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

[Herve Pages]

Hi Jenny,

Concerning the first problem you had:

  Warning: unable to access index for repository

http://www.bioconductor.org/packages/data/experiment/stable/bin/macosx/powerpc/contrib/2.2

since the data/experiment repository doesn't contain Mac OS X packages,
what you can do if you need to install a package from this repository
is try to install the source package:

> install.packages("package_name",
>                  
repos="http://bioconductor.org/packages/data/experiment/stable",
>                  type="source")

Concerning the simpleaffy_2.2.0.tgz package missing from our Mac OS X
repository, I don't know what happened but I'm almost sure that we
used to have this package here. However when I checked this morning
it was missing. I restored it so yoou should be able to install it
now.
Let me know if you run into any other problem.
Regards,

H.


Jenny Drnevich wrote:

> 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 said:
>
> Warning: unable to access index for repository 
> http://www.bioconductor.org/
> packages/data/experiment/stable/bin/macosx/powerpc/contrib/2.2
> trying URL 'http://www.bioconductor.org/packages/bioc/stable/bin/macosx/
> powerpc/contrib/2.2/simpleaffy_2.2.0.tgz'
>
> but I think it said that even when it was able to download/install the 
> other
> packages.
>
> **Here's the error message:
>
> Error in download.file(url, destfile, method, mode = "wb") :
>         cannot open URL 
> 'http://www.bioconductor.org/packages/bioc/stable/
> bin/macosx/powerpc/contrib/2.2/simpleaffy_2.2.0.tgz'
>
>
> 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).
>>
>> Regards,
>>
>> Hervé
>
>
> 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
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>



-- 
------------------------
Hervé Pagès
E-mail: hpages at fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319