Package: r-cran-dt Version: 0.9+dfsg-1 Severity: normal Hi,
I'm trying to use r-cran-dt to generate a report. The Debian package has problems (see the script at the end to reproduce the issue): - one css file is missing: $ Rscript -e "rmarkdown::render('small_test.rmd')" [...] /usr/bin/pandoc +RTS -K512m -RTS small_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output small_test.html --email-obfuscation none --self-contained --standalone --section-divs --template /usr/lib/R/site-library/rmarkdown/rmd/h/default.html --highlight-style tango --css style.css --variable 'theme:cerulean' --include-in-header /tmp/RtmpDhs6QV/rmarkdown-str692d16ebe87a.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/latex-div.lua pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/css/jquery.dataTables.extra.css: openBinaryFile: does not exist (No such file or directory) Erreur : pandoc document conversion failed with error 1 Exécution arrêtée Indeed, jquery.dataTables.extra.css is removed from the Debian r-cran-dt package, however, according to apt-file and https://pacakages.debian.org, no Debian package is providing this file. Continuing with $ sudo touch /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/css/jquery.dataTables.extra.css to workaround this problem - one javascript file is not in the expected path: $ Rscript -e "rmarkdown::render('small_test.rmd')" [...] /usr/bin/pandoc +RTS -K512m -RTS small_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output small_test.html --email-obfuscation none --self-contained --standalone --section-divs --template /usr/lib/R/site-library/rmarkdown/rmd/h/default.html --highlight-style tango --css style.css --variable 'theme:cerulean' --include-in-header /tmp/RtmpI2EroN/rmarkdown-str6bbf3216f5ad.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/latex-div.lua pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/js/jquery.dataTables.min.js: openBinaryFile: does not exist (No such file or directory) Erreur : pandoc document conversion failed with error 1 Exécution arrêtée Indeed, the javascript file is in /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/js/jquery.dataTables.min.js and not /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/jquery.dataTables.min.js Continuing with $ sudo ln -s . /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/js to workarround the problem - another javascript file is still not in the expected place: Rscript -e "rmarkdown::render('small_test.rmd')" [...] /usr/bin/pandoc +RTS -K512m -RTS small_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output small_test.html --email-obfuscation none --self-contained --standalone --section-divs --template /usr/lib/R/site-library/rmarkdown/rmd/h/default.html --highlight-style tango --css style.css --variable 'theme:cerulean' --include-in-header /tmp/RtmpS0d9gK/rmarkdown-str6e161233a5ca.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/latex-div.lua pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/jszip.min.js: openBinaryFile: does not exist (No such file or directory) Erreur : pandoc document conversion failed with error 1 Exécution arrêtée dpkg -S tells me that this file is (on Debian system) in libjs-jquery-datatables-extensions: /usr/share/javascript/jquery-datatables-extensions/JSZip/jszip.min.js (with a copy in 3 others packages on my machine) Continuing with $ sudo ln -s /usr/share/javascript/jquery-datatables-extensions/JSZip/jszip.min.js /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/jszip.min.js to workarround the problem - another javascript file is still not in the expected place: Rscript -e "rmarkdown::render('small_test.rmd')" [...] /usr/bin/pandoc +RTS -K512m -RTS small_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output small_test.html --email-obfuscation none --self-contained --standalone --section-divs --template /usr/lib/R/site-library/rmarkdown/rmd/h/default.html --highlight-style tango --css style.css --variable 'theme:cerulean' --include-in-header /tmp/RtmpMKo2nV/rmarkdown-str6e7f218627e7.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/latex-div.lua pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/pdfmake.min.js: openBinaryFile: does not exist (No such file or directory) Erreur : pandoc document conversion failed with error 1 Exécution arrêtée dpkg -S tells me that this file is (on Debian system) in libjs-jquery-datatables-extensions: /usr/share/javascript/jquery-datatables-extensions/pdfmake/build/pdfmake.min.js Continuing with $ sudo ln -s /usr/share/javascript/jquery-datatables-extensions/pdfmake/build/pdfmake.min.js /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/pdfmake.min.js - another javascript file is missing (vfs_fonts.js) and does not seem to be available in Debian $ Rscript -e "rmarkdown::render('small_test.rmd')" [...] /usr/bin/pandoc +RTS -K512m -RTS small_test.utf8.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash+smart --output small_test.html --email-obfuscation none --self-contained --standalone --section-divs --template /usr/lib/R/site-library/rmarkdown/rmd/h/default.html --highlight-style tango --css style.css --variable 'theme:cerulean' --include-in-header /tmp/RtmpiA4YrW/rmarkdown-str6ed3608bac42.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/pagebreak.lua --lua-filter /usr/lib/R/site-library/rmarkdown/rmd/lua/latex-div.lua pandoc: /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/vfs_fonts.js: openBinaryFile: does not exist (No such file or directory) Erreur : pandoc document conversion failed with error 1 Exécution arrêtée Continuing with $ sudo touch /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/vfs_fonts.js Eventually the html document is generated. So, it seems to me that: - some files are removed from the r-cran-dt source packages whereas they are not provided by any other Debian packages (at least jquery.dataTables.extra.css and vfs_fonts.js) - some files are not available in the expected path (through symlinks), at least jquery.dataTables.min.js, jszip.min.js and pdfmake.min.js Note that removing all workarounds: $ sudo rm /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/css/jquery.dataTables.extra.css /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables/js /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/jszip.min.js /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/pdfmake.min.js /usr/lib/R/site-library/DT/htmlwidgets/lib/datatables-extensions/Buttons/js/vfs_fonts.js and installing locally the DT package (install.packages('DT') from R) makes the script working. So the bugs come from the packaging. Regards, Vincent PS: in attachment, the Rcmd script file and the data file to reproduce this bug -- System Information: Debian Release: bullseye/sid APT prefers stable-updates APT policy: (500, 'stable-updates'), (500, 'oldstable-updates'), (500, 'unstable'), (500, 'testing'), (500, 'stable'), (500, 'oldstable'), (1, 'experimental') Architecture: amd64 (x86_64) Foreign Architectures: i386, armel, mipsel Kernel: Linux 5.2.0-3-amd64 (SMP w/4 CPU cores) Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8), LANGUAGE=fr_FR.utf8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) Versions of packages r-cran-dt depends on: ii libjs-jquery 3.3.1~dfsg-3 ii libjs-jquery-datatables 1.10.20+dfsg-1 ii libjs-jquery-datatables-extensions 0.0+20150910+dfsg-2 ii libjs-jquery-selectize.js 0.12.6+dfsg-1 ii r-base-core [r-api-3.5] 3.6.1-6 ii r-cran-crosstalk 1.0.0+dfsg-4 ii r-cran-htmltools 0.4.0-1 ii r-cran-htmlwidgets 1.5+dfsg-1 ii r-cran-jsonlite 1.6+dfsg-1 ii r-cran-magrittr 1.5-5 ii r-cran-promises 1.1.0-1 Versions of packages r-cran-dt recommends: ii r-cran-knitr 1.25+dfsg-1 ii r-cran-rmarkdown 1.16+dfsg-1 Versions of packages r-cran-dt suggests: ii r-cran-shiny 1.3.2+dfsg-1 -- no debconf information
--- title: "Test" author: "Cellule de Bioinformatique" date: "`r format(Sys.time(), '%d %B %Y')`" output: html_document: theme: cerulean highlight: tango --- ```{r setup, include=FALSE} knitr::opts_chunk$set(echo = FALSE) library(dplyr) library(tidyr) library(DT) ``` # Métriques de séquençage ```{r metrics, echo=FALSE} Identitovigilance = read.delim("Identitovigilance.tsv", header=TRUE) Identitovigilance %>% datatable(extensions = 'Buttons', options = list(dom = 'Bfrtip',buttons = c('copy', 'csv', 'excel', 'pdf', 'print'),pageLength=10, scrollX='400px', columnDefs = list(list(className = 'dt-center', targets = "_all"))),rownames = FALSE) ```
Echantillon Sexe Couv. autosomes Couv. chrX NAN094 H 44.2339823740566 22.0109940293309 NAQ095 F 45.6972749039199 45.2938556050553 NAQ102 H 46.4503791247102 23.3367492729385 NAQ104 F 42.6604621137042 41.59214873412 NAQ114 H 47.4454524288081 23.2806965771802 NAQ115 H 45.3128157396608 22.5878060713352 NAQ116 H 44.5120151092971 22.1902206625124 NAQ117 H 44.5667556457501 22.3253287035313 NAQ124 H 44.1547140407541 22.0612210097021 NAQ127 H 45.1406368058383 22.5020949697436 NAQ131 H 45.1472097072126 22.4443120795604 NAQ133 F 41.2195065918166 40.9188784430404 NAQ141 F 42.749084378469 43.7119043619277 NAR013 H 43.5951059938956 21.9606501487595 NAR018 H 45.3550866503083 22.3055364037361 NAR019 H 45.4337543537171 22.9515217254307 NAR028 F 38.4230276904003 37.9964613205878 NAR032 F 44.0734609415596 44.4685709835858 NAR041 F 43.9393289823221 42.9609225995391 NAR046 F 44.1486633776115 43.7450775977989 NAR047 H 43.3750988313457 22.4532127447165 NAR048 F 39.6169267993457 40.7340405197216 NAR053 F 43.2499594551444 42.0961465556751 NAR059 H 41.6948703311421 21.9658016456802