[Debian-med-packaging] [devteam-bioc] Help needed to build BSgenome

[Hervé Pagès]

On 07/08/2014 12:30 AM, Andreas Tille wrote:
> Hi,
>
> thanks for your quick reply.
>
> On Tue, Jul 08, 2014 at 12:05:34AM -0700, Hervé Pagès wrote:
>> Hi Andreas,
>>
>> How are you trying to update BSgenome?
>>
>> Seems to me that you're mixing stuff from BioC 2.14 (current
>> release) and BioC 3.0 (current devel).
>>
>> In BioC 2.14, GenomicAlignments depends on BSgenome, but in
>> BioC 3.0 it's now the other way around i.e. BSgenome depends
>> on GenomicAlignments. So trying to install the current devel
>> version of BSgenome on top of a BioC 2.14 installation is like
>> trying to solve a chicken and egg problem.
>
> I tried BSgenome 1.32.0 downloaded from
>
>     http://bioconductor.org/packages/release/bioc/html/BSgenome.html
>
> which states
>
>      Bioconductor version: Release (2.14)
>
> In Debian I would only provide released versions.
> So at least what I can see this is no chicken and egg problem.

The chicken and egg problem you have could come from packages
that BSgenome depends on (e.g. Rsamtools), not necessarily from
BSgenome itself.

Again, it looks very much like you are mixing stuff from different BioC
versions. Running biocValid() (from the BiocInstaller package) might
help you find the installed packages that don't belong to BioC 2.14.

Cheers,
H.

>
> Any further hint?
>
> Kind regards
>
>       Andreas.
>
>> Cheers,
>> H.
>>
>> On 07/07/2014 11:22 PM, Maintainer wrote:
>>> Hi,
>>>
>>> as you might know the Debian Med team is creating Debian packages from
>>> selected BioConductor modules.  When trying to update BSgenome I
>>> stumbled about a problem I have no clue how to solve.
>>>
>>> ...
>>> * installing *source* package 'BSgenome' ...
>>> ** R
>>> ** inst
>>> ** preparing package for lazy loading
>>> Error : objects 'GAlignments', 'GAlignmentPairs', 'Union', 'IntersectionNotEmpty', 'IntersectionStrict', 'findSpliceOverlaps' are not exported by 'namespace:GenomicRanges'
>>> ERROR: lazy loading failed for package 'BSgenome'
>>> * removing '/tmp/buildd/r-bioc-bsgenome-1.32.0/debian/r-bioc-bsgenome/usr/lib/R/site-library/BSgenome'
>>>
>>>
>>> Since I upgraded GenomicRanges before to version 1.16.3 the requirement
>>> GenomicRanges(>= 1.15.9) mentioned on the BSgenome web page is
>>> fullfilled.
>>>
>>> >From the names of the first two objects it seems like it could be a
>>> dependency of GenomicAlignments.  However, I can not build
>>> GenomicAlignments without having BSgenome installed.
>>>
>>> Any idea what might went wrong here?
>>>
>>> Kind regards
>>>
>>>         Andreas.
>>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages at fhcrc.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319