Hervé Pagès
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/XVector |
| Branch: master |
| Last Commit: 5bdbf5c |
| Last Changed Date: 2019-10-29 13:36:51 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:37:02 -0500 (Thu, 16 Jan 2020).
| Package 1811/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| XVector 0.27.0 Hervé Pagès
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | NA | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | WARNINGS | [ OK ] |
| Package: XVector |
| Version: 0.27.0 |
| Command: rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XVector_0.27.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R XVector.buildbin-libdir |
| StartedAt: 2020-01-16 12:01:44 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 12:02:12 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 28.3 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: XVector_0.27.0.tgz |
| PackageFileSize: 641.8 KiB |
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### Running command:
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### rm -rf XVector.buildbin-libdir && mkdir XVector.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh XVector_0.27.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R XVector.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=XVector.buildbin-libdir XVector_0.27.0.tar.gz'
>>>>>>>
* installing *source* package ‘XVector’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c XDouble_class.c -o XDouble_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c XInteger_class.c -o XInteger_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c XRaw_class.c -o XRaw_class.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/IRanges/include' -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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 XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.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-3.11-bioc/meat/XVector.buildbin-libdir/00LOCK-XVector/00new/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 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 (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/4.0/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/4.0/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/4.0/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/4.0/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/4.0/Resources/lib/libquadmath.0.dylib" "XVector.buildbin-libdir/XVector/libs//XVector.so"