[BioC] the error caused by makeProbePackage

[Wolfgang Huber]

Dear Yingtao,

could it be that you don't have all the necessary software tools for 
building and checking R packages on your Windows computer (e.g. a Perl 
interpreter)? While these tools are standard with practically every 
Unix, they do not come with MS-Windows and need to be installed by yourself.

See http://www.murdoch-sutherland.com/Rtools, perhaps also
http://www.biostat.jhsph.edu/~kbroman/Rintro/Rwinpack.html

For probe packages, you will not need the compilers, and the "Windows 
help" stuff is optional.

I agree that it must appear somewhat cumbersome that R is not 
self-contained when it comes to building packages; but that's how it is 
currently. And the packaging system (with versioning, documentation, 
etc.) is just THE obvious approach to making and distributing the probe 
annotation data.

I am afraid that the documentation of the "makeProbePackage" function is 
not very helpful on this point, and I will include a remark about this.

Best wishes
  Wolfgang



Yingtao Bi wrote:
> The version of R is 2.0.1, bioconductor is 1.5 and OS is WinXp. I am
> the administrator of that computer.
> I have tried the example in the vignette, but it did not work either.
> The followings are the input and output:
> 
> filename <- system.file("extdata", "HG-U95Av2_probe_tab.gz",package =
> "matchprobes")
> outdir <- tempdir()
> me <- "Wolfgang Huber <w.huber at dkfz.de>"
> makeProbePackage("HG-U95Av2", datafile = gzfile(filename, open = "r"),
> outdir = outdir, maintainer = me, version = "0.0.1", force = TRUE)
> 
> the output of these commands:
> 
> Importing the data.
> Loading required package: affy
> Loading required package: reposTools
> Creating package in C:\DOCUME~1\NINGYA~1\LOCALS~1\Temp\Rtmp23504/hgu95av2probe
> Writing the data.
> Checking the package.
> Error in makeProbePackage("HG-U95Av2", datafile = gzfile(filename,
> open = "r"),  :
>        Expected but did not find the log-file
> hgu95av2probe.Rcheck/00check.log after R CMD check
> 
> The same error happened, eventhough I changed the parameter "output".
> 
> Today I tried that example on a linux platform, it worked.
> Also I have downloaded the hgu133atagprobe package from the
> bioconductor website.
> 
> Thanks for your help
> Yingtao Bi
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


-- 
Best regards
   Wolfgang

-------------------------------------
Wolfgang Huber
European Bioinformatics Institute
European Molecular Biology Laboratory
Cambridge CB10 1SD
England
Phone: +44 1223 494642
Fax:   +44 1223 494486
Http:  www.ebi.ac.uk/huber