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

James W. MacDonald jmacdon at uw.edu
Tue Feb 2 15:50:21 CET 2016

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



On Tue, Feb 2, 2016 at 5:19 AM, Witold E Wolski <wewolski at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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