| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-12 11:58 -0500 (Wed, 12 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 293/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CBN2Path 1.0.0 (landing page) William Choi-Kim
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the CBN2Path package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CBN2Path.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: CBN2Path |
| Version: 1.0.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data CBN2Path |
| StartedAt: 2025-11-11 00:15:02 -0000 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 00:18:55 -0000 (Tue, 11 Nov 2025) |
| EllapsedTime: 233.1 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 CBN2Path
###
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* checking for file ‘CBN2Path/DESCRIPTION’ ... OK
* preparing ‘CBN2Path’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CBN2Path.Rmd’ using rmarkdown
/usr/bin/gtar: This does not look like a tar archive
gzip: stdin: not in gzip format
/usr/bin/gtar: Child returned status 1
/usr/bin/gtar: Error is not recoverable: exiting now
Quitting from CBN2Path.Rmd:54-64 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `GDCprepare()`:
! I couldn't find all the files from the query. Please check if the directory parameter is right or `GDCdownload` downloaded the samples.
---
Backtrace:
▆
1. └─CBN2Path::getRawTCGAData("TCGA-BLCA")
2. └─TCGAbiolinks::GDCprepare(query)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'CBN2Path.Rmd' failed with diagnostics:
I couldn't find all the files from the query. Please check if the directory parameter is right or `GDCdownload` downloaded the samples.
--- failed re-building ‘CBN2Path.Rmd’
SUMMARY: processing the following file failed:
‘CBN2Path.Rmd’
Error: Vignette re-building failed.
Execution halted