sybilSBML not available on CRAN for R>=4.0

[cdiener]

First of all thanks for making gapseq!

While installing I noticed I needed a few workarounds for newer R versions. In particular, it would be helpful if the installation instructions could mention some workarounds for the sybilSBML drop from CRAN for R>=4.0. The links to CRAN in the docs also lead to a removal notice on CRAN (https://cran.r-project.org/web/packages/sybilSBML/index.html). Since it is a self-hosted GitLab instance things like remotes::install_gitlab etc. won't work easily either. However,
R -e 'remotes::install_git("https://gitlab.cs.uni-duesseldorf.de/general/ccb/sybilSBML.git")' seems to work.

[Waschina]

Dear Christian,

yes, that sybilSBML was removed from and by CRAN is very unfortunate... The source package is still available from the CRAN archives, from where it can also be downloaded and installed. I added this workaround in the gapseq's installation documentation (https://gapseq.readthedocs.io/en/latest/install.html#a-name-sbmlsupport-a-sbml-support)

Apparently, the package was removed because its installation on macOS returned an error in CRAN's routine installation checks. I will contact the sybilSBML maintainers; perhaps they are already working on the issue.

Thank you for the feedback and help!
Silvio

[cdiener]

Awesome, thanks!

[hariszaf]

Hi, I have the same issue with installing sybilSBML in R 4.1.2.
I tried @cdiener command but doesn't work.
I also tried this gist but didn't work either..
Do you have any suggestions?

[jotech]

Do you have sbml-dev libraries linstalled and tried our conda installation?

[hariszaf]

Hi @jotech
Thanks for the reply.
I tried the conda installation after all and it worked.