[Bioc-devel] problem installing VariantAnnotation devel version
Martin Morgan
mtmorgan at fhcrc.org
Mon Aug 6 01:36:27 CEST 2012
On 08/05/2012 12:47 PM, Augusto Rendon wrote:
> Thank you for your quick answer.
>
> Bioconductor 2.10 is installed for all users
>
> I am using useDevel() and that installed devel versions of Biostrings,
> IRanges, RSamtools, GenomicRanges, BiocInstaller.
>
> Session info after loading these packages:
>
> > sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] Rsamtools_1.9.25 GenomicRanges_1.9.41 Biostrings_2.25.8
> [4] IRanges_1.15.25 BiocGenerics_0.2.0 BiocInstaller_1.5.12
>
> loaded via a namespace (and not attached):
> [1] bitops_1.0-4.1 stats4_2.15.1 tools_2.15.1 zlibbioc_1.2.0
Here's my sessionInfo() after starting R --vanilla and successfully
evaluating
biocLite("VariantAnnotation"); library(VariantAnnontation)
I notice you don't have rtracklayer in your sessionInfo above, in
addition to the mix of release and devel package versions Dan mentions.
Martin
> sessionInfo()
R version 2.15.1 Patched (2012-06-22 r59603)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] VariantAnnotation_1.3.18 Rsamtools_1.9.25 Biostrings_2.25.8
[4] GenomicRanges_1.9.41 IRanges_1.15.25 BiocGenerics_0.3.0
[7] BiocInstaller_1.5.12
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.19.28 Biobase_2.17.6 biomaRt_2.13.1
[4] bitops_1.0-4.1 BSgenome_1.25.3 DBI_0.2-5
[7] GenomicFeatures_1.9.28 grid_2.15.1 lattice_0.20-6
[10] Matrix_1.0-6 RCurl_1.91-1 RSQLite_0.11.1
[13] rtracklayer_1.17.15 snpStats_1.7.3 splines_2.15.1
[16] stats4_2.15.1 survival_2.36-14 tools_2.15.1
[19] XML_3.9-4 zlibbioc_1.3.0
>
>
> The fist element of .libPaths() is the intended one for the devel version.
>
> thxs
>
> On 5 August 2012 20:17, Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>> wrote:
>
> On 08/05/2012 12:04 PM, Vincent Carey wrote:
>
> We would need a full sessionInfo() result. FWIW this is the same
> problem I continue to have with my hand-built R-devel for
> MacOSX, and I
> have gone back to a scratch build to see if I can reproduce it
> even now.
> I will provide more data on the outcome of this ASAP.
>
>
> For what it's worth there is this in the svn log of Biostrings
>
> r67139 | hpages at fhcrc.org <mailto:hpages at fhcrc.org> | 2012-06-28
> 18:14:49 -0700 (Thu, 28 Jun 2012) | 3 lin
> es
>
> Rename xsbasetype() -> seqtype(), and
> get_xsbasetypes_conversion___lookup() ->
> get_seqtype_conversion_lookup(__).
>
> with ShortRead, Rsamtools, and rtracklayer using
> get_seqtype_conversion_lookup (and no mention of get_xbase* in the
> Bioconductor source tree).
>
>
> On Sun, Aug 5, 2012 at 2:51 PM, Martin Morgan
> <mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>
> <mailto:mtmorgan at fhcrc.org <mailto:mtmorgan at fhcrc.org>>> wrote:
>
> On 08/05/2012 11:36 AM, Augusto Rendon wrote:
>
> Hello,
>
> I am trying to install the development version of the
> VariantAnnotation
> devel (1.3.18) package
>
> and I keep getting this error:
> Error : object ‘get_xsbasetypes_conversion_____lookup’
> is not
>
> exported by
> 'namespace:Biostrings'
> ERROR: lazy loading failed for package ‘VariantAnnotation’
>
> any clues?
>
>
> Likely it is an out-of-date package. Try
>
> source('http://bioconductor.____org/biocLite.R
>
> <http://bioconductor.org/__biocLite.R
> <http://bioconductor.org/biocLite.R>>')
> biocLite(character())
>
> to be prompted to update old packages.
>
> Does biocLite know that you are using the devel version of
> Bioconductor?
>
> http://bioconductor.org/____developers/useDevel/
> <http://bioconductor.org/__developers/useDevel/>
>
> <http://bioconductor.org/__developers/useDevel/
> <http://bioconductor.org/developers/useDevel/>>
>
> Martin
>
>
> thanks,
>
> a
>
> [[alternative HTML version deleted]]
>
>
>
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> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>
>
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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