[BioC] can't get simpleaffy for Macs; was: Re: problem with loading affyQCReport

Jenny Drnevich drnevich at uiuc.edu
Fri Dec 16 21:55:41 CET 2005

Hi Herve,

I'm relaying on a problem about downloading simpleaffy for Macs; thought it 
might be related what happened before. Adrienne was able to download and 
install other Bioconductor packages, but not simpleaffy.

Hello Jenny,
Thank you! Well, I managed to get almost everything to install okay on my Mac
(OS X, PowerPC G4, 512 MB SDRAM). I figured out that there is a Package
Installer in the menu bar. By selecting Bioconductor (binaries), I was able 
to get
a long list that included all of the packages listed in #7 of your 
instructions. I
selected each of them and clicked install. This worked for all of the packages
except simpleaffy. The error message** popped up in the R console. It also 

Warning: unable to access index for repository http://www.bioconductor.org/
trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/macosx/

but I think it said that even when it was able to download/install the other

**Here's the error message:

Error in download.file(url, destfile, method, mode = "wb") :
         cannot open URL 'http://www.bioconductor.org/packages/bioc/stable/

Here's her sessionInfo():

R version 2.2.0, 2005-10-06, powerpc-apple-darwin7.9.0

attached base packages:
[1] "tcltk"     "tools"     "methods"   "stats"     "graphics"
[6] "grDevices" "utils"     "datasets"  "base"

other attached packages:
         plier          affy     tkWidgets        DynDoc    reposTools
       "1.2.0"       "1.8.1"       "1.8.0"       "1.8.0"       "1.8.0"
   widgetTools       convert        marray       Biobase         made4
       "1.6.0"       "1.4.0"       "1.8.0"       "1.8.0"       "1.4.0"
scatterplot3d          ade4         limma
      "0.3-24"       "1.4-0"       "2.4.4"

At 06:10 PM 12/14/2005, Herve Pages wrote:
>Hi Tuomas,
>Thanks for telling us!
>Due to recent minor fixes in packages "GeneR", "DEDS" and "simpleaffy",
>I recently had to rebuild them in order to provide updated source and binary
>(Windows) packages on our BioC 1.7 repository.
>But given the error message you got while trying to load the "simpleaffy"
>package, I guess I probably used R-2.3 instead of R-2.2 to rebuild.
>My mistake, sorry!
>Packages affected by this mistake are: GeneR (1.4.1), DEDS (1.2.1) and
>simpleaffy (2.4.1).
>Today I rebuilt them with R-2.2 and pushed them to our repository
>(http://bioconductor.org). The new (and hopefully working *) packages
>are: GeneR (1.4.2), DEDS (1.2.2) and simpleaffy (2.4.2).

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu

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