John Tillinghast
2006-Sep-21 21:01 UTC
[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]]
Deepayan Sarkar
2006-Sep-21 21:58 UTC
[R] Adding .R to source file keeps R from reading it?
On 9/21/06, John Tillinghast <tilling at gmail.com> 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
Duncan Murdoch
2006-Sep-21 22:46 UTC
[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
Henrik Bengtsson
2006-Sep-22 00:35 UTC
[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 <tilling at gmail.com> 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 at 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. >
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