Package: DOQTL

Version: 1.20.0

Command: rm -rf DOQTL.buildbin-libdir && mkdir DOQTL.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DOQTL_1.20.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DOQTL.buildbin-libdir

StartedAt: 2019-10-16 08:30:15 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 08:31:34 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 79.3 seconds

RetCode: 0

Status:  OK

PackageFile: DOQTL_1.20.0.tgz

PackageFileSize: 4.006 MiB

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### Running command:
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###   rm -rf DOQTL.buildbin-libdir && mkdir DOQTL.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DOQTL_1.20.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R DOQTL.buildbin-libdir
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>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DOQTL.buildbin-libdir DOQTL_1.20.0.tar.gz'
>>>>>>> 

* installing *source* package ‘DOQTL’ ...
** using staged installation
** libs
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 DOrec.c -o DOrec.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 DOstep.c -o DOstep.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 DOstep_Rwrappers.c -o DOstep_Rwrappers.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 addlog.c -o addlog.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 emission_prob.c -o emission_prob.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 emission_prob2.c -o emission_prob2.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 filter.smooth.allele.c -o filter.smooth.allele.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 filter.smooth.intensity.c -o filter.smooth.intensity.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 kinship.c -o kinship.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 ri4hap.c -o ri4hap.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 transition.c -o transition.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 update.alleles.c -o update.alleles.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 update.c -o update.o
clang -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 DOQTL.so DOrec.o DOstep.o DOstep_Rwrappers.o addlog.o emission_prob.o emission_prob2.o filter.smooth.allele.o filter.smooth.intensity.o init.o kinship.o ri4hap.o transition.o update.alleles.o update.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.9-bioc/meat/DOQTL.buildbin-libdir/00LOCK-DOQTL/00new/DOQTL/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Note: possible error in 'scanOne(y = pheno, x = addcovar, ': unused argument (intcovar = intcovar) 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'DOQTL' is deprecated and will be removed from Bioconductor
  version 3.10
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: Package 'DOQTL' is deprecated and will be removed from Bioconductor
  version 3.10
** testing if installed package keeps a record of temporary installation path
* DONE (DOQTL)


>>>>>>> 
>>>>>>> FIXING LINKS FOR DOQTL.buildbin-libdir/DOQTL/libs//DOQTL.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" "DOQTL.buildbin-libdir/DOQTL/libs//DOQTL.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "DOQTL.buildbin-libdir/DOQTL/libs//DOQTL.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" "DOQTL.buildbin-libdir/DOQTL/libs//DOQTL.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "DOQTL.buildbin-libdir/DOQTL/libs//DOQTL.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "DOQTL.buildbin-libdir/DOQTL/libs//DOQTL.so"