[Bioc-devel] topGO and cat() and print() statements in program code

Morgan, Martin Martin.Morgan at roswellpark.org
Wed Feb 3 22:57:39 CET 2016

Hi Witold -- if you'd like to submit a patch, I will apply this to the package and notify the maintainer. I suggest you either use svn to check out the 'devel' version of the package, make your changes, and forward to me (martin.morgan at roswellpark.org) the output of svn diff (basic instructions here http://bioconductor.org/developers/how-to/source-control/), or do similar against the Bioconductor github mirror https://github.com/Bioconductor-mirror/topGO; for the latter you cannot submit a 'pull' request to the mirror, but you could point me to your repository.


From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Witold E Wolski <wewolski at gmail.com>
Sent: Tuesday, February 2, 2016 5:19 AM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] topGO and cat() and print() statements in program code


I am using the very usefull package topGO to generate a report (R
markdown). There is not much to complain about topGO (on the contrary)
except that the package uses cat instead of message to display
progress information. which ruins the report.

Also the bioconductor package guidelines state:
cat() or print() are used only when displaying an object to the user,
e.g., in a show method.

This makes it difficult to integrate topGO.

I did contact the maintainer asking to update topGO. However I did not
get an reply. It seems that the maintainer is occupied with other
problems. I did offer to replace the cat with message for these
functions I am using myself. No reply.

So what I am wondering is... If I do the corrections, and would like
to commit the code... Sure I could create a branch but since I do not
have write access to svn no chance to push (commit) it for review.
And who is going to review it if the maintainer does not have time?


Witold Eryk Wolski

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