Re: [Rd] [Bioc-devel] promptClass
Dear Martin
Thank you for sending the fast fix to the problem.
Best regards
Christian
Martin Morgan wrote:
> promptClass fails to identify methods associated with the class. Here
> is a fix:
>
> Index: promptClass.R
> ===
> --- promptClass.R (revision 41719)
> +++ promptClass.R (working copy)
> @@ -165,7 +165,7 @@
> if (nmeths > 0) {
> .meths.body <- " \\describe{"
> for (i in 1:nmeths) {
> - .sigmat <- sigsList(methnms[i], where)
> + .sigmat <- sigsList(methnms[i], where=whereClass)
> for (j in seq_along(.sigmat)) {
> if (!all(is.na(match(.sigmat[[j]],clName {
> methn.i <- escape(methnms[i])
> Index: RMethodUtils.R
> ===
> --- RMethodUtils.R (revision 41719)
> +++ RMethodUtils.R (working copy)
> @@ -621,7 +621,7 @@
> getMethodsMetaData <-
>## get the methods meta-data for function f on database where
>function(f, where = topenv(parent.frame())) {
> -mname <- mlistMetaName(f, where)
> +mname <- mlistMetaName(f, getPackageName(where))
> if(exists(mname, where = where, inherits = missing(where)))
> get(mname, where)
> else
>
> Seth Falcon <[EMAIL PROTECTED]> writes:
>
>
>> cstrato <[EMAIL PROTECTED]> writes:
>>
>>
>>> Dear all,
>>>
>>> What is the best way to write the docs for S4 classes?
>>>
>>> Concretely, is it possible to include the methods in the class
>>> documentation?
>>> For example, the documentation for class "AffyBatch" contains all methods.
>>> However, when I do:
>>>promptClass("AffyBatch")
>>> the relevant output of file "AffyBatch-class.Rd" is:
>>>\section{Methods}{
>>>No methods defined with class "AffyBatch" in the signature.
>>>}
>>>
>> promptClass used to provide more useful output. You might want to
>> report the issue on one of the R lists.
>>
>>
>>> Since PromptClass() contains a parameter "where" is it possible to use
>>> it, and how?
>>>
>> I'm not sure that is relevant here.
>>
>> One thing that can be useful here is showMethods(classes="AffyBatch").
>> The problem with static documentation for methods is that what methods
>> are available can change based on what packages are attached.
>>
>> If showMethods or a wrapper for it could be convinced to output a link
>> to a help file, then it might actually be a good way to go...
>>
>> + seth
>>
>> --
>> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
>> http://bioconductor.org
>>
>> ___
>> [EMAIL PROTECTED] mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>
__
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[Rd] Problem with installing a package for R 2.5.0
Hi All, I developed a package which did pass all the tests for R 2.4.1. When I tried to re-compile it for R 2.5.0 it kept giving me the following message: *** C:\Program Files\R\R-2.5.0\bin>R CMD install mlmmm_0.1-1.tar.gz installing to 'c:/PROGRA~1/R/R-25~1.0/library' -- Making package mlmmm adding build stamp to DESCRIPTION installing NAMESPACE file and metadata making DLL ... g77 -O3 -Wall -c mlm.f -o mlm.o g77 -O3 -Wall -c mlmmm.f -o mlmmm.o windres -I c:/PROGRA~1/R/R-25~1.0/include -i mlmmm_res.rc -o mlmmm_res.o gcc -shared -s -o mlmmm.dll mlmmm.def mlm.o mlmmm.o mlmmm_res.o -Lc:/PROGRA~1 /R/R-25~1.0/bin -lg2c -lR ... DLL made installing DLL installing R files installing inst files FIND: Parameter format not correct make[2]: *** [c:/PROGRA~1/R/R-25~1.0/library/mlmmm/inst] Error 2 make[1]: *** [all] Error 2 make: *** [pkg-mlmmm] Error 2 *** Installation of mlmmm failed *** Removing 'c:/PROGRA~1/R/R-25~1.0/library/mlmmm' Restoring previous 'c:/PROGRA~1/R/R-25~1.0/library/mlmmm' * Similar failure was seen in Mac as well. Anybody else has similar problems? I would greatly appreciate any solution proposals... Best. -- Recai M. Yucel,Ph.D. Assistant Professor of Biostatistics Biostatistics and Epidemiology School of Public Health and Health Sciences University of Massachusetts-Amherst __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Problem with installing a package for R 2.5.0
On 27/05/2007 5:40 PM, Recai Yucel wrote: > Hi All, > > I developed a package which did pass all the tests for R 2.4.1. When I > tried to re-compile it for R 2.5.0 it kept giving me the following message: > > *** > C:\Program Files\R\R-2.5.0\bin>R CMD install mlmmm_0.1-1.tar.gz > installing to 'c:/PROGRA~1/R/R-25~1.0/library' > > > -- Making package mlmmm > adding build stamp to DESCRIPTION > installing NAMESPACE file and metadata > making DLL ... > g77 -O3 -Wall -c mlm.f -o mlm.o > g77 -O3 -Wall -c mlmmm.f -o mlmmm.o > windres -I c:/PROGRA~1/R/R-25~1.0/include -i mlmmm_res.rc -o mlmmm_res.o > gcc -shared -s -o mlmmm.dll mlmmm.def mlm.o mlmmm.o mlmmm_res.o > -Lc:/PROGRA~1 > /R/R-25~1.0/bin -lg2c -lR > ... DLL made > installing DLL > installing R files > installing inst files > FIND: Parameter format not correct > make[2]: *** [c:/PROGRA~1/R/R-25~1.0/library/mlmmm/inst] Error 2 > make[1]: *** [all] Error 2 > make: *** [pkg-mlmmm] Error 2 > *** Installation of mlmmm failed *** That's a pretty clear sign that your PATH isn't set up correctly: you're using the FIND that comes with Windows rather than the find that comes with the R toolset. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
