Hervé Pagès
| Snapshot Date: 2023-04-12 13:00:02 -0400 (Wed, 12 Apr 2023) |
| git_url: https://git.bioconductor.org/packages/HDF5Array |
| git_branch: RELEASE_3_16 |
| git_last_commit: 38b7bd6 |
| git_last_commit_date: 2022-11-01 11:13:03 -0400 (Tue, 01 Nov 2022) |
| Back to Mac ARM64 build report for BioC 3.16 |
|
This page was generated on 2023-04-19 11:01:55 -0400 (Wed, 19 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson | macOS 13.0 Ventura | arm64 | 4.2.2 (2022-10-31) -- "Innocent and Trusting" | 4256 |
| 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 | ||||
|
To the developers/maintainers of the HDF5Array package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 892/2183 | Hostname | OS / Arch | INSTALL | BUILD | BUILD BIN | ||||||||
| HDF5Array 1.26.0 (landing page) Hervé Pagès
| kjohnson | macOS 13.0 Ventura / arm64 | OK | OK | OK | | |||||||
| Package: HDF5Array |
| Version: 1.26.0 |
| Command: rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HDF5Array_1.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HDF5Array.buildbin-libdir |
| StartedAt: 2023-04-18 16:23:28 -0400 (Tue, 18 Apr 2023) |
| EndedAt: 2023-04-18 16:24:33 -0400 (Tue, 18 Apr 2023) |
| EllapsedTime: 65.1 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: HDF5Array_1.26.0.tgz |
| PackageFileSize: 9.518 MiB |
##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HDF5Array_1.26.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HDF5Array.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=HDF5Array.buildbin-libdir HDF5Array_1.26.0.tar.gz'
>>>>>>>
* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c S4Vectors_stubs.c -o S4Vectors_stubs.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c H5File.c -o H5File.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c global_errmsg_buf.c -o global_errmsg_buf.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c H5DSetDescriptor.c -o H5DSetDescriptor.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5dimscales.c -o h5dimscales.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c uaselection.c -o uaselection.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5mread_helpers.c -o h5mread_helpers.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5mread_startscounts.c -o h5mread_startscounts.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ChunkIterator.c -o ChunkIterator.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5mread_index.c -o h5mread_index.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:123:13: warning: unused function 'NOT_USED_make_nzindex_from_buf' [-Wunused-function]
static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
^
h5mread_sparse.c:179:13: warning: unused function 'NOT_USED_make_nzdata_from_IntAE_bufs' [-Wunused-function]
static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
^
h5mread_sparse.c:206:13: warning: unused function 'NOT_USED_make_nzindex_from_bufs' [-Wunused-function]
static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
^
3 warnings generated.
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5mread.c -o h5mread.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c h5summarize.c -o h5summarize.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_init_HDF5Array.c -o R_init_HDF5Array.o
clang -arch arm64 -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 HDF5Array.so S4Vectors_stubs.o H5File.o global_errmsg_buf.o H5DSetDescriptor.o h5dimscales.o uaselection.o h5mread_helpers.o h5mread_startscounts.o ChunkIterator.o h5mread_index.o h5mread_sparse.o h5mread.o h5summarize.o R_init_HDF5Array.o /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/lib/libhdf5_hl.a /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/lib -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: -undefined dynamic_lookup may not work with chained fixups
installing to /Volumes/External/bbs-3.16-bioc-m1/meat/HDF5Array.buildbin-libdir/00LOCK-HDF5Array/00new/HDF5Array/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 (HDF5Array)
>>>>>>>
>>>>>>> FIXING LINKS FOR HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so
>>>>>>>
install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so"
install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so"
install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so"