Your message dated Fri, 10 Apr 2020 16:35:38 +0000
with message-id <e1jmwd0-000bm0...@fasolo.debian.org>
and subject line Bug#942469: fixed in r-cran-rmarkdown 2.1+dfsg-2
has caused the Debian Bug report #942469,
regarding r-cran-rmarkdown: directory to symlink conversion not correctly
handled on upgrade
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
942469: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=942469
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: r-cran-rmarkdown
Version: 1.16+dfsg-1
Severity: normal
Hi,
While trying to reproduce a bug in another package (r-cran-dt, I will
submit it after this one), I notice an error while pandoc is invoked:
[...]
/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/Rtmpo7H2Mq/rmarkdown-str53cc33e4db8.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/rmarkdown/rmd/h/bootstrap/css/../fonts/glyphicons-halflings-regular.eot:
openBinaryFile: does not exist (No such file or directory)
Erreur : pandoc document conversion failed with error 1
Exécution arrêtée
Looking with apt-file, I see that
/usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/css/../fonts/glyphicons-halflings-regular.eot
was provided by r-cran-rmarkdown.
Looking at the git history of r-cran-rmarkdown, I see that in 7bd53b7c34
these files where removed and replaced by a symlink. However,
for file in fonts/ subdir, this is the whole subdir that is
symlinked and not the files themselves.
dpkg do not correctly handle dir to symlink when upgrading
(due to the fact that the sysadmin can decide to replace
dir by symlinks to manage its disks if I remember).
So support in preinst/postinst is required.
And indeed, on my machine, I can see that
/usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/fonts
is still a (empty) real directory :
$ ls -ld /usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/fonts
drwxr-xr-x 2 root root 4096 juil. 9 15:20
/usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/fonts
I fix the bug by removing the directory and reinstalling the
package :
$ sudo rmdir /usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/fonts
$ sudo apt install --reinstall r-cran-rmarkdown
[...]
Dépaquetage de r-cran-rmarkdown (1.16+dfsg-1) sur (1.16+dfsg-1) ...
[...]
$ ls -ld /usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/fonts
lrwxrwxrwx 1 root root 53 oct. 7 15:00
/usr/lib/R/site-library/rmarkdown/rmd/h/bootstrap/fonts ->
../../../../../../../share/javascript/bootstrap/fonts
So, for people upgrading the package, you will have to
fix this dir to symlink conversion in a pre/post-inst script.
Regards,
Vincent
-- 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-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+dfsg1-4
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 pandoc 2.5-2+b1
ii r-base-core [r-api-3.5] 3.6.1-6
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+dfsg-1
ii r-cran-knitr 1.25+dfsg-1
ii r-cran-mime 0.7-1
ii r-cran-shiny 1.3.2+dfsg-1
ii r-cran-stringr 1.4.0-1
ii r-cran-tinytex 0.16-1
ii r-cran-xfun 0.10-1
ii r-cran-yaml 2.2.0-1
Versions of packages r-cran-rmarkdown recommends:
ii r-cran-testthat 2.2.1-1
Versions of packages r-cran-rmarkdown suggests:
ii r-cran-callr 3.3.2-1
ii r-cran-digest 0.6.21-1
pn r-cran-dygraphs <none>
ii r-cran-fs 1.3.1+dfsg-1
ii r-cran-shiny 1.3.2+dfsg-1
ii r-cran-tibble 2.1.3-1
pn r-cran-tufte <none>
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: r-cran-rmarkdown
Source-Version: 2.1+dfsg-2
Done: =?utf-8?q?Dylan_A=C3=AFssi?= <dai...@debian.org>
We believe that the bug you reported is fixed in the latest version of
r-cran-rmarkdown, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 942...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Dylan Aïssi <dai...@debian.org> (supplier of updated r-cran-rmarkdown package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Fri, 10 Apr 2020 18:15:44 +0200
Source: r-cran-rmarkdown
Architecture: source
Version: 2.1+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net>
Changed-By: Dylan Aïssi <dai...@debian.org>
Closes: 942469 943550
Changes:
r-cran-rmarkdown (2.1+dfsg-2) unstable; urgency=medium
.
* Team upload.
* Add Testsuite: autopkgtest-pkg-r.
* Add salsa-ci file (routine-update)
* Rules-Requires-Root: no (routine-update)
* Re-add node-html5shiv to deps (Closes: #943550)
* Add symlink_to_dir and dir_to_symlink (Closes: #942469)
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