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This page was generated on 2024-03-01 11:36:01 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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 935/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HDF5Array 1.30.1  (landing page)
Hervé Pagès
Snapshot Date: 2024-02-29 14:05:06 -0500 (Thu, 29 Feb 2024)
git_url: https://git.bioconductor.org/packages/HDF5Array
git_branch: RELEASE_3_18
git_last_commit: 1aee703
git_last_commit_date: 2024-02-14 00:03:31 -0500 (Wed, 14 Feb 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    ERROR    OK  
kjohnson1macOS 13.6.1 Ventura / arm64see weekly results here

INSTALL results for HDF5Array on nebbiolo2


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.

raw results


Summary

Package: HDF5Array
Version: 1.30.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL HDF5Array
StartedAt: 2024-02-29 15:09:42 -0500 (Thu, 29 Feb 2024)
EndedAt: 2024-02-29 15:10:08 -0500 (Thu, 29 Feb 2024)
EllapsedTime: 26.2 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL HDF5Array
###
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘HDF5Array’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c H5File.c -o H5File.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c global_errmsg_buf.c -o global_errmsg_buf.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c H5DSetDescriptor.c -o H5DSetDescriptor.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c h5dimscales.c -o h5dimscales.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c uaselection.c -o uaselection.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c h5mread_helpers.c -o h5mread_helpers.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c h5mread_startscounts.c -o h5mread_startscounts.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c ChunkIterator.c -o ChunkIterator.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c h5mread_index.c -o h5mread_index.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c h5mread_sparse.c -o h5mread_sparse.o
h5mread_sparse.c:206:13: warning: ‘NOT_USED_make_nzindex_from_bufs’ defined but not used [-Wunused-function]
  206 | static SEXP NOT_USED_make_nzindex_from_bufs(const IntAEAE *nzindex_bufs,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:179:13: warning: ‘NOT_USED_make_nzdata_from_IntAE_bufs’ defined but not used [-Wunused-function]
  179 | static SEXP NOT_USED_make_nzdata_from_IntAE_bufs(const IntAEAE *nzdata_bufs,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h5mread_sparse.c:123:13: warning: ‘NOT_USED_make_nzindex_from_buf’ defined but not used [-Wunused-function]
  123 | static SEXP NOT_USED_make_nzindex_from_buf(const IntAE *nzindex_buf,
      |             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c h5mread.c -o h5mread.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c h5summarize.c -o h5summarize.o
gcc -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/include' -I/usr/local/include    -fpic  -g -O2  -Wall -c R_init_HDF5Array.c -o R_init_HDF5Array.o
gcc -shared -L/home/biocbuild/bbs-3.18-bioc/R/lib -L/usr/local/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 /home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/lib/libhdf5_hl.a /home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/lib/libhdf5.a -L/home/biocbuild/bbs-3.18-bioc/R/site-library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -L/home/biocbuild/bbs-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-library/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)