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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel