docker-galaxy-stable: libXrender.so.1: cannot open shared object file: No such file or directory
Hi @bgruening , thanks for creating this great docker image! I have a tool that uses the R Markdown package. Whenever I use the rmarkdown::render()
this function in my code, it gives me this error:
/export/tool_deps/_conda/envs/mulled-v1-e42906f66f0b4446c0f35f93ca0dfe5a7ae97d6c546c525c30341daef2d11b95/bin/pandoc +RTS -K512m -RTS tool_template.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output /export/galaxy-central/database/files/000/dataset_10.dat --smart --email-obfuscation none --self-contained --standalone --section-divs --template /tool_deps/_conda/envs/mulled-v1-e42906f66f0b4446c0f35f93ca0dfe5a7ae97d6c546c525c30341daef2d11b95/lib/R/library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /tmp/Rtmp0DvuNB/rmarkdown-str5ee12aa8c2c.html --mathjax --variable 'mathjax-url:https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
Output created: /export/galaxy-central/database/files/000/dataset_10.dat
Warning messages:
1: In grDevices::png(f) :
unable to load shared object '/export/tool_deps/_conda/envs/mulled-v1-e42906f66f0b4446c0f35f93ca0dfe5a7ae97d6c546c525c30341daef2d11b95/lib/R/library/grDevices/libs//cairo.so':
libXrender.so.1: cannot open shared object file: No such file or directory
2: In grDevices::png(f) : failed to load cairo DLL
Because of this error, all R markdown galaxy tools stop working.
About this issue
- Original URL
- State: closed
- Created 6 years ago
- Comments: 23 (7 by maintainers)
Cool, thanks @jdblischak for your help.
@jdblischak
rmarkdown 1.6
works!! Thanks 😃@MingChen0919 The version of rmarkdown available from conda-forge is currently 1.6. We are ready to update to 1.8, but we wanted to get the 1.6 version operational first. Can you please confirm that your Galaxy tool can work with rmarkdown 1.6? Once it’s working, we’ll update to 1.8.