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This page was generated on 2025-04-02 19:35 -0400 (Wed, 02 Apr 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4764
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4495
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4522
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4449
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4426
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 1215/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaseqR2 1.18.1  (landing page)
Panagiotis Moulos
Snapshot Date: 2025-03-31 13:00 -0400 (Mon, 31 Mar 2025)
git_url: https://git.bioconductor.org/packages/metaseqR2
git_branch: RELEASE_3_20
git_last_commit: 3863e41
git_last_commit_date: 2025-03-26 00:05:00 -0400 (Wed, 26 Mar 2025)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
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
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped

BUILD results for metaseqR2 on taishan

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: 1.18.1
Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data metaseqR2
StartedAt: 2025-04-01 00:40:25 -0000 (Tue, 01 Apr 2025)
EndedAt: 2025-04-01 00:45:20 -0000 (Tue, 01 Apr 2025)
EllapsedTime: 295.1 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 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/RtmpciOV1y/test1/plots/qc/correlation_correlogram.png (deflated 2%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/qc/correlation_heatmap.png (deflated 11%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/qc/correlation_pairs.png (deflated 1%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/qc/filtered_genes.png (deflated 8%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/qc/mds.png (deflated 47%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/boxplot_normalized.png (deflated 21%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/boxplot_raw.png (deflated 22%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/gcbias_normalized.png (deflated 16%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/gcbias_raw.png (deflated 15%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/lengthbias_normalized.png (deflated 12%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/lengthbias_raw.png (deflated 12%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 4%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 4%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 4%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 4%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meanvar_normalized.png (deflated 9%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meanvar_raw.png (deflated 7%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 9%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 7%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 6%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 8%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/qc/correlation_correlogram.pdf (deflated 4%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/qc/correlation_heatmap.pdf (deflated 26%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/qc/correlation_pairs.pdf (deflated 4%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/qc/filtered_genes.pdf (deflated 7%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/qc/mds.pdf (deflated 12%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/boxplot_normalized.pdf (deflated 12%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/boxplot_raw.pdf (deflated 12%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/gcbias_normalized.pdf (deflated 4%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/gcbias_raw.pdf (deflated 4%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/lengthbias_normalized.pdf (deflated 1%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/lengthbias_raw.pdf (deflated 1%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 21%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.pdf (deflated 21%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meanvar_normalized.pdf (deflated 44%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/normalization/meanvar_raw.pdf (deflated 39%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.pdf (deflated 9%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
  adding: home/biocbuild/tmp/RtmpciOV1y/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%)
  adding: home/biocbuild/tmp/RtmpciOV1y/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 268 KB

trying URL 'https://code.highcharts.com/highcharts-more.js'
downloaded 92 KB

trying URL 'https://code.highcharts.com/modules/exporting.js'
downloaded 19 KB

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

trying URL 'https://code.highcharts.com/modules/export-data.js'
downloaded 12 KB

trying URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'

Quitting from metaseqr2-statistics.Rmd:228-284 [example-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `download.file()`:
! cannot open URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
---
Backtrace:
    ▆
 1. └─metaseqR2::metaseqr2(...)
 2.   └─metaseqR2:::.downloadJsLibs(PROJECT_PATH, reportDb)
 3.     └─utils::download.file(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metaseqr2-statistics.Rmd' failed with diagnostics:
cannot open URL 'https://unpkg.com/dexie@2.0.4/dist/dexie.min.js'
--- 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