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###
### Running command:
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###   C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/CNVtools_1.84.0.tar.gz && rm -rf CNVtools.buildbin-libdir && mkdir CNVtools.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=CNVtools.buildbin-libdir CNVtools_1.84.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL CNVtools_1.84.0.zip && rm CNVtools_1.84.0.tar.gz CNVtools_1.84.0.zip
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install for i386

* installing *source* package 'CNVtools' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fitmodel.cpp -o fitmodel.o
In file included from fitmodel.cpp:9:
gmath.h: In function 'double gmath::psi(double)':
gmath.h:204:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if (x < 0.0)
     ^~
gmath.h:206:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
         return ps;
         ^~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c glm_test.cpp -o glm_test.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mla.cpp -o mla.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c routine.cpp -o routine.o
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c zeroin.c -o zeroin.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CNVtools.dll tmp.def fitmodel.o glm_test.o mla.o routine.o zeroin.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CNVtools.buildbin-libdir/00LOCK-CNVtools/00new/CNVtools/libs/i386
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'CNVtools'
    finding HTML links ... done
    A112                                    html  
    CNV.fitModel                            html  
    CNVtest.binary                          html  
    CNVtest.binary.T                        html  
    CNVtest.qt                              html  
    CNVtest.qt.T                            html  
    CNVtest.select.model                    html  
    CNVtools-package                        html  
    EM.starting.point                       html  
    ExpandData                              html  
    apply.ldf                               html  
    apply.pca                               html  
    cnv.plot                                html  
    compact.data.frame                      html  
    get.model.spec                          html  
    getQualityScore                         html  
    getparams                               html  
    qt.plot                                 html  
    test.posterior                          html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'CNVtools' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'CNVtools' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'CNVtools' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fitmodel.cpp -o fitmodel.o
In file included from fitmodel.cpp:9:
gmath.h: In function 'double gmath::psi(double)':
gmath.h:204:5: warning: this 'if' clause does not guard... [-Wmisleading-indentation]
     if (x < 0.0)
     ^~
gmath.h:206:9: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'if'
         return ps;
         ^~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c glm_test.cpp -o glm_test.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c mla.cpp -o mla.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c routine.cpp -o routine.o
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c zeroin.c -o zeroin.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o CNVtools.dll tmp.def fitmodel.o glm_test.o mla.o routine.o zeroin.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/CNVtools.buildbin-libdir/CNVtools/libs/x64
** testing if installed package can be loaded
Warning: Package 'CNVtools' is deprecated and will be removed from Bioconductor
  version 3.13
* MD5 sums
packaged installation of 'CNVtools' as CNVtools_1.84.0.zip
* DONE (CNVtools)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'CNVtools' successfully unpacked and MD5 sums checked