| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-05 11:32 -0500 (Wed, 05 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| 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 1830/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RTCGAToolbox 2.41.0 (landing page) Marcel Ramos
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the RTCGAToolbox package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RTCGAToolbox.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: RTCGAToolbox |
| Version: 2.41.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RTCGAToolbox |
| StartedAt: 2025-11-04 19:38:31 -0500 (Tue, 04 Nov 2025) |
| EndedAt: 2025-11-04 19:39:09 -0500 (Tue, 04 Nov 2025) |
| EllapsedTime: 38.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RTCGAToolbox
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* checking for file ‘RTCGAToolbox/DESCRIPTION’ ... OK
* preparing ‘RTCGAToolbox’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘RTCGAToolbox-vignette.Rmd’ using rmarkdown
trying URL 'https://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/READ/20160128/gdac.broadinstitute.org_READ.Clinical_Pick_Tier1.Level_4.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 31541 bytes (30 KB)
==================================================
downloaded 30 KB
trying URL 'https://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/READ/20160128/gdac.broadinstitute.org_READ.Mutation_Packager_Calls.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 896526 bytes (875 KB)
==================================================
downloaded 875 KB
Quitting from RTCGAToolbox-vignette.Rmd:212-216 [unnamed-chunk-8]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
---
Backtrace:
▆
1. ├─RTCGAToolbox::biocExtract(accmini, "CNASNP")
2. │ └─RTCGAToolbox:::.hasRangeNames(object)
3. └─base::loadNamespace(x)
4. └─base::namespaceImportFrom(...)
5. └─base::importIntoEnv(impenv, impnames, ns, impvars)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'RTCGAToolbox-vignette.Rmd' failed with diagnostics:
object 'microRNAs' is not exported by 'namespace:GenomicFeatures'
--- failed re-building ‘RTCGAToolbox-vignette.Rmd’
SUMMARY: processing the following file failed:
‘RTCGAToolbox-vignette.Rmd’
Error: Vignette re-building failed.
Execution halted