Dear Martin, Thanks a lot for fixing it in the trunk. I do appreciate it. It really makes it a lot easier to use topGO when creating markdown files.
Witold PS. I did delete the github fork. On 5 February 2016 at 12:47, Morgan, Martin <martin.mor...@roswellpark.org> wrote: > I followed your lead and updated topGO in Bioc devel branch to version > 2.23.3, replacing cat() with message() directly rather a wrapper > .cat2message(). I did not change use of cat() in print() and show() methods, > where output to stdout is appropriate. > > Generally, using message() simplified code, replacing multiple calls to cat() > and nested paste() statements with a single call to message(). > > Martin > > ________________________________________ > From: Bioc-devel <bioc-devel-boun...@r-project.org> on behalf of Witold E > Wolski <wewol...@gmail.com> > Sent: Friday, February 5, 2016 5:50 AM > To: Dan Tenenbaum; henrik.bengts...@gmail.com > Cc: bioc-devel; James W. MacDonald > Subject: Re: [Bioc-devel] topGO and cat() and print() statements in program > code > > I did replace the call to cat in topGO with with a call to a package > private .cat2message function (which makes some adjustments to the > passed arguments so that the messages look as before). The patched > package is available from here. > https://github.com/wolski/topGO > Upstream commits made on 3 February by h.bengtsson are merged. > AFAIK all is working OK (checks pass and my code using topGO is still working) > > > Witold > > > > > > > On 4 February 2016 at 11:56, Witold E Wolski <wewol...@gmail.com> wrote: >> Hi Dan, >> >> Excellent suggestion. This is very similar to how I am plan to do the >> refactoring. Write a function cat2message which has a signature like >> cat but uses message in the implementation and than replace all calls >> to cat in the topGO package. >> >> best >> >> On 4 February 2016 at 00:56, Dan Tenenbaum <dtene...@fredhutch.org> wrote: >>> Another dirty hack is to redefine cat() in your own code to do nothing: >>> >>> cat <- function(....) {} >>> >>> Dan >>> >>> >>> ----- Original Message ----- >>>> From: "James W. MacDonald" <jmac...@uw.edu> >>>> To: "Witold E Wolski" <wewol...@gmail.com> >>>> Cc: "bioc-devel" <bioc-devel@r-project.org> >>>> Sent: Tuesday, February 2, 2016 6:50:21 AM >>>> Subject: Re: [Bioc-devel] topGO and cat() and print() statements in >>>> program code >>> >>>> I can't speak to the issue of changing somebody else's code without forking >>>> (which you are free to do), or getting their OK. But do note that there are >>>> usually ways around this. First, you can use include = FALSE in your chunk >>>> options statement, which will run all the code, but silence everything. >>>> This isn't a good use case if you need to print, but that can usually be >>>> split out. Something like >>>> >>>> ```r{noisypart, include = FALSE} >>>> >>>> noisy code goes here >>>> >>>> ``` >>>> >>>> ```r{quietpart, echo = FALSE, fig.cap = ""} >>>> >>>> plots go here >>>> >>>> ``` >>>> >>>> An alternative is to use GOstats, which may be less noisy, but which still >>>> has 18 calls to cat() (vs 121 for topGO) and 2 calls to print() (vs 29 for >>>> topGO). >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> >>>> >>>> On Tue, Feb 2, 2016 at 5:19 AM, Witold E Wolski <wewol...@gmail.com> wrote: >>>> >>>>> 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 >>>>> >>>> >>>> >>>> >>>> -- >>>> James W. MacDonald, M.S. >>>> Biostatistician >>>> University of Washington >>>> Environmental and Occupational Health Sciences >>>> 4225 Roosevelt Way NE, # 100 >>>> Seattle WA 98105-6099 >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> >> >> -- >> Witold Eryk Wolski > > > > -- > 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
