Back to Multiple platform build/check report for BioC 3.9
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

INSTALL report for BioQC on tokay2

This page was generated on 2019-10-16 12:34:32 -0400 (Wed, 16 Oct 2019).

Package 166/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioQC 1.12.0
Jitao David Zhang
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/BioQC
Branch: RELEASE_3_9
Last Commit: 54cb13d
Last Changed Date: 2019-05-02 11:53:59 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  ERROR  skipped 
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] ERROR  skipped  skipped 
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  ERROR  skipped  skipped 

Summary

Package: BioQC
Version: 1.12.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/BioQC_1.12.0.tar.gz && rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioQC.buildbin-libdir BioQC_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BioQC_1.12.0.zip && rm BioQC_1.12.0.tar.gz BioQC_1.12.0.zip
StartedAt: 2019-10-15 18:48:39 -0400 (Tue, 15 Oct 2019)
EndedAt: 2019-10-15 18:49:32 -0400 (Tue, 15 Oct 2019)
EllapsedTime: 53.3 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/BioQC_1.12.0.tar.gz && rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioQC.buildbin-libdir BioQC_1.12.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL BioQC_1.12.0.zip && rm BioQC_1.12.0.tar.gz BioQC_1.12.0.zip
###
##############################################################################
##############################################################################


  % 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  590k  100  590k    0     0  8511k      0 --:--:-- --:--:-- --:--:-- 9525k

install for i386

* installing *source* package 'BioQC' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.9-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:155:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:188:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:257:0: 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-3~1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/BioQC.buildbin-libdir/00LOCK-BioQC/00new/BioQC/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpo79yBz/R.INSTALL115c37372277/BioQC/man/IndexList.Rd:6: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpo79yBz/R.INSTALL115c37372277/BioQC/man/IndexList.Rd:7: All text must be in a section
Warning: C:/Users/biocbuild/bbs-3.9-bioc/tmpdir/Rtmpo79yBz/R.INSTALL115c37372277/BioQC/man/IndexList.Rd:9: All text must be in a section
*** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'BioQC' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.9-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-3~1.9-B/R/include" -DNDEBUG `C:/Users/BIOCBU~1/BBS-3~1.9-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:155:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:188:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 ^
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:257:0: 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-3~1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/BioQC.buildbin-libdir/BioQC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioQC' as BioQC_1.12.0.zip
* DONE (BioQC)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'BioQC' successfully unpacked and MD5 sums checked