| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-01 11:32 -0400 (Sat, 01 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" | 4774 |
| 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 931/2321 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GSVA 2.5.0 (landing page) Robert Castelo
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
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To the developers/maintainers of the GSVA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GSVA.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: GSVA |
| Version: 2.5.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data GSVA |
| StartedAt: 2025-10-31 18:10:06 -0400 (Fri, 31 Oct 2025) |
| EndedAt: 2025-10-31 18:11:40 -0400 (Fri, 31 Oct 2025) |
| EllapsedTime: 94.1 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 GSVA
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* checking for file ‘GSVA/DESCRIPTION’ ... OK
* preparing ‘GSVA’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* running ‘cleanup’
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘GSVA.Rmd’ using rmarkdown
Quitting from GSVA.Rmd:345-352 [unnamed-chunk-7]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `library()`:
! there is no package called 'GSVAdata'
---
Backtrace:
▆
1. └─base::library(GSVAdata)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GSVA.Rmd' failed with diagnostics:
there is no package called 'GSVAdata'
--- failed re-building ‘GSVA.Rmd’
--- re-building ‘GSVA_scRNAseq.Rmd’ using rmarkdown
Quitting from GSVA_scRNAseq.Rmd:164-172 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `file()`:
! cannot open the connection
---
Backtrace:
▆
1. └─GSVA::readGMT(fname)
2. ├─base::strsplit(readLines(con, ...), sep)
3. └─base::readLines(con, ...)
4. └─base::file(con, "r")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'GSVA_scRNAseq.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘GSVA_scRNAseq.Rmd’
SUMMARY: processing the following files failed:
‘GSVA.Rmd’ ‘GSVA_scRNAseq.Rmd’
Error: Vignette re-building failed.
Execution halted