the error caused by makeProbePackage

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Yingtao Bi ▴ 20

@yingtao-bi-1065

Last seen 10.2 years ago

Dear All, Since the hgu133atagprobe package is not available from the bioconductor website, I am trying to construct it by using makeProbePackage. But this function return the following error: "Expected but did not find the log-file hgu133atagprobe.Rcheck/00check.log after R CMD check" (bug??) So I let the check = FALSE, it's ok this time, but the constructed package can't be loaded by R. I am wondering if the package constructed by this function can't meet the requirement of R 2.0.1??? Thanks for your help and Regard University of California, Riveriside

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ADD COMMENT • link 19.9 years ago Yingtao Bi ▴ 20

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rgentleman ★ 5.5k

@rgentleman-7725

Last seen 9.6 years ago

United States

Well, we need a bit more information, version of R, of the makeProbePackage, what files you downloaded from Affymetrix, what commands you issued and what other error messages or warnings showed up along the way. It looks rather like something went wrong earlier, but it is impossible to tell from what you have decided to tell us. Please try to provide a complete description of what your system is and what you did. And the answer to your last question is that yes this function produces packages that are suitable for the version of R that was used to build them. Did you try the example in the vignette? Did that work for you? That is usually the place to start. Robert On Jan 6, 2005, at 12:28 AM, Yingtao Bi wrote: > Dear All, > > Since the hgu133atagprobe package is not available from the > bioconductor website, > I am trying to construct it by using makeProbePackage. > > But this function return the following error: > "Expected but did not find the log-file > hgu133atagprobe.Rcheck/00check.log after R CMD check" (bug??) > > So I let the check = FALSE, it's ok this time, but the constructed > package can't be loaded by R. > > I am wondering if the package constructed by this function can't meet > the requirement of R 2.0.1??? > > Thanks for your help and Regard > > > University of California, Riveriside > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+

ADD COMMENT • link 19.9 years ago rgentleman ★ 5.5k

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Yingtao Bi ▴ 20

@yingtao-bi-1065

Last seen 10.2 years ago

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@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

ADD COMMENT • link 19.9 years ago Yingtao Bi ▴ 20

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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@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@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

ADD REPLY • link 19.9 years ago Wolfgang Huber ★ 13k

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