Mike Smith
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/rhdf5 |
| git_branch: RELEASE_3_20 |
| git_last_commit: d0313f0 |
| git_last_commit_date: 2024-12-09 08:14:05 -0500 (Mon, 09 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 1742/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| rhdf5 2.50.1 (landing page) Mike Smith
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the rhdf5 package: - 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 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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: rhdf5 |
| Version: 2.50.1 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL rhdf5 |
| StartedAt: 2025-01-08 19:58:55 -0000 (Wed, 08 Jan 2025) |
| EndedAt: 2025-01-08 19:59:12 -0000 (Wed, 08 Jan 2025) |
| EllapsedTime: 16.5 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL rhdf5 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’ * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’ using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’ /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5.c -o H5.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5A.c -o H5A.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5D.c -o H5D.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5E.c -o H5E.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5F.c -o H5F.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5G.c -o H5G.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5I.c -o H5I.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5L.c -o H5L.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5O.c -o H5O.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5P.c -o H5P.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5PL.c -o H5PL.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5R.c -o H5R.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5S.c -o H5S.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5S_extras.c -o H5S_extras.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5T.c -o H5T.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5T_extras.c -o H5T_extras.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5Z.c -o H5Z.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c H5constants.c -o H5constants.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c HandleList.cpp -o HandleList.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c HandleListWrap.c -o HandleListWrap.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c bit64conversion.c -o bit64conversion.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c external_filters.c -o external_filters.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5dump.c -o h5dump.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5ls.c -o h5ls.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5testLock.c -o h5testLock.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c h5writeDataFrame.c -o h5writeDataFrame.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c printdatatype.c -o printdatatype.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c utils.c -o utils.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c wrap.c -o wrap.o /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5PL.o H5R.o H5S.o H5S_extras.o H5T.o H5T_extras.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 /home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/R/R-4.4.2/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/R/R/lib -lR installing to /home/biocbuild/R/R-4.4.2/site-library/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)