[Bioc-devel] problem installing VariantAnnotation devel version

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

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

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