Alexey Sergushichev
| Snapshot Date: 2025-08-29 13:45 -0400 (Fri, 29 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/gatom |
| git_branch: devel |
| git_last_commit: 6509ada |
| git_last_commit_date: 2025-04-15 13:23:11 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-30 12:08 -0400 (Sat, 30 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4615 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4562 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4541 |
| 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 779/2320 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| gatom 1.7.0 (landing page) Alexey Sergushichev
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the gatom package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gatom.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: gatom |
| Version: 1.7.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data gatom |
| StartedAt: 2025-08-28 23:59:00 -0000 (Thu, 28 Aug 2025) |
| EndedAt: 2025-08-29 00:17:53 -0000 (Fri, 29 Aug 2025) |
| EllapsedTime: 1133.4 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 gatom
###
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* checking for file ‘gatom/DESCRIPTION’ ... OK
* preparing ‘gatom’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gatom-tutorial.Rmd’ using rmarkdown
Quitting from gatom-tutorial.Rmd:458-471 [unnamed-chunk-38]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `readRDS()`:
! cannot read from connection
---
Backtrace:
▆
1. └─base::readRDS(url("http://artyomovlab.wustl.edu/publications/supp_materials/GATOM/network.combined.rds"))
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'gatom-tutorial.Rmd' failed with diagnostics:
cannot read from connection
--- failed re-building ‘gatom-tutorial.Rmd’
SUMMARY: processing the following file failed:
‘gatom-tutorial.Rmd’
Error: Vignette re-building failed.
Execution halted