Jacques Serizay
| Snapshot Date: 2025-03-17 13:00 -0400 (Mon, 17 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/HiContacts |
| git_branch: RELEASE_3_20 |
| git_last_commit: c4ca14f |
| git_last_commit_date: 2024-10-29 11:14:31 -0400 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-20 12:12 -0400 (Thu, 20 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4756 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4514 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4441 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4406 |
| 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 958/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| HiContacts 1.8.0 (landing page) Jacques Serizay
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | 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 | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the HiContacts package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HiContacts.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: HiContacts |
| Version: 1.8.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiContacts |
| StartedAt: 2025-03-18 01:35:48 -0000 (Tue, 18 Mar 2025) |
| EndedAt: 2025-03-18 01:39:04 -0000 (Tue, 18 Mar 2025) |
| EllapsedTime: 195.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data HiContacts
###
##############################################################################
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* checking for file ‘HiContacts/DESCRIPTION’ ... OK
* preparing ‘HiContacts’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘HiContacts.Rmd’ using rmarkdown
Warning in for (i in seq_along(slots)) { :
closing unused connection 4 (/home/biocbuild/.cache/R/ExperimentHub/37cbb2193e94e6_7751)
Quitting from HiContacts.Rmd:120-127 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `h()`:
! error in evaluating the argument 'con' in selecting a method for function 'import': HDF5. File accessibility. Unable to open file.
---
Backtrace:
▆
1. ├─BiocIO::import(...)
2. ├─BiocIO::import(...)
3. │ ├─BiocIO::import(FileForFormat(con, format), ...)
4. │ └─BiocIO::FileForFormat(con, format)
5. │ └─get(constructorName, ns)(path)
6. │ └─HiCExperiment:::.check_cool_file(path)
7. │ └─HiCExperiment:::.is_cool(path)
8. │ └─HiCExperiment:::.lsCoolFiles(path)
9. │ ├─(function(x) {...
10. │ │ └─base::gsub("//", "/", x)
11. │ │ └─base::is.factor(x)
12. │ ├─base::unique(...)
13. │ ├─dplyr::pull(...)
14. │ ├─dplyr::mutate(rhdf5::h5ls(file), path = paste0(group, "/", name))
15. │ └─rhdf5::h5ls(file)
16. │ └─rhdf5:::h5checktypeOrOpenLoc(...)
17. │ └─rhdf5::H5Fopen(file, flags = flags, fapl = fapl, native = native)
18. └─base::.handleSimpleError(...)
19. └─base (local) h(simpleError(msg, call))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'HiContacts.Rmd' failed with diagnostics:
error in evaluating the argument 'con' in selecting a method for function 'import': HDF5. File accessibility. Unable to open file.
--- failed re-building ‘HiContacts.Rmd’
SUMMARY: processing the following file failed:
‘HiContacts.Rmd’
Error: Vignette re-building failed.
Execution halted