Package: genefilter

Version: 1.68.0

Command: rm -rf genefilter.buildbin-libdir && mkdir genefilter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh genefilter_1.68.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R genefilter.buildbin-libdir

StartedAt: 2020-04-15 07:33:27 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 07:34:24 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 57.5 seconds

RetCode: 0

Status:  OK

PackageFile: genefilter_1.68.0.tgz

PackageFileSize: 1.766 MiB

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### Running command:
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###   rm -rf genefilter.buildbin-libdir && mkdir genefilter.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh genefilter_1.68.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R genefilter.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=genefilter.buildbin-libdir genefilter_1.68.0.tar.gz'
>>>>>>> 

* installing *source* package ‘genefilter’ ...
** using staged installation
** libs
clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c half_range_mode.cpp -o half_range_mode.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c nd.c -o nd.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c pAUC.c -o pAUC.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c rowPAUCs.c -o rowPAUCs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include  -fPIC  -Wall -g -O2  -c rowttests.c -o rowttests.o
gfortran  -fPIC  -Wall -g -O2  -c ttest.f -o ttest.o
ttest.f:47:12:

          dm=dm1-dm2
            1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:50:12:

          dm=dm1/dm2
            1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:59:13:

          tst=(dm1-dm2)/sqrt((1.d0/ng1+1.d0/ng2)*(dss1+dss2)/(ng1+ng2-2))
             1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
ttest.f:62:10:

       tst=(dm1-dm2)/sqrt(dss1/((ng1-1)*ng1)+dss2/((ng2-1)*ng2))
          1
Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1) [-Wconversion]
clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.10-bioc/meat/genefilter.buildbin-libdir/00LOCK-genefilter/00new/genefilter/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genefilter)


>>>>>>> 
>>>>>>> FIXING LINKS FOR genefilter.buildbin-libdir/genefilter/libs//genefilter.so
>>>>>>> 

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib" "genefilter.buildbin-libdir/genefilter/libs//genefilter.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "genefilter.buildbin-libdir/genefilter/libs//genefilter.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib" "genefilter.buildbin-libdir/genefilter/libs//genefilter.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "genefilter.buildbin-libdir/genefilter/libs//genefilter.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "genefilter.buildbin-libdir/genefilter/libs//genefilter.so"
install_name_tool -change "/usr/local/gfortran/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "genefilter.buildbin-libdir/genefilter/libs//genefilter.so"
install_name_tool -change "/usr/local/gfortran/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "genefilter.buildbin-libdir/genefilter/libs//genefilter.so"