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

[Andreas Tille]

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.

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
> 

-- 
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