Xiuwen Zheng
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/SeqArray |
| git_branch: RELEASE_3_17 |
| git_last_commit: 644f430 |
| git_last_commit_date: 2023-06-09 02:36:28 -0400 (Fri, 09 Jun 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1884/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SeqArray 1.40.1 (landing page) Xiuwen Zheng
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the SeqArray package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SeqArray |
| Version: 1.40.1 |
| Command: rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SeqArray_1.40.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SeqArray.buildbin-libdir |
| StartedAt: 2023-10-19 17:09:28 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 17:11:11 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 103.0 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: SeqArray_1.40.1.tgz |
| PackageFileSize: 3.87 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SeqArray_1.40.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SeqArray.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SeqArray.buildbin-libdir SeqArray_1.40.1.tar.gz' >>>>>>> * installing *source* package ‘SeqArray’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConvToGDS.cpp -o ConvToGDS.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FileMerge.cpp -o FileMerge.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GetData.cpp -o GetData.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Index.cpp -o Index.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LinkSNPRelate.cpp -o LinkSNPRelate.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Methods.cpp -o Methods.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_SeqArray.c -o R_SeqArray.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBySample.cpp -o ReadBySample.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadByUnit.cpp -o ReadByUnit.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadByVariant.cpp -o ReadByVariant.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SeqArray.cpp -o SeqArray.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pkg_test.cpp -o pkg_test.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c samtools_ext.c -o samtools_ext.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vectorization.c -o vectorization.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 ReadByUnit.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-3.17-bioc-mac-arm64/meat/SeqArray.buildbin-libdir/00LOCK-SeqArray/00new/SeqArray/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 (SeqArray) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so >>>>>>> >>>>>>> Paths before fix: SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so: SeqArray.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so" >>>>>>> Paths after fix: SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so: SeqArray.so (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) /usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)