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INSTALL report for sigPathway on tokay1

This page was generated on 2020-04-15 12:17:40 -0400 (Wed, 15 Apr 2020).

Package 1592/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sigPathway 1.54.0
Weil Lai
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/sigPathway
Branch: RELEASE_3_10
Last Commit: 2217a34
Last Changed Date: 2019-10-29 13:07:43 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sigPathway
Version: 1.54.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/sigPathway_1.54.0.tar.gz && rm -rf sigPathway.buildbin-libdir && mkdir sigPathway.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sigPathway.buildbin-libdir sigPathway_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL sigPathway_1.54.0.zip && rm sigPathway_1.54.0.tar.gz sigPathway_1.54.0.zip
StartedAt: 2020-04-14 18:29:27 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 18:29:56 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 28.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/sigPathway_1.54.0.tar.gz && rm -rf sigPathway.buildbin-libdir && mkdir sigPathway.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sigPathway.buildbin-libdir sigPathway_1.54.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL sigPathway_1.54.0.zip && rm sigPathway_1.54.0.tar.gz sigPathway_1.54.0.zip
###
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100  456k  100  456k    0     0  8444k      0 --:--:-- --:--:-- --:--:-- 9136k

install for i386

* installing *source* package 'sigPathway' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c calc_gene_set_internal.c -o calc_gene_set_internal.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c calc_gene_set_stat.c -o calc_gene_set_stat.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c calc_probe_stat.c -o calc_probe_stat.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c calc_weights.c -o calc_weights.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c matrix_fn.c -o matrix_fn.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c permute.c -o permute.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c shuffle.c -o shuffle.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sigPathway.c -o sigPathway.o
C:/Rtools/mingw_32/bin/gcc -shared -s -static-libgcc -o sigPathway.dll tmp.def calc_gene_set_internal.o calc_gene_set_stat.o calc_probe_stat.o calc_weights.o matrix_fn.o permute.o shuffle.o sigPathway.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/sigPathway.buildbin-libdir/00LOCK-sigPathway/00new/sigPathway/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'sigPathway'
    finding HTML links ... done
    MuscleExample                           html  
    calcTNullFast                           html  
    calcTStatFast                           html  
    calculate.GSEA                          html  
    calculate.NGSk                          html  
    calculatePathwayStatistics              html  
    estimateNumPerm                         html  
    getPathwayStatistics.NGSk               html  
    getPathwayStatistics                    html  
    importGeneSets                          html  
    rankPathways.NGSk                       html  
    rankPathways                            html  
    runSigPathway                           html  
    selectGeneSets                          html  
    writeSigPathway                         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 'sigPathway' ...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c calc_gene_set_internal.c -o calc_gene_set_internal.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c calc_gene_set_stat.c -o calc_gene_set_stat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c calc_probe_stat.c -o calc_probe_stat.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c calc_weights.c -o calc_weights.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c matrix_fn.c -o matrix_fn.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c permute.c -o permute.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c shuffle.c -o shuffle.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sigPathway.c -o sigPathway.o
C:/Rtools/mingw_64/bin/gcc -shared -s -static-libgcc -o sigPathway.dll tmp.def calc_gene_set_internal.o calc_gene_set_stat.o calc_probe_stat.o calc_weights.o matrix_fn.o permute.o shuffle.o sigPathway.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/sigPathway.buildbin-libdir/sigPathway/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sigPathway' as sigPathway_1.54.0.zip
* DONE (sigPathway)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'sigPathway' successfully unpacked and MD5 sums checked