Back to Multiple platform build/check report for BioC 3.14
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2021-10-19 12:04:48 -0400 (Tue, 19 Oct 2021).

INSTALL results for BioQC on riesling1

To the developers/maintainers of the BioQC package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BioQC.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.

raw results

Package 187/2060HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BioQC 1.21.4  (landing page)
Jitao David Zhang
Snapshot Date: 2021-10-18 14:50:10 -0400 (Mon, 18 Oct 2021)
git_url: https://git.bioconductor.org/packages/BioQC
git_branch: master
git_last_commit: 91a7127
git_last_commit_date: 2021-08-18 08:15:12 -0400 (Wed, 18 Aug 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: BioQC
Version: 1.21.4
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BioQC_1.21.4.tar.gz && rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioQC.buildbin-libdir BioQC_1.21.4.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BioQC_1.21.4.zip && rm BioQC_1.21.4.tar.gz BioQC_1.21.4.zip
StartedAt: 2021-10-18 16:56:04 -0400 (Mon, 18 Oct 2021)
EndedAt: 2021-10-18 16:59:05 -0400 (Mon, 18 Oct 2021)
EllapsedTime: 181.1 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/BioQC_1.21.4.tar.gz && rm -rf BioQC.buildbin-libdir && mkdir BioQC.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BioQC.buildbin-libdir BioQC_1.21.4.tar.gz && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL BioQC_1.21.4.zip && rm BioQC_1.21.4.tar.gz BioQC_1.21.4.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
 63 4348k   63 2760k    0     0  5074k      0 --:--:-- --:--:-- --:--:-- 5065k
100 4348k  100 4348k    0     0  6090k      0 --:--:-- --:--:-- --:--:-- 6081k

install for i386

* installing *source* package 'BioQC' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gini.c -o gini.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_gmt.cpp -o read_gmt.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c stat_rank.c -o stat_rank.o
"C:/rtools40/mingw32/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:118: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'wmw_test':
wmw_test.c:168: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:201: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:270: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -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 -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/BioQC.buildbin-libdir/00LOCK-BioQC/00new/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  
    appendGmtList                           html  
    as.GmtList                              html  
    entropy                                 html  
    entropyDiversity                        html  
    entropySpecificity                      html  
    filterBySize                            html  
    filterPmat                              html  
    getLeadingEdgeIndexFromVector           html  
    gini                                    html  
    gmtlist2signedGenesets                  html  
    gsDesc                                  html  
    gsGeneCount                             html  
    gsGenes                                 html  
    gsName                                  html  
    gsNamespace                             html  
    hasNamespace                            html  
    isValidBaseIndexList                    html  
    isValidGmtList                          html  
    isValidIndexList                        html  
    isValidSignedGenesets                   html  
    isValidSignedIndexList                  html  
    matchGenes                              html  
    offset-set                              html  
    offset                                  html  
    prettySigNames                          html  
    readCurrentSignatures                   html  
    readGmt                                 html  
    readSignedGmt                           html  
    sampleSpecialization                    html  
    setDescAsNamespace                      html  
    setGsNamespace                          html  
    setNamespace                            html  
    show-GmtList-method                     html  
    show-IndexList-method                   html  
    show-SignedGenesets-method              html  
    show-SignedIndexList-method             html  
    simplifyMatrix                          html  
    sub-.GmtList                            html  
    sub-sub-.GmtList                        html  
    uniqGenesetsByNamespace                 html  
    valTypes                                html  
    wmwLeadingEdge                          html  
    wmwTest                                 html  
    wmwTestInR                              html  
*** copying figures
** 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:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c gini.c -o gini.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c init.c -o init.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_gmt.cpp -o read_gmt.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c stat_rank.c -o stat_rank.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG `D:/biocbuild/bbs-3.14-bioc/R/bin/Rscript -e 'Rcpp:::CxxFlags()'` -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c wmw_test.c -o wmw_test.o
wmw_test.c: In function 'wmw_test_list':
wmw_test.c:118: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'wmw_test':
wmw_test.c:168: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'signed_wmw_test_list':
wmw_test.c:201: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
wmw_test.c: In function 'signed_wmw_test':
wmw_test.c:270: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
 #pragma omp parallel for
 
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -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 -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/BioQC.buildbin-libdir/BioQC/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BioQC' as BioQC_1.21.4.zip
* DONE (BioQC)
* installing to library 'D:/biocbuild/bbs-3.14-bioc/R/library'
package 'BioQC' successfully unpacked and MD5 sums checked