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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/SAGx_1.66.0.tar.gz && rm -rf SAGx.buildbin-libdir && mkdir SAGx.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SAGx.buildbin-libdir SAGx_1.66.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL SAGx_1.66.0.zip && rm SAGx_1.66.0.tar.gz SAGx_1.66.0.zip
###
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install for i386

* installing *source* package 'SAGx' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c minigsea.c -o minigsea.o
minigsea.c: In function 'MiniGSEA':
minigsea.c:8:12: warning: variable 'k' set but not used [-Wunused-but-set-variable]
    int i,j,k,I;
            ^
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c newboot.c -o newboot.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"c:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c samrocNboot.c -o samrocNboot.o
C:/rtools40/mingw32/bin/gcc -shared -s -static-libgcc -o SAGx.dll tmp.def minigsea.o newboot.o samrocNboot.o -Lc:/extsoft/lib/i386 -Lc:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/SAGx.buildbin-libdir/00LOCK-SAGx/00new/SAGx/libs/i386
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'SAGx'
    finding HTML links ... done
    Fstat                                   html  
    GSEA.mean.t                             html  
    JT.test                                 html  
    R2BASE                                  html  
    R2mim                                   html  
    Xprep                                   html  
    Xprep.resid                             html  
    clin2mim                                html  
    cluster.q                               html  
    estimatep0                              html  
    fetchSignal                             html  
    firstpass                               html  
    fom                                     html  
    fp.fn                                   html  
    gap                                     html  
    list.experiments                        html  
    list.intersection.p                     html  
    mat2TeX                                 html  
    myclus                                  html  
    normalise                               html  
    one.probeset.per.gene                   html  
    outlier                                 html  
    p0.mom                                  html  
    pava.fdr                                html  
    pava                                    html  
    rank.genes                              html  
    rank.trend                              html  
    rsd.test                                html  
    samroc.result-class                     html  
    samrocn                                 html  
    samrocnboot                             html  
    union.of.pways                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'SAGx' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package can be loaded from final location
Warning: Package 'SAGx' is deprecated and will be removed from Bioconductor
  version 3.14
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'SAGx' ...
** libs
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c minigsea.c -o minigsea.o
minigsea.c: In function 'MiniGSEA':
minigsea.c:8:12: warning: variable 'k' set but not used [-Wunused-but-set-variable]
    int i,j,k,I;
            ^
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c newboot.c -o newboot.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.13-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c samrocNboot.c -o samrocNboot.o
C:/rtools40/mingw64/bin/gcc -shared -s -static-libgcc -o SAGx.dll tmp.def minigsea.o newboot.o samrocNboot.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.13-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.13-bioc/meat/SAGx.buildbin-libdir/SAGx/libs/x64
** testing if installed package can be loaded
Warning: Package 'SAGx' is deprecated and will be removed from Bioconductor
  version 3.14
* MD5 sums
packaged installation of 'SAGx' as SAGx_1.66.0.zip
* DONE (SAGx)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'SAGx' successfully unpacked and MD5 sums checked