Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:45 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 932/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HDF5Array 1.35.2 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the HDF5Array package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HDF5Array.git to reflect on this report. See Troubleshooting Build Report for more information. - 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: HDF5Array |
Version: 1.35.2 |
Command: rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HDF5Array_1.35.2.tar.gz /Library/Frameworks/R.framework/Resources/bin/R HDF5Array.buildbin-libdir |
StartedAt: 2024-12-23 22:30:21 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 22:30:34 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 13.3 seconds |
RetCode: 0 |
Status: OK |
PackageFile: HDF5Array_1.35.2.tgz |
PackageFileSize: 11.38 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf HDF5Array.buildbin-libdir && mkdir HDF5Array.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh HDF5Array_1.35.2.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_1.35.2.tar.gz' >>>>>>> * installing *source* package ‘HDF5Array’ ... ** using staged installation ** libs using C compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’ using SDK: ‘MacOSX11.3.sdk’ clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c H5DSetDescriptor.c -o H5DSetDescriptor.o H5DSetDescriptor.c:698:45: warning: format specifies type 'long' but the argument has type 'hid_t' (aka 'long long') [-Wformat] Rprintf("%s * h5type_id = %ld\n", margin, h5type->h5type_id); ~~~ ^~~~~~~~~~~~~~~~~ %lld H5DSetDescriptor.c:1166:31: warning: format specifies type 'long' but the argument has type 'hid_t' (aka 'long long') [-Wformat] Rprintf("- dset_id = %ld\n", h5dset->dset_id); ~~~ ^~~~~~~~~~~~~~~ %lld H5DSetDescriptor.c:1184:34: warning: format specifies type 'long' but the argument has type 'hid_t' (aka 'long long') [-Wformat] Rprintf("- h5space_id = %ld\n", h5dset->h5space_id); ~~~ ^~~~~~~~~~~~~~~~~~ %lld H5DSetDescriptor.c:1188:34: warning: format specifies type 'long' but the argument has type 'hid_t' (aka 'long long') [-Wformat] Rprintf("- h5plist_id = %ld\n", h5dset->h5plist_id); ~~~ ^~~~~~~~~~~~~~~~~~ %lld 4 warnings generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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 h5mread_startscounts.c:296:16: warning: variable 'num_hyperslabs' set but not used [-Wunused-but-set-variable] long long int num_hyperslabs = 0; ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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 clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/library/S4Vectors/include' -I'/Library/Frameworks/R.framework/Versions/4.5-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 -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/4.5-arm64/Resources/library/Rhdf5lib/lib/libhdf5_hl.a /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Users/biocbuild/bbs-3.21-bioc/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 PATHS TO DYNAMIC LIBRARIES FOR HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so >>>>>>> >>>>>>> Paths before fix: HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so: HDF5Array.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/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so" >>>>>>> Paths after fix: HDF5Array.buildbin-libdir/HDF5Array/libs/HDF5Array.so: HDF5Array.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/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0) /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)