Mike Smith
| Snapshot Date: 2022-07-06 14:00:06 -0400 (Wed, 06 Jul 2022) |
| git_url: https://git.bioconductor.org/packages/rhdf5 |
| git_branch: master |
| git_last_commit: c572550 |
| git_last_commit_date: 2022-06-20 10:38:08 -0400 (Mon, 20 Jun 2022) |
| Back to Multiple platform build/check report for BioC 3.16 |
|
This page was generated on 2022-07-07 11:11:52 -0400 (Thu, 07 Jul 2022).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.2.0 Patched (2022-06-02 r82447) -- "Vigorous Calisthenics" | 4343 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.0 Patched (2022-06-02 r82447 ucrt) -- "Vigorous Calisthenics" | 4148 |
| lconway | macOS 12.2.1 Monterey | x86_64 | 4.2.0 Patched (2022-05-29 r82424) -- "Vigorous Calisthenics" | 4160 |
| kjohnson | macOS 12.4 Monterey | arm64 | 4.2.0 Patched (2022-06-09 r82473) -- "Vigorous Calisthenics" | 3115 |
| 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 rhdf5 package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rhdf5.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1627/2124 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rhdf5 2.41.1 (landing page) Mike Smith
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.2.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson | macOS 12.4 Monterey / arm64 | OK | OK | NA | ERROR | |||||||||
| Package: rhdf5 |
| Version: 2.41.1 |
| Command: rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rhdf5_2.41.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rhdf5.buildbin-libdir |
| StartedAt: 2022-07-07 08:53:23 -0400 (Thu, 07 Jul 2022) |
| EndedAt: 2022-07-07 08:53:44 -0400 (Thu, 07 Jul 2022) |
| EllapsedTime: 20.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rhdf5_2.41.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rhdf5.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rhdf5.buildbin-libdir rhdf5_2.41.1.tar.gz' >>>>>>> * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5.c -o H5.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5A.c -o H5A.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5D.c -o H5D.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5E.c -o H5E.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5F.c -o H5F.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5G.c -o H5G.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5I.c -o H5I.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5L.c -o H5L.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5O.c -o H5O.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5P.c -o H5P.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5R.c -o H5R.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5S.c -o H5S.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5S_extras.c -o H5S_extras.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5T.c -o H5T.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5Z.c -o H5Z.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 H5constants.c -o H5constants.o clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 HandleList.cpp -o HandleList.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 HandleListWrap.c -o HandleListWrap.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 bit64conversion.c -o bit64conversion.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 external_filters.c -o external_filters.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 h5dump.c -o h5dump.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 h5ls.c -o h5ls.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 h5testLock.c -o h5testLock.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 h5writeDataFrame.c -o h5writeDataFrame.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 printdatatype.c -o printdatatype.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 utils.c -o utils.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -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 wrap.c -o wrap.o clang++ -arch arm64 -std=gnu++14 -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 rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5R.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /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 installing to /Users/biocbuild/bbs-3.16-bioc/meat/rhdf5.buildbin-libdir/00LOCK-rhdf5/00new/rhdf5/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (rhdf5) >>>>>>> >>>>>>> FIXING LINKS FOR rhdf5.buildbin-libdir/rhdf5/libs/rhdf5.so >>>>>>> ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib not found!