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INSTALL report for BioQC on tokay2

This page was generated on 2018-10-17 08:41:25 -0400 (Wed, 17 Oct 2018).

Package 146/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioQC 1.8.0
Jitao David Zhang
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/BioQC
Branch: RELEASE_3_7
Last Commit: f043d16
Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BioQC
Version: 1.8.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/BioQC_1.8.0.tar.gz && rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioQC.buildbin-libdir BioQC_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL BioQC_1.8.0.zip && rm BioQC_1.8.0.tar.gz BioQC_1.8.0.zip
StartedAt: 2018-10-16 18:40:43 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 18:41:46 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 63.0 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/BioQC_1.8.0.tar.gz && rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioQC.buildbin-libdir BioQC_1.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL BioQC_1.8.0.zip && rm BioQC_1.8.0.tar.gz BioQC_1.8.0.zip
###
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install for i386

* installing *source* package 'BioQC' ...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c gini.c -o gini.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c read_gmt.cpp -o read_gmt.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c stat_rank.c -o stat_rank.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:105:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'wmw_test':
wmw_test.c:152:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:185:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:248:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BioQC.dll tmp.def gini.o init.o read_gmt.o stat_rank.o wmw_test.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/BioQC.buildbin-libdir/BioQC/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BioQC'
    finding HTML links ... done
    BaseIndexList-class                     html  
    GmtList-class                           html  
    GmtList                                 html  
    IndexList-class                         html  
    IndexList                               html  
    SignedGenesets-class                    html  
    SignedGenesets                          html  
    SignedIndexList-class                   html  
    SignedIndexList                         html  
    absLog10p                               html  
    as.gmtlist                              html  
    entropy                                 html  
    filterPmat                              html  
    gini                                    html  
    gmtlist2signedGenesets                  html  
    matchGenes                              html  
    offset-BaseIndexList-method             html  
    offset-set                              html  
    readGmt                                 html  
    readSignedGmt                           html  
    simplifyMatrix                          html  
    valTypes                                html  
    wmwTest                                 html  
    wmwTestInR                              html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'BioQC' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c gini.c -o gini.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c init.c -o init.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c read_gmt.cpp -o read_gmt.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c stat_rank.c -o stat_rank.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG `C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/Rscript -e 'Rcpp:::CxxFlags()'`    -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:105:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'wmw_test':
wmw_test.c:152:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:185:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:248:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BioQC.dll tmp.def gini.o init.o read_gmt.o stat_rank.o wmw_test.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/BioQC.buildbin-libdir/BioQC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioQC' as BioQC_1.8.0.zip
* DONE (BioQC)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'BioQC' successfully unpacked and MD5 sums checked
In R CMD INSTALL