Xiuwen Zheng
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/SAIGEgds |
| git_branch: RELEASE_3_17 |
| git_last_commit: 8011316 |
| git_last_commit_date: 2023-05-01 20:07:45 -0400 (Mon, 01 May 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:11 -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 1800/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SAIGEgds 2.0.1 (landing page) Xiuwen Zheng
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the SAIGEgds 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: SAIGEgds |
| Version: 2.0.1 |
| Command: rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SAIGEgds_2.0.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SAIGEgds.buildbin-libdir |
| StartedAt: 2023-10-19 16:49:16 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 16:51:47 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 151.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: SAIGEgds_2.0.1.tgz |
| PackageFileSize: 2.254 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf SAIGEgds.buildbin-libdir && mkdir SAIGEgds.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SAIGEgds_2.0.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SAIGEgds.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SAIGEgds.buildbin-libdir SAIGEgds_2.0.1.tar.gz' >>>>>>> * installing *source* package ‘SAIGEgds’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SPATest.cpp -o SPATest.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c saige_fitnull.cpp -o saige_fitnull.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c saige_main.cpp -o saige_main.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c saige_misc.cpp -o saige_misc.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vec_ext_avx2.cpp -o vec_ext_avx2.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vec_ext_avx512bw.cpp -o vec_ext_avx512bw.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vec_ext_def.cpp -o vec_ext_def.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DARMA_64BIT_WORD=1 -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppParallel/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vectorization.cpp -o vectorization.o clang++ -arch arm64 -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/opt/R/arm64/lib -o SAIGEgds.so SPATest.o saige_fitnull.o saige_main.o saige_misc.o vec_ext_avx2.o vec_ext_avx512bw.o vec_ext_def.o vectorization.o -lm -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame installing to /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/SAIGEgds.buildbin-libdir/00LOCK-SAIGEgds/00new/SAIGEgds/libs ** R ** 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 (SAIGEgds) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so >>>>>>> >>>>>>> Paths before fix: SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so: SAIGEgds.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /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/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0) >>>>>>> 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" "SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so" >>>>>>> Paths after fix: SAIGEgds.buildbin-libdir/SAIGEgds/libs/SAIGEgds.so: SAIGEgds.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /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/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)