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@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@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@fhcrc.org
>> <mailto:mtmorgan@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]]
>>
>>
>>
>>         ______________________________**___________________
>>         Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.**org<Bioc-devel@r-project.org>
>> >
>>         mailing list
>>         https://stat.ethz.ch/mailman/_**_listinfo/bioc-devel<https://stat.ethz.ch/mailman/__listinfo/bioc-devel>
>>
>>         <https://stat.ethz.ch/mailman/**listinfo/bioc-devel<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>> >
>>
>>
>>
>>     --
>>     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 <tel:%28206%29%20667-2793>
>>
>>     ______________________________**___________________
>>     Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.**org<Bioc-devel@r-project.org>>
>> mailing list
>>     https://stat.ethz.ch/mailman/_**_listinfo/bioc-devel<https://stat.ethz.ch/mailman/__listinfo/bioc-devel>
>>     <https://stat.ethz.ch/mailman/**listinfo/bioc-devel<https://stat.ethz.ch/mailman/listinfo/bioc-devel>
>> >
>>
>>
>>
>
> --
> 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
>

	[[alternative HTML version deleted]]

