[BioC] Installation Problems

[McGee, Monnie]

Thank you, Herve.   I figured it was something like this, because I couldn't see anything wrong on my end.

I re-ran the commands from the R Gui and programs are installing right now.

Best,
Monnie

Monnie McGee, Ph.D.
Assistant Professor
Department of Statistical Science
Southern Methodist University
Ph: 214-768-2462
Fax: 214-768-4035



-----Original Message-----
From: Herve Pages [mailto:hpages at fhcrc.org]
Sent: Tue 8/29/2006 2:15 PM
To: McGee, Monnie
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Installation Problems
 
Hi Monnie,

Sorry for the late answer. 2 days ago our main server experienced a
hardware failure (this has been reported yesterday on the BioC list).
We are still in the process of recovering the data and transferring
them on a spare machine. Apparently a lot of things are still missing
(e.g. symlinks) which is the cause of your problem.

We'll do our best to get things fully restored before tomorrow.

Thanks for your patience and sorry for the inconvenience.

H.

McGee, Monnie wrote:
> Dear List,
>
> I am trying to update my version of R and Bioconductor on a PowerPC G5 running MAC OS 10.4.7.  I successfully installed R version 2.3.1.  In trying install BioC from Cocoa R GUI, I receive the following errors.  I get the same errors when I try installing biocLite.  I also tried installation using X11, and the errors I received from that process are given at the end of this e-mail.
>
> Thanks for your help,
> Monnie
>
>   
>> source("http://www.bioconductor.org/getBioC.R")
>> getBioC()
>>     
> Running getBioC version 0.1.6 with R version 2.3.1 
> Running biocinstall version 1.8.4 with R version 2.3.1 
> Your version of R requires version 1.8 of Bioconductor.
> Will install the following packages:
>  [1] "affy"        "affydata"    "affyPLM"     "annaffy"     "annotate"    "Biobase"    
>  [7] "Biostrings"  "DynDoc"      "edd"         "gcrma"       "genefilter"  "geneplotter"
> [13] "globaltest"  "hgu95av2"    "limma"       "makecdfenv"  "marray"      "matchprobes"
> [19] "multtest"    "pamr"        "ROC"         "siggenes"    "sma"         "statmod"    
> [25] "tkWidgets"   "vsn"         "widgetTools" "xtable"     
> Please wait...
>
> Warning: unable to access index for repository http://bioconductor.org/packages/1.8/bioc/bin/macosx/powerpc/contrib/2.3
> Warning: unable to access index for repository http://bioconductor.org/packages/1.8/data/annotation/bin/macosx/powerpc/contrib/2.3
> Warning: unable to access index for repository http://bioconductor.org/packages/1.8/data/experiment/bin/macosx/powerpc/contrib/2.3
> Warning: unable to access index for repository http://bioconductor.org/packages/1.8/omegahat/bin/macosx/powerpc/contrib/2.3
> Warning: unable to access index for repository http://bioconductor.org/packages/1.8/lindsey/bin/macosx/powerpc/contrib/2.3
> Warning: unable to access index for repository http://cran.fhcrc.org/bin/macosx/powerpc/contrib/2.3
> dependencies ''affy'' are not availabledependencies ''affydata'' are not availabledependencies ''affyPLM'' are not availabledependencies ''annaffy'' are not availabledependencies ''annotate'' are not availabledependencies ''Biobase'' are not availabledependencies ''Biostrings'' are not availabledependencies ''DynDoc'' are not availabledependencies ''edd'' are not availabledependencies ''gcrma'' are not availabledependencies ''genefilter'' are not availabledependencies ''geneplotter'' are not availabledependencies ''globaltest'' are not availabledependencies ''hgu95av2'' are not availabledependencies ''limma'' are not availabledependencies ''makecdfenv'' are not availabledependencies ''marray'' are not availabledependencies ''matchprobes'' are not availabledependencies ''multtest'' are not availabledependencies ''pamr'' are not availabledependencies ''ROC'' are not availabledependencies ''siggenes'' are not availabledependencies ''sma'' are not availabledependencies ''statmod'' are not availabledependencies ''tkWidgets'' are not availabledependencies ''vsn'' are not availabledependencies ''widgetTools'' are not availabledependencies ''xtable'' are not available
>
> Errors from X11 installation:
>
>   
>> source("http://www.bioconductor.org/getBioC.R")
>> getBioC()
>>     
> Running getBioC version 0.1.6 with R version 2.3.1 
> Running biocinstall version 1.8.4 with R version 2.3.1 
> Your version of R requires version 1.8 of Bioconductor.
> Will install the following packages:
>  [1] "affy"        "affydata"    "affyPLM"     "annaffy"     "annotate"   
>  [6] "Biobase"     "Biostrings"  "DynDoc"      "edd"         "gcrma"      
> [11] "genefilter"  "geneplotter" "globaltest"  "hgu95av2"    "limma"      
> [16] "makecdfenv"  "marray"      "matchprobes" "multtest"    "pamr"       
> [21] "ROC"         "siggenes"    "sma"         "statmod"     "tkWidgets"  
> [26] "vsn"         "widgetTools" "xtable"     
> Please wait...
>
>
>  *** caught segfault ***
> address 0x5f4d4550, cause 'memory not mapped'
>
> Traceback:
>  1: download.file(url = paste(repos, "PACKAGES.gz", sep = "/"), destfile = tmpf,     method = method, cacheOK = FALSE, quiet = TRUE, mode = "wb")
>  2: try(download.file(url = paste(repos, "PACKAGES.gz", sep = "/"),     destfile = tmpf, method = method, cacheOK = FALSE, quiet = TRUE,     mode = "wb"), silent = TRUE)
>  3: available.packages(contriburl = contriburl, method = method)
>  4: .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl,     method = method, available = available, destdir = destdir,     installWithVers = installWithVers, dependencies = dependencies)
>  5: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,     type = type, ...)
>  6: biocinstall(...)
>  7: getBioC()
>
> Possible actions:
> 1: abort (with core dump)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
>
> Monnie McGee, Ph.D.
> Assistant Professor
> Department of Statistical Science
> Southern Methodist University
> Ph: 214-768-2462
> Fax: 214-768-4035
>
>
>
>   
> ------------------------------------------------------------------------
>
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-- 
------------------------
Hervé Pagès
E-mail: hpages at fhcrc.org
 Phone: (206) 667-5791
   Fax: (206) 667-1319