[BioC] geneLenDataBase installation issues

[Martin Morgan]

On 04/17/2012 01:01 AM, Matthew Young wrote:
> Hi Diana,
>
> I'm reasonably sure that all your problems are all to do with your first
> error message.  The geneLenDataBase package Namespace file imports from
> various packages, such as rtracklayer, which the first error seems to
> indicate aren't being installed.  Have you been able to get other
> bioconductor packages to install with biocLite?
>
> Anyway, your first error message indicates that the installer can't find
> any of the core dependencies at the repository "
> http://cran.hostingzero.com/bin/macosx/leopard/contrib/2.15", which seems
> to be resulting in none of the needed dependencies being installed (not
> just geneLenDataBase).  The first thing I'd try is run chooseBioCmirror()
> and chooseCRANmirror(), after source("http://bioconductor.org/biocLite.R")
> and choose a different mirror and see if that solves your problem.  I've
> cc'ed the bioconductor mailing list in case others have encountered your
> problem and know of a solution.
>
> Cheers,
>
> Matt
>
> On Mon, Apr 16, 2012 at 11:31 PM, Diana T. Dugas<Diana.Dugas at sparc.usda.gov
>> wrote:
>
>>   Hi, Matthew-
>> I am a huge fan of your goseq package.  I used it often under an earlier
>> installation of R (2.13.0) and have since upgraded to the latest version
>> 2.15.0.  Due to this, I'm finding myself in need of updating a lot of my
>> favorite packages.  While trying to download and install goseq, from
>> source("http://bioconductor.org/biocLite.R") I received the following
>> notice:
>>   biocLite("goseq")
>>   BioC_mirror: http://bioconductor.org
>>   Using R version 2.15, BiocInstaller version 1.4.3.
>>   Installing package(s) 'goseq'
>>   Warning: unable to access index for repository
>> http://cran.hostingzero.com/bin/macosx/leopard/contrib/2.15
>>   Warning: dependencies ‘BiasedUrn’, ‘DBI’, ‘RSQLite’, ‘XML’, ‘RCurl’,
>> ‘bitops’ are not available
>>   also installing the dependencies ‘GenomicRanges’, ‘Biostrings’,
>> ‘BSgenome’, ‘zlibbioc’, ‘Rsamtools’, ‘biomaRt’, ‘rtracklayer’,
>> ‘GenomicFeatures’, ‘BiocGenerics’, ‘Biobase’, ‘IRanges’, ‘geneLenDataBase’,
>> ‘AnnotationDbi’

to update these packages, run

   source("http://bioconductor.org/biocLite.R")
   biocLite(character())

answer 'a' (for 'all') to the resulting prompt; let us know if some of 
the packages do not update.

Martin

>>
>>   If I go in and either download and "R CMD INSTALL" or run
>> biocLite("geneLenDataBase") I don't get any errors.  When I try to load
>> the goseq library, though I receive the following error message:
>>   Error in get(Info[i, 1], envir = env) :
>>     internal error -3 in R_decompress1
>>   Error: package/namespace load failed for ‘geneLenDataBase’
>>
>>   I have a NAMESPACE file within the appropriate directory.  I don't
>> understand what the problem is.  Could you please help direct me in what to
>> do to fix the issue?  I'm looking forward to using your goseq library
>> again, but won't be able to until this issue is resolved.  The more
>> frustrating issue is that I work with Sorghum, so I don't think I ever
>> actually use the geneLenDataBase package for anything other than as a
>> dependency for goseq.
>>
>>   I don't want to down-grade my R program, but I'm starting to seriously
>> consider doing so if it will allow me access to the libraries I need.
>>   Please let me know if you think this is the correct route to take.  Thank
>> you for any help and guidance you can provide.
>> -Diana
>>
>>   --
>> Diana Toups Dugas
>> Post Doctoral Associate
>> Robert Klein Lab
>> USDA-ARS
>> College Station, TX 77843-2123
>> 979-862-4802
>>
>>
>
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