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

mail.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 >

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

; 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

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

to do nothing: >> >> cat <- function() {} >> >> Dan >> >> >> - Original Message - >>> From: "James W. MacDonald" >>> To: "Witold E Wolski" >>> Cc: "bioc-devel" >>> Sent: Tuesd

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

" >> 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), o

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

lf of Witold E > Wolski > 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

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

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

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

your repository. Martin From: Bioc-devel on behalf of Witold E Wolski 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 topG

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.

[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: