Re: [R] Adding .R to source file keeps R from reading it?
So...are you trying to modify a contributed package by adding a *.R file to the 'R' subdirectory in the package? One thing to consider besides the previous tip is that the package might be using a NAMESPACE, which lives in the package root directory (one directory up from the 'R' subdirectory). If so, then you must add the name of your function to the argument list of the call to 'export' in the NAMESPACE file e.g. export(sortgenes, pvalues, MyFunction) -Original Message- From: John Tillinghast [mailto:[EMAIL PROTECTED] Sent: Thu 9/21/2006 9:55 PM To: r-help@stat.math.ethz.ch Subject: Re: [R] Adding .R to source file keeps R from reading it? Yes, this was exactly the problem: I was using the unzipped package, not the source. Now it works! -- Forwarded message -- From: Deepayan Sarkar [EMAIL PROTECTED] Date: Sep 21, 2006 2:58 PM Subject: Re: [R] Adding .R to source file keeps R from reading it? To: John Tillinghast [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch On 9/21/06, John Tillinghast [EMAIL PROTECTED] wrote: Hi, I'm updating the LMGene package from Bioconductor. Writing R Extensions suggests that all source files (the ones in the R directory) have a .R ending, so I added it to the (one) source file. The next time I installed and ran R, R didn't understand any of the functions. I tried various things and eventually went back to the file and dropped the .R ending, installed, ran R. It worked! For purposes of distributing the package, do I want to leave the name without the .R, or add the .R and change something else? I'm guessing that the source you are working on has been obtained by unzipping the windows binary zip file. Despite appearances, that is not the source code. For the proper source code, download the file that's marked as source. In this case, http://bioconductor.org/packages/1.8/bioc/html/LMGene.html clearly labels the following as Source (and the corresponding zip file as Windows Binary) http://bioconductor.org/packages/1.8/bioc/src/contrib/LMGene_1.0.0.tar.gz This likely answers your other question as well. -Deepayan [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Adding .R to source file keeps R from reading it?
Hi, I'm updating the LMGene package from Bioconductor. Writing R Extensions suggests that all source files (the ones in the R directory) have a .R ending, so I added it to the (one) source file. The next time I installed and ran R, R didn't understand any of the functions. I tried various things and eventually went back to the file and dropped the .R ending, installed, ran R. It worked! For purposes of distributing the package, do I want to leave the name without the .R, or add the .R and change something else? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding .R to source file keeps R from reading it?
On 9/21/06, John Tillinghast [EMAIL PROTECTED] wrote: Hi, I'm updating the LMGene package from Bioconductor. Writing R Extensions suggests that all source files (the ones in the R directory) have a .R ending, so I added it to the (one) source file. The next time I installed and ran R, R didn't understand any of the functions. I tried various things and eventually went back to the file and dropped the .R ending, installed, ran R. It worked! For purposes of distributing the package, do I want to leave the name without the .R, or add the .R and change something else? I'm guessing that the source you are working on has been obtained by unzipping the windows binary zip file. Despite appearances, that is not the source code. For the proper source code, download the file that's marked as source. In this case, http://bioconductor.org/packages/1.8/bioc/html/LMGene.html clearly labels the following as Source (and the corresponding zip file as Windows Binary) http://bioconductor.org/packages/1.8/bioc/src/contrib/LMGene_1.0.0.tar.gz This likely answers your other question as well. -Deepayan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding .R to source file keeps R from reading it?
On 9/21/2006 5:01 PM, John Tillinghast wrote: Hi, I'm updating the LMGene package from Bioconductor. Writing R Extensions suggests that all source files (the ones in the R directory) have a .R ending, so I added it to the (one) source file. The next time I installed and ran R, R didn't understand any of the functions. I tried various things and eventually went back to the file and dropped the .R ending, installed, ran R. It worked! For purposes of distributing the package, do I want to leave the name without the .R, or add the .R and change something else? You aren't giving us very much information, but I would guess you edited the installed copy of the package rather than the source. (Where did you find the file with the source in it? If it was in $(RHOME)/library/LMGene/R, then that's the installed copy, and you shouldn't edit it.) When R installs a package, it copies all the source into one file and doesn't put the .R extension on it. I imagine if you try running after renaming such a file, R wouldn't see it. Your other message about seeing a help directory confirms this. You should get the source to the LMGene package, and make modifications to that, or just write your own functions and put them in your own file. Duncan Murdoch __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding .R to source file keeps R from reading it?
Hmm... sounds like you're on Windows and have the Explorer setup such that it is hiding file extensions. You can try to use list.files() from R to see if the files actually have file extension. If this is your problem, open My Computer - Tools - Folder Options... and select tab View. Make sure that Hide extensions for known file types is *NOT* selected. /H On 9/21/06, John Tillinghast [EMAIL PROTECTED] wrote: Hi, I'm updating the LMGene package from Bioconductor. Writing R Extensions suggests that all source files (the ones in the R directory) have a .R ending, so I added it to the (one) source file. The next time I installed and ran R, R didn't understand any of the functions. I tried various things and eventually went back to the file and dropped the .R ending, installed, ran R. It worked! For purposes of distributing the package, do I want to leave the name without the .R, or add the .R and change something else? [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Adding .R to source file keeps R from reading it?
Yes, this was exactly the problem: I was using the unzipped package, not the source. Now it works! -- Forwarded message -- From: Deepayan Sarkar [EMAIL PROTECTED] Date: Sep 21, 2006 2:58 PM Subject: Re: [R] Adding .R to source file keeps R from reading it? To: John Tillinghast [EMAIL PROTECTED] Cc: r-help@stat.math.ethz.ch On 9/21/06, John Tillinghast [EMAIL PROTECTED] wrote: Hi, I'm updating the LMGene package from Bioconductor. Writing R Extensions suggests that all source files (the ones in the R directory) have a .R ending, so I added it to the (one) source file. The next time I installed and ran R, R didn't understand any of the functions. I tried various things and eventually went back to the file and dropped the .R ending, installed, ran R. It worked! For purposes of distributing the package, do I want to leave the name without the .R, or add the .R and change something else? I'm guessing that the source you are working on has been obtained by unzipping the windows binary zip file. Despite appearances, that is not the source code. For the proper source code, download the file that's marked as source. In this case, http://bioconductor.org/packages/1.8/bioc/html/LMGene.html clearly labels the following as Source (and the corresponding zip file as Windows Binary) http://bioconductor.org/packages/1.8/bioc/src/contrib/LMGene_1.0.0.tar.gz This likely answers your other question as well. -Deepayan [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
