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BUILD BIN report for XVector on merida2

This page was generated on 2018-10-17 08:51:33 -0400 (Wed, 17 Oct 2018).

Package 1554/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
XVector 0.20.0
Hervé Pagès
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/XVector
Branch: RELEASE_3_7
Last Commit: a83a7ea
Last Changed Date: 2018-04-30 10:35:30 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: XVector
Version: 0.20.0
Command: rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XVector_0.20.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R XVector.buildbin-libdir
StartedAt: 2018-10-17 02:20:09 -0400 (Wed, 17 Oct 2018)
EndedAt: 2018-10-17 02:21:08 -0400 (Wed, 17 Oct 2018)
EllapsedTime: 58.9 seconds
RetCode: 0
Status:  OK 
PackageFile: XVector_0.20.0.tgz
PackageFileSize: 624.9 KiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XVector_0.20.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R XVector.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=XVector.buildbin-libdir XVector_0.20.0.tar.gz'
>>>>>>> 

* installing *source* package ‘XVector’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c RDS_random_access.c -o RDS_random_access.o
RDS_random_access.c:796:18: warning: unused variable 'ans' [-Wunused-variable]
        SEXP subscript, ans;
                        ^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c R_init_XVector.c -o R_init_XVector.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SharedDouble_class.c -o SharedDouble_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SharedInteger_class.c -o SharedInteger_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SharedRaw_class.c -o SharedRaw_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c SharedVector_class.c -o SharedVector_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c XRawList_comparison.c -o XRawList_comparison.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c XVectorList_class.c -o XVectorList_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c XVector_class.c -o XVector_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c io_utils.c -o io_utils.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c slice_methods.c -o slice_methods.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c vector_copy.c -o vector_copy.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/S4Vectors/include" -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/IRanges/include" -I/usr/local/include   -fPIC  -Wall -g -O2  -c view_summarization_methods.c -o view_summarization_methods.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 XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XRawList_comparison.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.7-bioc/meat/XVector.buildbin-libdir/XVector/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (XVector)


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

install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "XVector.buildbin-libdir/XVector/libs//XVector.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "XVector.buildbin-libdir/XVector/libs//XVector.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "XVector.buildbin-libdir/XVector/libs//XVector.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "XVector.buildbin-libdir/XVector/libs//XVector.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "XVector.buildbin-libdir/XVector/libs//XVector.so"