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

Witold E Wolski wewolski at gmail.com
Thu Feb 4 11:52:56 CET 2016

Dear Martin,

That's great that you can update the svn and are willing to do so. I
will go with the github mirror, fork it, make the changes and send you
a link to the fork as soon as I am done replacing the cat with
message. I will try to be done sometimes next week.


Would it not be more convenient If bioconductor could move from svn to
github so pull requests could be made?

On 3 February 2016 at 22:57, Morgan, Martin
<Martin.Morgan at roswellpark.org> wrote:
> 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.
> Martin
> ________________________________________
> 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
> Hi,
> 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?
> best
> Witold
> --
> Witold Eryk Wolski
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Witold Eryk Wolski

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