[BioC] Problems installing bioconductor

[Martin Morgan]

Daniel and I identified the problem: a filter on Daniel's end did not
allow downloading of the PACKAGES.gz file needed to retrieve
packages.

For the record, the filter complained that the MIME class
application/x-gzip was not permitted. It only reported this for the
http://cran.fhcrc.org address.

Also for the record, we found this out by typing

> warnings()

after biocLite() failed. This suggested that read.dcf (called in
available.packages) tried to parse a file that contained the html
message generated by the filter. We then used
debug(available.packages); biocLite() and stepped through the function
until we found the repository that was causing the problem.

Martin

Martin Morgan <mtmorgan at fhcrc.org> writes:

> Hi Daniel --
>
> Daniel Silberschmidt wrote:
>> Hello everybody,
>> 	tried to install bioconductor from three different machines (all 64
>> bits) and different OS (Linux different kernels, Windows XP)  but always
>> got a message like this one:
>> 
>>>> source("http://bioconductor.org/biocLite.R")
>>>> biocLite()
>>> Running biocinstall version 2.2.9 with R version 2.7.0 Your version
>>> of R requires version 2.2 of BioConductor.
>>> Will install the following packages:
>>>  [1] "affy"         "affydata"     "affyPLM"      "annaffy"
>>> "annotate"     [6] "Biobase"      "Biostrings"   "DynDoc"
>>> "gcrma"        "genefilter"  [11] "geneplotter"  "hgu95av2.db"
>>> "limma"        "marray"       "matchprobes" [16] "multtest"
>>> "ROC"          "vsn"          "xtable"       "affyQCReport"
>>> Please wait...
>>>
>>> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies,  :
>>>   argument 'lib' is missing: using '/home/xxxxxxxx'
>>> Error: subscript out of bounds
>>> In addition: There were 15 warnings (use warnings() to see them)
>>>
>> 	Think that is something related to the  place because at home
>> (linux ubuntu 8.04, 32 bits) I was able to  install it without
>> problem
>
> Hard to know for sure. After the error, what does traceback() say?
>
> Also,  is /home/xxxxxxx really the directory where you are installing
> libraries? Perhaps a helpful system administrator has written a
> Rprofile file for the site that sets 'your' home directory to
> this. What does .libPaths() say? The packages will be installed in the
> first directory returned by .libPaths(), and you must have write
> permissions. If this is the issue, you'll want to configure R to know
> about a more sensible directory; see ?Startup and ?.libPaths for more.
>
> Hope that helps...
>
> Martin
>
>
>> 	Any idea? Thanks
>> Daniel Silberschmidt
>> _______________________________________________
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>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>
>
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M2 B169
Phone: (206) 667-2793