Affy autodownload cdf problem
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@sean-davis-490
Last seen 12 weeks ago
United States
I haven't used the affy packages in a while, so just wondered about the behavior of justRMA (and maybe others that auto-download from bioconductor) on MacOS. The details are below. I can download the cdf by hand and install, but the auto-install seems to fail. I know I am missing some detail, but would love to hear what that is. Thanks, Sean > sessionInfo() R version 2.2.0, 2005-08-11, powerpc-apple-darwin7.9.0 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: affy Biobase "1.8.1" "1.8.0" > eset <- justRMA(filenames=dir('../Results'),celfile.path='../Results',verbose= T) Warning: unable to access index for repository http://bioconductor.org/packages/bioc/1.7/bin/macosx/2.2 Warning: unable to access index for repository http://bioconductor.org/packages/data/annotation/1.7/bin/macosx/2.2 Warning: unable to access index for repository http://bioconductor.org/packages/data/experiment/1.7/bin/macosx/2.2 Warning: unable to access index for repository http://bioconductor.org/packages/omegahat/1.7/bin/macosx/2.2 Warning: unable to access index for repository http://bioconductor.org/packages/lindsey/1.7/bin/macosx/2.2 Warning: unable to access index for repository http://cran.fhcrc.org/bin/macosx/2.2 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HG-U133_Plus_2 Library - package hgu133plus2cdf not installed Data for package affy did not contain hgu133plus2cdf Bioconductor - hgu133plus2cdf not available
cdf affy cdf affy • 1.0k views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
Hi Sean, On 30 Nov 2005, sdavis2 at mail.nih.gov wrote: > I haven't used the affy packages in a while, so just wondered about > the behavior of justRMA (and maybe others that auto-download from > bioconductor) on MacOS. The details are below. I can download the > cdf by hand and install, but the auto-install seems to fail. I know > I am missing some detail, but would love to hear what that is. We'll look into this, thanks for the report. + seth
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
Hi Sean, Can you start R and send me the following output: getOption("pkgType") contrib.url("foo") I think you should see mac.binary for pkgType and something like: foo/bin/macosx/powerpc/contrib/2.2. If not, are you using a ~/.Rprofile file or similar? On 30 Nov 2005, sdavis2 at mail.nih.gov wrote: >> eset <- > justRMA(filenames=dir('../Results'),celfile.path='../Results',verbos e=T) > Warning: unable to access index for repository > http://bioconductor.org/packages/bioc/1.7/bin/macosx/2.2 Warning: > unable to access index for repository The location of OS X binary packages in a CRAN-style repository (what we use) changed recently and instead of bin/macosx/x.y it is bin/macosx/powerpc/contrib/x.y. I believe the change is in anticipation of the intel-based macs that will, eventually, be out in the wild. + seth
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On 11/30/05 11:53 AM, "Seth Falcon" <sfalcon at="" fhcrc.org=""> wrote: > Hi Sean, > > Can you start R and send me the following output: > > getOption("pkgType") > contrib.url("foo") > > I think you should see mac.binary for pkgType and something like: > foo/bin/macosx/powerpc/contrib/2.2. If not, are you using a > ~/.Rprofile file or similar? > getOption('pkgType') [1] "mac.binary" > contrib.url('foo') [1] "foo/bin/macosx/2.2" Sean
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