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.
best 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.mor...@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-boun...@r-project.org> on behalf of Witold E > Wolski <wewol...@gmail.com> > Sent: Tuesday, February 2, 2016 5:19 AM > To: bioc-devel@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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. -- Witold Eryk Wolski _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
