Multiple platform build/check report for BioC 3.21 - BUILD results for metaseqR2 on kunpeng2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.1 (2025-06-13) -- "Great Square Root"	4833
merida1	macOS 12.7.6 Monterey	x86_64	4.5.1 RC (2025-06-05 r88288) -- "Great Square Root"	4614
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"	4555
kunpeng2	Linux (openEuler 24.03 LTS)	aarch64	R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences"	4586
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*

BUILD results for metaseqR2 on kunpeng2

To the developers/maintainers of the metaseqR2 package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/metaseqR2.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: metaseqR2

Version: 1.20.0

Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data metaseqR2

StartedAt: 2025-10-14 02:16:57 -0000 (Tue, 14 Oct 2025)

EndedAt: 2025-10-14 02:28:42 -0000 (Tue, 14 Oct 2025)

EllapsedTime: 705.2 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 metaseqR2
###
##############################################################################
##############################################################################


* checking for file ‘metaseqR2/DESCRIPTION’ ... OK
* preparing ‘metaseqR2’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘metaseqr2-annotation.Rmd’ using rmarkdown
trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/ncbiGene.txt.gz'
Content type 'application/x-gzip' length 238 bytes
==================================================
downloaded 238 bytes

trying URL 'http://hgdownload.cse.ucsc.edu/goldenPath/eboVir3/database/chromInfo.txt.gz'
Content type 'application/x-gzip' length 71 bytes
==================================================
downloaded 71 bytes

/home/biocbuild/bin/genePredToGtf: error while loading shared libraries: libssl.so.1.1: cannot open shared object file: No such file or directory

Quitting from metaseqr2-annotation.Rmd:190-254 [example-4]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection
---
Backtrace:
     ▆
  1. └─metaseqR2::buildCustomAnnotation(...)
  2.   └─metaseqR2:::parseCustomGtf(gtfFile)
  3.     ├─BiocIO::import(gtfFile, colnames = desiredColumns, feature.type = .GFF_FEATURE_TYPES)
  4.     └─BiocIO::import(gtfFile, colnames = desiredColumns, feature.type = .GFF_FEATURE_TYPES)
  5.       ├─BiocIO::import(FileForFormat(con), ...)
  6.       └─rtracklayer::import(FileForFormat(con), ...)
  7.         └─rtracklayer (local) .local(con, format, text, ...)
  8.           └─BiocIO:::connection(m, con, "r")
  9.             └─BiocIO:::connectionForResource(manager, resource(x), open = open)
 10.               ├─base::open(con, open)
 11.               └─base::open.connection(con, open)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metaseqr2-annotation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘metaseqr2-annotation.Rmd’

--- re-building ‘metaseqr2-statistics.Rmd’ using rmarkdown
Warning: call dbDisconnect() when finished working with a connection
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/qc/correlation_correlogram.png (deflated 2%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/qc/correlation_heatmap.png (deflated 11%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/qc/correlation_pairs.png (deflated 1%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/qc/filtered_genes.png (deflated 8%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/qc/mds.png (deflated 47%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/boxplot_normalized.png (deflated 21%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/boxplot_raw.png (deflated 22%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/gcbias_normalized.png (deflated 16%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/gcbias_raw.png (deflated 15%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/lengthbias_normalized.png (deflated 12%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/lengthbias_raw.png (deflated 12%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 4%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 4%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 4%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 4%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meanvar_normalized.png (deflated 9%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meanvar_raw.png (deflated 7%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 9%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 7%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 6%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 8%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/qc/correlation_correlogram.pdf (deflated 4%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/qc/correlation_heatmap.pdf (deflated 26%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/qc/correlation_pairs.pdf (deflated 4%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/qc/filtered_genes.pdf (deflated 7%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/qc/mds.pdf (deflated 12%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/boxplot_normalized.pdf (deflated 12%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/boxplot_raw.pdf (deflated 12%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/gcbias_normalized.pdf (deflated 4%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/gcbias_raw.pdf (deflated 4%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/lengthbias_normalized.pdf (deflated 1%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/lengthbias_raw.pdf (deflated 1%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 21%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.pdf (deflated 21%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meanvar_normalized.pdf (deflated 44%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/normalization/meanvar_raw.pdf (deflated 39%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.pdf (deflated 9%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%)
  adding: home/biocbuild/tmp/RtmpcVyj77/test1/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.pdf (deflated 2%)
trying URL 'https://raw.github.com/HubSpot/pace/v1.0.0/pace.min.js'
Content type 'text/plain; charset=utf-8' length 12363 bytes (12 KB)
==================================================
downloaded 12 KB

trying URL 'https://code.highcharts.com/highcharts.js'
downloaded 272 KB

trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 96 KB

trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 26 KB

trying URL 'https://code.highcharts.com/modules/offline-exporting.js'
downloaded 5942 bytes

trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 13 KB

trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
Content type 'text/javascript; charset=utf-8' length 56670 bytes (55 KB)
==================================================
downloaded 55 KB


Quitting from metaseqr2-statistics.Rmd:228-284 [example-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `pm[[2]]`:
! subscript out of bounds
---
Backtrace:
     ▆
  1. ├─metaseqR2::metaseqr2(...)
  2. │ └─rmarkdown::render(...)
  3. │   └─knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
  4. │     └─knitr:::process_file(text, output)
  5. │       ├─xfun:::handle_error(...)
  6. │       ├─base::withCallingHandlers(...)
  7. │       └─knitr:::process_group(group)
  8. │         └─knitr:::call_block(x)
  9. │           └─knitr:::block_exec(params)
 10. │             └─knitr:::eng_r(options)
 11. │               ├─knitr:::in_input_dir(...)
 12. │               │ └─knitr:::in_dir(input_dir(), expr)
 13. │               └─knitr (local) evaluate(...)
 14. │                 └─evaluate::evaluate(...)
 15. │                   ├─base::withRestarts(...)
 16. │                   │ └─base (local) withRestartList(expr, restarts)
 17. │                   │   ├─base (local) withOneRestart(withRestartList(expr, restarts[-nr]), restarts[[nr]])
 18. │                   │   │ └─base (local) doWithOneRestart(return(expr), restart)
 19. │                   │   └─base (local) withRestartList(expr, restarts[-nr])
 20. │                   │     └─base (local) withOneRestart(expr, restarts[[1L]])
 21. │                   │       └─base (local) doWithOneRestart(return(expr), restart)
 22. │                   ├─evaluate:::with_handlers(...)
 23. │                   │ ├─base::eval(call)
 24. │                   │ │ └─base::eval(call)
 25. │                   │ └─base::withCallingHandlers(...)
 26. │                   ├─base::withVisible(eval(expr, envir))
 27. │                   └─base::eval(expr, envir)
 28. │                     └─base::eval(expr, envir)
 29. │                       ├─... %>% layout(width = 640, height = 480)
 30. │                       ├─heatmaply::heatmaply(...)
 31. │                       └─heatmaply:::heatmaply.default(...)
 32. │                         ├─heatmaply::heatmaply(...)
 33. │                         └─heatmaply:::heatmaply.heatmapr(...)
 34. │                           ├─... %>% layout(showlegend = FALSE)
 35. │                           ├─plotly::ggplotly(...)
 36. │                           └─plotly:::ggplotly.ggplot(...)
 37. │                             └─plotly::gg2list(...)
 38. ├─plotly::layout(., width = 640, height = 480)
 39. └─plotly::layout(., showlegend = FALSE)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metaseqr2-statistics.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘metaseqr2-statistics.Rmd’

SUMMARY: processing the following files failed:
  ‘metaseqr2-annotation.Rmd’ ‘metaseqr2-statistics.Rmd’

Error: Vignette re-building failed.
Execution halted