[Bioc-devel] problem installing VariantAnnotation devel version

[Dan Tenenbaum]

On Sun, Aug 5, 2012 at 12:47 PM, Augusto Rendon <ar506 at cam.ac.uk> 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
>
>
> The fist element of .libPaths() is the intended one for the devel version.
>

It looks like you have mixed release (BiocGenerics, zlibbioc) and
devel packages.
This can and will cause problems.
http://bioconductor.org/developers/useDevel/
should tell you how to keep release and devel packages completely separate.

That said, there seems to be some recent change in devel that is
breaking a number of packages. That's all I know at this point.

Dan


> thxs
>
> On 5 August 2012 20:17, Martin Morgan <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 | 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>> 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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>>
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>> Computational Biology / Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N.
>> PO Box 19024 Seattle, WA 98109
>>
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>> Phone: (206) 667-2793
>>
>
>         [[alternative HTML version deleted]]
>
>
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