Back to Multiple platform build/check report for BioC 3.21:   simplified   long
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2025-02-03 12:37 -0500 (Mon, 03 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4704
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4467
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4478
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 1214/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
metaseqR2 1.19.0  (landing page)
Panagiotis Moulos
Snapshot Date: 2025-02-02 13:40 -0500 (Sun, 02 Feb 2025)
git_url: https://git.bioconductor.org/packages/metaseqR2
git_branch: devel
git_last_commit: 22e1b29
git_last_commit_date: 2024-10-29 10:46:48 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped

BUILD results for metaseqR2 on nebbiolo1

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.

raw results


Summary

Package: metaseqR2
Version: 1.19.0
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data metaseqR2
StartedAt: 2025-02-02 17:57:52 -0500 (Sun, 02 Feb 2025)
EndedAt: 2025-02-02 18:04:51 -0500 (Sun, 02 Feb 2025)
EllapsedTime: 419.4 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/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

trying URL 'http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToGtf'
Content type 'unknown' length 39236624 bytes (37.4 MB)
==================================================
downloaded 37.4 MB

Warning: call dbDisconnect() when finished working with a connection
--- finished re-building ‘metaseqr2-annotation.Rmd’

--- re-building ‘metaseqr2-statistics.Rmd’ using rmarkdown
  adding: tmp/Rtmp3syg0I/test1/plots/qc/correlation_correlogram.png (deflated 1%)
  adding: tmp/Rtmp3syg0I/test1/plots/qc/correlation_heatmap.png (deflated 9%)
  adding: tmp/Rtmp3syg0I/test1/plots/qc/correlation_pairs.png (deflated 1%)
  adding: tmp/Rtmp3syg0I/test1/plots/qc/filtered_genes.png (deflated 5%)
  adding: tmp/Rtmp3syg0I/test1/plots/qc/mds.png (deflated 44%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/boxplot_normalized.png (deflated 17%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/boxplot_raw.png (deflated 17%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/gcbias_normalized.png (deflated 13%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/gcbias_raw.png (deflated 12%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/lengthbias_normalized.png (deflated 10%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/lengthbias_raw.png (deflated 10%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.png (deflated 3%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.png (deflated 3%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.png (deflated 3%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.png (deflated 3%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meanvar_normalized.png (deflated 6%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meanvar_raw.png (deflated 5%)
  adding: tmp/Rtmp3syg0I/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.png (deflated 6%)
  adding: tmp/Rtmp3syg0I/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.png (deflated 5%)
  adding: tmp/Rtmp3syg0I/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.png (deflated 5%)
  adding: tmp/Rtmp3syg0I/test1/plots/statistics/volcano_plot_adult_8_weeks_vs_e14.5.png (deflated 7%)
  adding: tmp/Rtmp3syg0I/test1/plots/qc/correlation_correlogram.pdf (deflated 4%)
  adding: tmp/Rtmp3syg0I/test1/plots/qc/correlation_heatmap.pdf (deflated 26%)
  adding: tmp/Rtmp3syg0I/test1/plots/qc/correlation_pairs.pdf (deflated 4%)
  adding: tmp/Rtmp3syg0I/test1/plots/qc/filtered_genes.pdf (deflated 7%)
  adding: tmp/Rtmp3syg0I/test1/plots/qc/mds.pdf (deflated 12%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/boxplot_normalized.pdf (deflated 12%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/boxplot_raw.pdf (deflated 12%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/gcbias_normalized.pdf (deflated 4%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/gcbias_raw.pdf (deflated 4%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/lengthbias_normalized.pdf (deflated 1%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/lengthbias_raw.pdf (deflated 1%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meandiff_normalized_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 21%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meandiff_normalized_e14.5_e14.5_1_e14.5_2.pdf (deflated 21%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meandiff_raw_adult_8_weeks_a8w_1_a8w_2.pdf (deflated 20%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meandiff_raw_e14.5_e14.5_1_e14.5_2.pdf (deflated 20%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meanvar_normalized.pdf (deflated 44%)
  adding: tmp/Rtmp3syg0I/test1/plots/normalization/meanvar_raw.pdf (deflated 39%)
  adding: tmp/Rtmp3syg0I/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_asis.pdf (deflated 9%)
  adding: tmp/Rtmp3syg0I/test1/plots/statistics/de_heatmap_adult_8_weeks_vs_e14.5_zscore.pdf (deflated 8%)
  adding: tmp/Rtmp3syg0I/test1/plots/statistics/mastat_plot_adult_8_weeks_vs_e14.5.pdf (deflated 5%)
  adding: tmp/Rtmp3syg0I/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 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js'

Quitting from lines 229-284 [example-1] (metaseqr2-statistics.Rmd)
Error: processing vignette 'metaseqr2-statistics.Rmd' failed with diagnostics:
cannot open URL 'http://jvenn.toulouse.inrae.fr/app/js/canvas2svg.js'
--- failed re-building ‘metaseqr2-statistics.Rmd’

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

Error: Vignette re-building failed.
Execution halted