Felix G.M. Ernst
| Snapshot Date: 2025-11-17 13:45 -0500 (Mon, 17 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/RNAmodR |
| git_branch: RELEASE_3_22 |
| git_last_commit: 683b357 |
| git_last_commit_date: 2025-10-29 10:52:38 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-20 12:06 -0500 (Thu, 20 Nov 2025).
| 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" | 4615 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.2 Patched (2025-11-05 r88990) -- "[Not] Part in a Rumble" | 4610 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble" | 4598 |
| 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 1819/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| RNAmodR 1.24.0 (landing page) Felix G.M. Ernst
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the RNAmodR package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAmodR.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 |
| Version: 1.24.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RNAmodR |
| StartedAt: 2025-11-18 00:20:51 -0500 (Tue, 18 Nov 2025) |
| EndedAt: 2025-11-18 00:22:07 -0500 (Tue, 18 Nov 2025) |
| EllapsedTime: 75.7 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data RNAmodR
###
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* checking for file ‘RNAmodR/DESCRIPTION’ ... OK
* preparing ‘RNAmodR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RNAmodR.Rmd’ using rmarkdown
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa2e4295cc_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa213cfc65_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa6c65bde5_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa2e4295cc_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa2e4295cc_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa213cfc65_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa213cfc65_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa6c65bde5_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa6c65bde5_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa2e4295cc_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa213cfc65_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa6c65bde5_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa2e4295cc_2521'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa213cfc65_2523'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14afa6c65bde5_2525'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add6302dbbe_2545'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add7953fbb4_2547'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add77844c31_2549'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add4d7d65df_2537'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add7ebccaff_2539'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add478e976e_2541'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add2ae910d4_2543'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add6302dbbe_2545'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add4d7d65df_2537'
[E::idx_find_and_load] Could not retrieve index file for '/Users/biocbuild/Library/Caches/org.R-project.R/R/ExperimentHub/14add478e976e_2541'
Quitting from RNAmodR.Rmd:254-256 [modifierset1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `reducer$value.cache[[as.character(idx)]] <- values`:
! wrong args for environment subassignment
---
Backtrace:
▆
1. └─RNAmodR::ModSetInosine(files, annotation = annotation, sequences = sequences)
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(...)
12. ├─BiocParallel::bploop(...)
13. └─BiocParallel:::bploop.lapply(...)
14. └─BiocParallel:::.bploop_impl(...)
15. └─BiocParallel:::.collect_result(manager, reducer, progress, BPPARAM)
16. ├─BiocParallel:::.reducer_add(reducer, njob, value)
17. └─BiocParallel:::.reducer_add(reducer, njob, value)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'RNAmodR.Rmd' failed with diagnostics:
wrong args for environment subassignment
--- failed re-building ‘RNAmodR.Rmd’
--- re-building ‘RNAmodR.creation.Rmd’ using rmarkdown
Warning in dir.create(biocDir) :
cannot create dir '/var/folders/dc/2xck8b8s0_3gymbxnrltzxhm0000gs/T//RtmpqLgKxX/BiocStyle', reason 'No such file or directory'
Warning in file(con, "w") :
cannot open file '/var/folders/dc/2xck8b8s0_3gymbxnrltzxhm0000gs/T//RtmpqLgKxX/BiocStyle/template.html': No such file or directory
Error: processing vignette 'RNAmodR.creation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘RNAmodR.creation.Rmd’
SUMMARY: processing the following files failed:
‘RNAmodR.Rmd’ ‘RNAmodR.creation.Rmd’
Error: Vignette re-building failed.
Execution halted