| Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-10-16 12:34:32 -0400 (Wed, 16 Oct 2019).
| Package 166/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| BioQC 1.12.0 Jitao David Zhang
| 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 |
| 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 |
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### Running command:
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### 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
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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