[BioC] Installation Problems

[McGee, Monnie]

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