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

Witold E Wolski wewolski at gmail.com
Tue Feb 2 11:19:34 CET 2016


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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