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INSTALL report for sigPathway on tokay2

This page was generated on 2020-10-17 11:57:49 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE sigPathway PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1658/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
sigPathway 1.56.0
Weil Lai
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/sigPathway
Branch: RELEASE_3_11
Last Commit: b2b529d
Last Changed Date: 2020-04-27 14:13:29 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: sigPathway
Version: 1.56.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/sigPathway_1.56.0.tar.gz && rm -rf sigPathway.buildbin-libdir && mkdir sigPathway.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sigPathway.buildbin-libdir sigPathway_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL sigPathway_1.56.0.zip && rm sigPathway_1.56.0.tar.gz sigPathway_1.56.0.zip
StartedAt: 2020-10-16 16:44:35 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 16:46:57 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 142.7 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/sigPathway_1.56.0.tar.gz && rm -rf sigPathway.buildbin-libdir && mkdir sigPathway.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=sigPathway.buildbin-libdir sigPathway_1.56.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL sigPathway_1.56.0.zip && rm sigPathway_1.56.0.tar.gz sigPathway_1.56.0.zip
###
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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  455k  100  455k    0     0  7193k      0 --:--:-- --:--:-- --:--:-- 8142k

install for i386

* installing *source* package 'sigPathway' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c calc_gene_set_internal.c -o calc_gene_set_internal.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c calc_gene_set_stat.c -o calc_gene_set_stat.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c calc_probe_stat.c -o calc_probe_stat.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c calc_weights.c -o calc_weights.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix_fn.c -o matrix_fn.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c permute.c -o permute.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c shuffle.c -o shuffle.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sigPathway.c -o sigPathway.o
C:/rtools40/mingw32/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-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c calc_gene_set_internal.c -o calc_gene_set_internal.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c calc_gene_set_stat.c -o calc_gene_set_stat.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c calc_probe_stat.c -o calc_probe_stat.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c calc_weights.c -o calc_weights.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c matrix_fn.c -o matrix_fn.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c permute.c -o permute.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c shuffle.c -o shuffle.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sigPathway.c -o sigPathway.o
C:/rtools40/mingw64/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-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/sigPathway.buildbin-libdir/sigPathway/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'sigPathway' as sigPathway_1.56.0.zip
* DONE (sigPathway)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'sigPathway' successfully unpacked and MD5 sums checked