Xiuwen Zheng
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/SeqArray |
| Branch: RELEASE_3_9 |
| Last Commit: 1ecfddf |
| Last Changed Date: 2019-07-11 22:49:49 -0400 (Thu, 11 Jul 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:51:14 -0400 (Wed, 16 Oct 2019).
| Package 1490/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| SeqArray 1.24.2 Xiuwen Zheng
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | [ OK ] | |
| Package: SeqArray |
| Version: 1.24.2 |
| Command: rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SeqArray_1.24.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SeqArray.buildbin-libdir |
| StartedAt: 2019-10-16 09:24:12 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 09:25:13 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 60.9 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: SeqArray_1.24.2.tgz |
| PackageFileSize: 3.984 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SeqArray_1.24.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R SeqArray.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SeqArray.buildbin-libdir SeqArray_1.24.2.tar.gz' >>>>>>> * installing *source* package ‘SeqArray’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ConvToGDS.cpp -o ConvToGDS.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c FileMerge.cpp -o FileMerge.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c GetData.cpp -o GetData.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Index.cpp -o Index.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c LinkSNPRelate.cpp -o LinkSNPRelate.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c Methods.cpp -o Methods.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c R_SeqArray.c -o R_SeqArray.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ReadBySample.cpp -o ReadBySample.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c ReadByVariant.cpp -o ReadByVariant.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c SeqArray.cpp -o SeqArray.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pkg_test.cpp -o pkg_test.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c samtools_ext.c -o samtools_ext.o clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/gdsfmt/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c vectorization.c -o vectorization.o 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 SeqArray.so ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.9-bioc/meat/SeqArray.buildbin-libdir/00LOCK-SeqArray/00new/SeqArray/libs ** R ** data ** 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 (SeqArray) >>>>>>> >>>>>>> FIXING LINKS FOR SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.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" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so" install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.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" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so" install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.dylib" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib" "SeqArray.buildbin-libdir/SeqArray/libs//SeqArray.so"