Aaron Lun
| Snapshot Date: 2024-05-11 09:00:03 -0400 (Sat, 11 May 2024) |
| git_url: https://git.bioconductor.org/packages/alabaster.base |
| git_branch: devel |
| git_last_commit: 04ff2d9 |
| git_last_commit_date: 2024-05-03 03:08:31 -0400 (Fri, 03 May 2024) |
| Back to Mac ARM64 build report for BioC 3.20 |
|
This page was generated on 2024-05-13 11:32:00 -0400 (Mon, 13 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4378 |
| 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 40/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| alabaster.base 1.5.1 (landing page) Aaron Lun
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the alabaster.base 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: alabaster.base |
| Version: 1.5.1 |
| Command: rm -rf alabaster.base.buildbin-libdir && mkdir alabaster.base.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh alabaster.base_1.5.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R alabaster.base.buildbin-libdir |
| StartedAt: 2024-05-13 07:05:15 -0400 (Mon, 13 May 2024) |
| EndedAt: 2024-05-13 07:06:58 -0400 (Mon, 13 May 2024) |
| EllapsedTime: 103.0 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: alabaster.base_1.5.1.tgz |
| PackageFileSize: 2.126 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf alabaster.base.buildbin-libdir && mkdir alabaster.base.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh alabaster.base_1.5.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R alabaster.base.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=alabaster.base.buildbin-libdir alabaster.base_1.5.1.tar.gz' >>>>>>> * installing *source* package ‘alabaster.base’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++17 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c check_csv.cpp -o check_csv.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c check_list.cpp -o check_list.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c choose_numeric_missing_placeholder.cpp -o choose_numeric_missing_placeholder.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c is_rfc3339.cpp -o is_rfc3339.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c load_csv.cpp -o load_csv.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c load_list.cpp -o load_list.o clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I../inst/include -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c validate.cpp -o validate.o clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o alabaster.base.so RcppExports.o check_csv.o check_list.o choose_numeric_missing_placeholder.o is_rfc3339.o load_csv.o load_list.o validate.o /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: ignoring duplicate libraries: '-lz' installing to /Users/biocbuild/bbs-3.20-bioc-mac-arm64/meat/alabaster.base.buildbin-libdir/00LOCK-alabaster.base/00new/alabaster.base/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 (alabaster.base) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so >>>>>>> >>>>>>> Paths before fix: alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so: alabaster.base.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so" >>>>>>> Paths after fix: alabaster.base.buildbin-libdir/alabaster.base/libs/alabaster.base.so: alabaster.base.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.0) /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)