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This page was generated on 2025-09-18 11:40 -0400 (Thu, 18 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4827
merida1macOS 12.7.5 Montereyx86_644.5.1 RC (2025-06-05 r88288) -- "Great Square Root" 4608
kjohnson1macOS 13.6.6 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4549
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4581
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 1807/2341HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RNAmodR.ML 1.22.0  (landing page)
Felix G.M. Ernst
Snapshot Date: 2025-09-15 13:40 -0400 (Mon, 15 Sep 2025)
git_url: https://git.bioconductor.org/packages/RNAmodR.ML
git_branch: RELEASE_3_21
git_last_commit: 4f3cd89
git_last_commit_date: 2025-04-15 11:47:23 -0400 (Tue, 15 Apr 2025)
nebbiolo1Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for RNAmodR.ML on kunpeng2

To the developers/maintainers of the RNAmodR.ML package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RNAmodR.ML.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.

raw results


Summary

Package: RNAmodR.ML
Version: 1.22.0
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data RNAmodR.ML
StartedAt: 2025-09-16 11:24:26 -0000 (Tue, 16 Sep 2025)
EndedAt: 2025-09-16 11:30:54 -0000 (Tue, 16 Sep 2025)
EllapsedTime: 388.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data RNAmodR.ML
###
##############################################################################
##############################################################################


* checking for file ‘RNAmodR.ML/DESCRIPTION’ ... OK
* preparing ‘RNAmodR.ML’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘RNAmodR.ML.Rmd’ using rmarkdown
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c49cba7de_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e5d33e220660_2523'
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525'
[W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c49cba7de_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e5d33e220660_2523'
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525'
[W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525
[E::bgzf_read] BGZF block offset 3489 set beyond block size 0
[E::bgzf_read] Read block operation failed with error 8 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 9 after 0 of 4 bytes
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c49cba7de_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c49cba7de_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e5d33e220660_2523'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e5d33e220660_2523'
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525'
[W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525
[E::bgzf_read_block] Failed to read BGZF block data at offset 27418923 expected 8124 bytes; hread returned 3779
[E::bgzf_read] Read block operation failed with error 4 after 38 of 44 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525'
[W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c49cba7de_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e5d33e220660_2523'
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525'
[W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c49cba7de_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e5d33e220660_2523'
[W::bam_hdr_read] EOF marker is absent. The input is probably truncated
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525'
[W::hts_idx_load3] The index file is older than the data file: /home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525
[E::bgzf_read_block] Failed to read BGZF block data at offset 36184006 expected 10472 bytes; hread returned 4136
[E::bgzf_read] Read block operation failed with error 4 after 0 of 32 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::bgzf_read] Read block operation failed with error 5 after 0 of 4 bytes
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c49cba7de_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c49cba7de_2521'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e5d33e220660_2523'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e5d33e220660_2523'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525'
[E::idx_find_and_load] Could not retrieve index file for '/home/biocbuild/.cache/R/ExperimentHub/7e64c7107d46d_2525'

Quitting from RNAmodR.ML.Rmd:331-339 [unnamed-chunk-19]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error:
! subscript contains invalid names
---
Backtrace:
     ▆
  1. ├─mod[c("1", "4")]
  2. └─mod[c("1", "4")]
  3.   ├─methods::callNextMethod(x = x, i = i)
  4.   │ └─base::eval(call, callEnv)
  5.   │   └─base::eval(call, callEnv)
  6.   └─S4Vectors (local) .nextMethod(x = x, i = i)
  7.     └─S4Vectors:::subset_along_ROWS(x, i, drop = drop)
  8.       ├─S4Vectors::extractROWS(x, i)
  9.       └─GenomicRanges (local) extractROWS(x, i)
 10.         └─IRanges (local) METHOD(x, i)
 11.           └─S4Vectors::normalizeSingleBracketSubscript(i, x, as.NSBS = TRUE)
 12.             ├─S4Vectors::NSBS(...)
 13.             └─S4Vectors::NSBS(...)
 14.               └─S4Vectors:::.subscript_error("subscript contains invalid ", what)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'RNAmodR.ML.Rmd' failed with diagnostics:
subscript contains invalid names
--- failed re-building ‘RNAmodR.ML.Rmd’

SUMMARY: processing the following file failed:
  ‘RNAmodR.ML.Rmd’

Error: Vignette re-building failed.
Execution halted