Package: r-cran-rmarkdown
Version: 2.1+dfsg-2
Severity: normal
Dear Maintainer,
* What led up to the situation?
Tests in nascent package pigx-rnaseq.
* What was the outcome of this action?
This error message in the log file while running
/usr/bin/Rscript --vanilla
/home/moeller/git/med-team/pigx/pigx-rnaseq/scripts/runDeseqReport.R
--logo=/home/moeller/git/med-team/pigx/pigx-rnaseq/images/Logo_PiGx.png
--prefix='analysis1.salmon.transcripts'
--reportFile=/home/moeller/git/med-team/pigx/pigx-rnaseq/scripts/deseqReport.Rmd
--countDataFile=/home/moeller/git/med-team/pigx/pigx-rnaseq/tests/output/feature_counts/raw_counts/counts_from_SALMON.transcripts.tsv
--colDataFile=/home/moeller/git/med-team/pigx/pigx-rnaseq/tests/output/colData.tsv
--gtfFile=/home/moeller/git/med-team/pigx/pigx-rnaseq/tests/sample_data/sample.gtf
--caseSampleGroups='HBR' --controlSampleGroups='UHR' --covariates=''
--workdir=/home/moeller/git/med-team/pigx/pigx-rnaseq/tests/output/report
--organism='' >>
/home/moeller/git/med-team/pigx/pigx-rnaseq/tests/output/logs/analysis1.report.salmon.transcripts.log
2>&1
Can't copy dependency files that don't exist:
'/usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/css',
'/usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/fonts',
'/usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/js',
'/usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/shim'
* What outcome did you expect instead?
Well, one could possibly address this also by a better script of pigx-rnaseq,
but the Debian package should not make unecessary compromises. We should have
symlinks in place that point to the respective files in other Debian packages,
such that the copy operation would have worked out just fine.
-- System Information:
Debian Release: bullseye/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Foreign Architectures: i386
Kernel: Linux 5.6.0-1-amd64 (SMP w/2 CPU cores)
Kernel taint flags: TAINT_OOT_MODULE, TAINT_UNSIGNED_MODULE
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8),
LANGUAGE=en_US:en (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled
Versions of packages r-cran-rmarkdown depends on:
ii fonts-font-awesome 5.0.10+really4.7.0~dfsg-1
ii libjs-bootstrap 3.4.1+dfsg-1
ii libjs-highlight.js 9.12.0+dfsg1-5
ii libjs-jquery 3.3.1~dfsg-3
ii libjs-jquery-ui 1.12.1+dfsg-5
ii libjs-modernizr 2.6.2+ds1-3
ii libjs-prettify 2015.12.04+dfsg-1.1
ii node-html5shiv 3.7.3+dfsg-3
ii pandoc 2.5-3+b1
ii r-base-core [r-api-3.5] 3.6.3-2
ii r-cran-base64enc 0.1-3-2
ii r-cran-evaluate 0.14-1
ii r-cran-htmltools 0.4.0-1
ii r-cran-jsonlite 1.6.1+dfsg-1
ii r-cran-knitr 1.28+dfsg-1
ii r-cran-mime 0.9-1
ii r-cran-shiny 1.4.0.2+dfsg-1
ii r-cran-stringr 1.4.0-1
ii r-cran-tinytex 0.22-1
ii r-cran-xfun 0.13-1
ii r-cran-yaml 2.2.1-1
Versions of packages r-cran-rmarkdown recommends:
ii r-cran-testthat 2.3.2-1
Versions of packages r-cran-rmarkdown suggests:
ii r-cran-callr 3.4.3-1
ii r-cran-digest 0.6.25-1
pn r-cran-dygraphs <none>
ii r-cran-fs 1.4.1+dfsg-1
ii r-cran-shiny 1.4.0.2+dfsg-1
ii r-cran-tibble 3.0.1-1
pn r-cran-tufte <none>
-- no debconf information
