Hugo Gruson
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/Rhdf5lib |
| git_branch: devel |
| git_last_commit: c0f2cf6 |
| git_last_commit_date: 2026-03-16 08:05:07 -0400 (Mon, 16 Mar 2026) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-18 11:37 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 1821/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rhdf5lib 1.33.6 (landing page) Hugo Gruson
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
| See other builds for Rhdf5lib in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Rhdf5lib package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rhdf5lib.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: Rhdf5lib |
| Version: 1.33.6 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL Rhdf5lib |
| StartedAt: 2026-04-16 20:17:47 -0000 (Thu, 16 Apr 2026) |
| EndedAt: 2026-04-16 20:18:15 -0000 (Thu, 16 Apr 2026) |
| EllapsedTime: 27.2 seconds |
| RetCode: 1 |
| Status: ERROR |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL Rhdf5lib ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’ * installing *source* package ‘Rhdf5lib’ ... ** this is package ‘Rhdf5lib’ version ‘1.33.6’ ** using staged installation -- The C compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Performing Test HAVE_DECL___BUILTIN_CLZLL -- Performing Test HAVE_DECL___BUILTIN_CLZLL - Success -- Looking for snprintf -- Looking for snprintf - found -- Configuring done (0.6s) -- Generating done (0.0s) -- Build files have been written to: /home/biocbuild/bbs-3.23-bioc/meat/Rhdf5lib/_build_libaec [ 11%] Building C object src/CMakeFiles/aec-static-objects.dir/encode.c.o [ 22%] Building C object src/CMakeFiles/aec-static-objects.dir/encode_accessors.c.o [ 33%] Building C object src/CMakeFiles/aec-static-objects.dir/decode.c.o [ 44%] Building C object src/CMakeFiles/aec-static-objects.dir/vector.c.o [ 44%] Built target aec-static-objects [ 55%] Linking C static library libaec.a [ 55%] Built target aec-static [ 66%] Building C object src/CMakeFiles/sz-static-objects.dir/sz_compat.c.o [ 66%] Built target sz-static-objects [ 77%] Linking C static library libsz.a [ 77%] Built target sz-static [ 88%] Building C object src/CMakeFiles/graec.dir/graec.c.o [100%] Linking C executable graec [100%] Built target graec -- Install configuration: "Release" -- Installing: /home/biocbuild/bbs-3.23-bioc/meat/Rhdf5lib/inst/lib/cmake/libaec/libaec-config.cmake -- Installing: /home/biocbuild/bbs-3.23-bioc/meat/Rhdf5lib/inst/lib/cmake/libaec/libaec-config-version.cmake -- Installing: /home/biocbuild/bbs-3.23-bioc/meat/Rhdf5lib/inst/include/libaec.h -- Installing: /home/biocbuild/bbs-3.23-bioc/meat/Rhdf5lib/inst/include/szlib.h -- Installing: /home/biocbuild/bbs-3.23-bioc/meat/Rhdf5lib/inst/lib/libaec.a -- Installing: /home/biocbuild/bbs-3.23-bioc/meat/Rhdf5lib/inst/lib/libsz.a -- Installing: /home/biocbuild/bbs-3.23-bioc/meat/Rhdf5lib/inst/lib/cmake/libaec/libaec-targets.cmake -- Installing: /home/biocbuild/bbs-3.23-bioc/meat/Rhdf5lib/inst/lib/cmake/libaec/libaec-targets-release.cmake -- The C compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Final: share -- Looking for include file sys/file.h -- Looking for include file sys/file.h - found -- Looking for include files sys/file.h, sys/ioctl.h -- Looking for include files sys/file.h, sys/ioctl.h - found -- Looking for 3 include files sys/file.h, ..., sys/resource.h -- Looking for 3 include files sys/file.h, ..., sys/resource.h - found -- Looking for 4 include files sys/file.h, ..., sys/socket.h -- Looking for 4 include files sys/file.h, ..., sys/socket.h - found -- Looking for 5 include files sys/file.h, ..., sys/stat.h -- Looking for 5 include files sys/file.h, ..., sys/stat.h - found -- Looking for 6 include files sys/file.h, ..., sys/time.h -- Looking for 6 include files sys/file.h, ..., sys/time.h - found -- Looking for 7 include files sys/file.h, ..., sys/types.h -- Looking for 7 include files sys/file.h, ..., sys/types.h - found -- Looking for 8 include files sys/file.h, ..., features.h -- Looking for 8 include files sys/file.h, ..., features.h - found -- Looking for 9 include files sys/file.h, ..., dirent.h -- Looking for 9 include files sys/file.h, ..., dirent.h - found -- Looking for 10 include files sys/file.h, ..., unistd.h -- Looking for 10 include files sys/file.h, ..., unistd.h - found -- Looking for 11 include files sys/file.h, ..., pwd.h -- Looking for 11 include files sys/file.h, ..., pwd.h - found -- Looking for 12 include files sys/file.h, ..., pthread.h -- Looking for 12 include files sys/file.h, ..., pthread.h - found -- Looking for 13 include files sys/file.h, ..., dlfcn.h -- Looking for 13 include files sys/file.h, ..., dlfcn.h - found -- Looking for 14 include files sys/file.h, ..., netinet/in.h -- Looking for 14 include files sys/file.h, ..., netinet/in.h - found -- Looking for 15 include files sys/file.h, ..., netdb.h -- Looking for 15 include files sys/file.h, ..., netdb.h - found -- Looking for 16 include files sys/file.h, ..., arpa/inet.h -- Looking for 16 include files sys/file.h, ..., arpa/inet.h - found -- Looking for include file quadmath.h -- Looking for include file quadmath.h - not found -- Looking for ceil in m; -- Looking for ceil in m; - found -- Looking for dlopen in dl;m -- Looking for dlopen in dl;m - found -- Looking for WSAStartup in ws2_32;m;dl -- Looking for WSAStartup in ws2_32;m;dl - not found -- Looking for gethostbyname in wsock32;m;dl -- Looking for gethostbyname in wsock32;m;dl - not found -- Looking for gethostname in ucb;m;dl -- Looking for gethostname in ucb;m;dl - not found -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of char -- Check size of char - done -- Check size of short -- Check size of short - done -- Check size of int -- Check size of int - done -- Check size of unsigned -- Check size of unsigned - done -- Check size of long -- Check size of long - done -- Check size of long long -- Check size of long long - done -- Check size of float -- Check size of float - done -- Check size of double -- Check size of double - done -- Check size of long double -- Check size of long double - done -- Check size of int8_t -- Check size of int8_t - done -- Check size of uint8_t -- Check size of uint8_t - done -- Check size of int_least8_t -- Check size of int_least8_t - done -- Check size of uint_least8_t -- Check size of uint_least8_t - done -- Check size of int_fast8_t -- Check size of int_fast8_t - done -- Check size of uint_fast8_t -- Check size of uint_fast8_t - done -- Check size of int16_t -- Check size of int16_t - done -- Check size of uint16_t -- Check size of uint16_t - done -- Check size of int_least16_t -- Check size of int_least16_t - done -- Check size of uint_least16_t -- Check size of uint_least16_t - done -- Check size of int_fast16_t -- Check size of int_fast16_t - done -- Check size of uint_fast16_t -- Check size of uint_fast16_t - done -- Check size of int32_t -- Check size of int32_t - done -- Check size of uint32_t -- Check size of uint32_t - done -- Check size of int_least32_t -- Check size of int_least32_t - done -- Check size of uint_least32_t -- Check size of uint_least32_t - done -- Check size of int_fast32_t -- Check size of int_fast32_t - done -- Check size of uint_fast32_t -- Check size of uint_fast32_t - done -- Check size of int64_t -- Check size of int64_t - done -- Check size of uint64_t -- Check size of uint64_t - done -- Check size of int_least64_t -- Check size of int_least64_t - done -- Check size of uint_least64_t -- Check size of uint_least64_t - done -- Check size of int_fast64_t -- Check size of int_fast64_t - done -- Check size of uint_fast64_t -- Check size of uint_fast64_t - done -- Check size of size_t -- Check size of size_t - done -- Check size of ssize_t -- Check size of ssize_t - done -- Check size of ptrdiff_t -- Check size of ptrdiff_t - done -- Check size of off_t -- Check size of off_t - done -- Check size of time_t -- Check size of time_t - done -- Check size of _Bool -- Check size of _Bool - done -- Looking for CLOCK_MONOTONIC -- Looking for CLOCK_MONOTONIC - not found -- Performing Test H5_HAVE_TM_GMTOFF -- Performing Test H5_HAVE_TM_GMTOFF - Success -- Performing Test H5_HAVE___TM_GMTOFF -- Performing Test H5_HAVE___TM_GMTOFF - Failed -- Performing Test H5_HAVE_STRUCT_TIMEZONE -- Performing Test H5_HAVE_STRUCT_TIMEZONE - Failed -- Looking for gettimeofday -- Looking for gettimeofday - found -- Performing Test H5_HAVE_STAT_ST_BLOCKS -- Performing Test H5_HAVE_STAT_ST_BLOCKS - Success -- Looking for ioctl -- Looking for ioctl - found -- Performing Test H5_HAVE_STRUCT_VIDEOCONFIG -- Performing Test H5_HAVE_STRUCT_VIDEOCONFIG - Failed -- Performing Test H5_HAVE_STRUCT_TEXT_INFO -- Performing Test H5_HAVE_STRUCT_TEXT_INFO - Failed -- Looking for _getvideoconfig -- Looking for _getvideoconfig - not found -- Looking for gettextinfo -- Looking for gettextinfo - not found -- Looking for _scrsize -- Looking for _scrsize - not found -- Looking for GetConsoleScreenBufferInfo -- Looking for GetConsoleScreenBufferInfo - not found -- Looking for TIOCGWINSZ -- Looking for TIOCGWINSZ - found -- Looking for TIOCGETD -- Looking for TIOCGETD - found -- Looking for alarm -- Looking for alarm - found -- Looking for fcntl -- Looking for fcntl - found -- Looking for flock -- Looking for flock - found -- Looking for fork -- Looking for fork - found -- Looking for gethostname -- Looking for gethostname - found -- Looking for getrusage -- Looking for getrusage - found -- Looking for pread -- Looking for pread - found -- Looking for pwrite -- Looking for pwrite - found -- Looking for rand_r -- Looking for rand_r - found -- Looking for random -- Looking for random - found -- Looking for strcasestr -- Looking for strcasestr - found -- Looking for strdup -- Looking for strdup - found -- Looking for symlink -- Looking for symlink - found -- Looking for tmpfile -- Looking for tmpfile - found -- Looking for asprintf -- Looking for asprintf - found -- Looking for vasprintf -- Looking for vasprintf - found -- Looking for waitpid -- Looking for waitpid - found -- Looking for sigsetjmp -- Looking for sigsetjmp - found -- Looking for clock_gettime -- Looking for clock_gettime - found -- Looking for clock_gettime in rt -- Looking for clock_gettime in rt - found -- Looking for clock_gettime in posix4 -- Looking for clock_gettime in posix4 - not found -- Check size of CLOCK_MONOTONIC_COARSE -- Check size of CLOCK_MONOTONIC_COARSE - done CMake Error at /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message): Could NOT find CURL (missing: CURL_LIBRARY CURL_INCLUDE_DIR) Call Stack (most recent call first): /usr/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:600 (_FPHSA_FAILURE_MESSAGE) /usr/share/cmake/Modules/FindCURL.cmake:182 (find_package_handle_standard_args) config/cmake/ConfigureChecks.cmake:630 (find_package) CMakeLists.txt:503 (include) -- Configuring incomplete, errors occurred! Error: failed to configure the HDF5 library with CMake Execution halted ERROR: configuration failed for package ‘Rhdf5lib’ * removing ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib’ * restoring previous ‘/home/biocbuild/R/R-devel_2025-02-19/site-library/Rhdf5lib’