505 passed | 3 failed
== testthat results ===========================================================
OK: 0 SKIPPED: 2 FAILED: 0
>
> proc.time()
user system elapsed
1.81 0.20 2.10
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CoGAPS.Rcheck/tests_x64/testthat.Rout
R version 3.5.1 Patched (2018-07-24 r75005) -- "Feather Spray"
Copyright (C) 2018 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)
Loading required package: Rcpp
Attaching package: 'CoGAPS'
The following object is masked from 'package:stats':
residuals
>
> test_check("CoGAPS")
˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
is a Catch v1.10.0 host application.
Run with -? for options
-------------------------------------------------------------------------------
Test GibbsSampler.h
GibbsSampler Statistics
-------------------------------------------------------------------------------
cpp_tests/testGibbsSampler.cpp:57
...............................................................................
cpp_tests/testGibbsSampler.cpp:105: FAILED:
REQUIRE( sampler.meanChiSq() == Approx(8371.568).epsilon(0.001) )
with expansion:
11813.07031f == Approx( 8371.568 )
===============================================================================
test cases: 7 | 6 passed | 1 failed
assertions: 94506 | 94505 passed | 1 failed
== testthat results ===========================================================
OK: 0 SKIPPED: 2 FAILED: 0
>
> proc.time()
user system elapsed
1.87 0.14 2.12
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CoGAPS.Rcheck/examples_i386/CoGAPS-Ex.timings
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CoGAPS.Rcheck/examples_x64/CoGAPS-Ex.timings
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