Hervé Pagès
| Snapshot Date: 2025-07-28 13:40 -0400 (Mon, 28 Jul 2025) |
| git_url: https://git.bioconductor.org/packages/HDF5Array |
| git_branch: RELEASE_3_21 |
| git_last_commit: 1e32d9f |
| git_last_commit_date: 2025-04-15 10:58:57 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-07-31 11:48 -0400 (Thu, 31 Jul 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4823 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4565 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4603 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4544 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 955/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HDF5Array 1.36.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: HDF5Array |
| Version: 1.36.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HDF5Array |
| StartedAt: 2025-07-29 01:25:40 -0000 (Tue, 29 Jul 2025) |
| EndedAt: 2025-07-29 01:26:39 -0000 (Tue, 29 Jul 2025) |
| EllapsedTime: 59.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HDF5Array
###
##############################################################################
##############################################################################
* checking for file ‘HDF5Array/DESCRIPTION’ ... OK
* preparing ‘HDF5Array’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HDF5Array_performance.Rmd’ using rmarkdown
Quitting from HDF5Array_performance.Rmd:112-115 [brain_s]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `rhdf5::H5Fopen()`:
! HDF5. File accessibility. Unable to open file.
---
Backtrace:
▆
1. └─HDF5Array::TENxMatrix(brain_s_path, group = "mm10")
2. └─HDF5Array::TENxMatrixSeed(filepath, group)
3. └─HDF5Array::H5SparseMatrixSeed(filepath, group)
4. └─HDF5Array:::.check_group(filepath, group)
5. └─h5mread::h5exists(filepath, group)
6. └─h5mread:::.H5Fopen(filepath, flags = "H5F_ACC_RDONLY")
7. ├─base::suppressMessages(rhdf5::H5Fopen(name, flags = flags, fapl = fapl))
8. │ └─base::withCallingHandlers(...)
9. └─rhdf5::H5Fopen(name, flags = flags, fapl = fapl)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'HDF5Array_performance.Rmd' failed with diagnostics:
HDF5. File accessibility. Unable to open file.
--- failed re-building ‘HDF5Array_performance.Rmd’
SUMMARY: processing the following file failed:
‘HDF5Array_performance.Rmd’
Error: Vignette re-building failed.
Execution halted