| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-02-12 11:58 -0500 (Thu, 12 Feb 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4889 |
| 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 1500/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| OmicsMLRepoR 1.4.2 (landing page) Sehyun Oh
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for OmicsMLRepoR in R Universe. | ||||||||||||||
|
To the developers/maintainers of the OmicsMLRepoR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmicsMLRepoR.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. |
| Package: OmicsMLRepoR |
| Version: 1.4.2 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 OmicsMLRepoR |
| StartedAt: 2026-02-09 19:29:28 -0500 (Mon, 09 Feb 2026) |
| EndedAt: 2026-02-09 19:31:15 -0500 (Mon, 09 Feb 2026) |
| EllapsedTime: 107.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 OmicsMLRepoR
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* checking for file ‘OmicsMLRepoR/DESCRIPTION’ ... OK
* preparing ‘OmicsMLRepoR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Browse_cBioPortal.Rmd’ using rmarkdown
Quitting from Browse_cBioPortal.Rmd:118-130 [breast_cancer]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
▆
1. ├─cbio %>% tree_filter(cancer_type, "breast cancer")
2. └─OmicsMLRepoR::tree_filter(., cancer_type, "breast cancer")
3. └─utils::read.csv(file.path(dir, fname), header = TRUE)
4. └─utils::read.table(...)
5. └─base::file(file, "rt")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Browse_cBioPortal.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Browse_cBioPortal.Rmd’
--- re-building ‘Quickstart.Rmd’ using rmarkdown
--- finished re-building ‘Quickstart.Rmd’
--- re-building ‘tree_filter.Rmd’ using rmarkdown
--- finished re-building ‘tree_filter.Rmd’
SUMMARY: processing the following file failed:
‘Browse_cBioPortal.Rmd’
Error: Vignette re-building failed.
Execution halted