Entering edit mode
Matthew Young
▴
50
@matthew-young-4865
Last seen 9.6 years ago
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@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
>
> 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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