| Back to Build/check report for BioC 3.23: simplified long |
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This page was generated on 2025-11-08 11:32 -0500 (Sat, 08 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" | 4821 |
| 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 1793/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RNAmodR.RiboMethSeq 1.25.0 (landing page) Felix G.M. Ernst
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
|
To the developers/maintainers of the RNAmodR.RiboMethSeq package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAmodR.RiboMethSeq.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: RNAmodR.RiboMethSeq |
| Version: 1.25.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data RNAmodR.RiboMethSeq |
| StartedAt: 2025-11-07 19:37:07 -0500 (Fri, 07 Nov 2025) |
| EndedAt: 2025-11-07 19:38:41 -0500 (Fri, 07 Nov 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 RNAmodR.RiboMethSeq
###
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* checking for file ‘RNAmodR.RiboMethSeq/DESCRIPTION’ ... OK
* preparing ‘RNAmodR.RiboMethSeq’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘RNAmodR.RiboMethSeq.Rmd’ using rmarkdown
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d75fbf076_2530'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4ea0fe5_2532'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d75fbf076_2530'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4ea0fe5_2532'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d75fbf076_2530'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/ca93d4ea0fe5_2532'
Quitting from RNAmodR.RiboMethSeq.Rmd:78-81 [unnamed-chunk-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! BiocParallel errors
2 remote errors, element index: 1, 2
0 unevaluated and other errors
first remote error:
Error in h(simpleError(msg, call)): error in evaluating the argument 'table' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'shortName': Biostrings internal error, please report
---
Backtrace:
▆
1. └─RNAmodR.RiboMethSeq::ModSetRiboMethSeq(...)
2. ├─RNAmodR::ModifierSet(...)
3. └─RNAmodR::ModifierSet(...)
4. └─RNAmodR:::.bamfiles_to_ModifierSet(...)
5. ├─BiocParallel::bpmapply(...)
6. └─BiocParallel::bpmapply(...)
7. ├─BiocParallel::bpmapply(...)
8. └─BiocParallel::bpmapply(...)
9. ├─BiocParallel::bplapply(...)
10. └─BiocParallel::bplapply(...)
11. └─BiocParallel:::.bpinit(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'RNAmodR.RiboMethSeq.Rmd' failed with diagnostics:
BiocParallel errors
2 remote errors, element index: 1, 2
0 unevaluated and other errors
first remote error:
Error in h(simpleError(msg, call)): error in evaluating the argument 'table' in selecting a method for function '%in%': error in evaluating the argument 'x' in selecting a method for function 'shortName': Biostrings internal error, please report
--- failed re-building ‘RNAmodR.RiboMethSeq.Rmd’
SUMMARY: processing the following file failed:
‘RNAmodR.RiboMethSeq.Rmd’
Error: Vignette re-building failed.
Execution halted