[Debian-med-packaging] [devteam-bioc] Please explain binary files without source in Rsamtools

[Andreas Tille]

Hi Martin,

On Wed, Oct 30, 2013 at 07:38:09AM -0700, Martin Morgan wrote:
> On 10/30/2013 03:12 AM, Maintainer wrote:
> >Hi,
> >
> >as formerly posted here I'm working onn the Debian packaging of
> >preconditions for the new version of cummeRbund.  The package Rsamtools
> >belongs to the tree of dependencies and inside its source I found some
> >binary files with unclear origin which will not be accepted.  Since
> >Martin Morgan pointed me in previous cases to the documentation inside
> >the package I tried to verify this first but failed.  Here are the
> >files in Question:
> 
> you don't mention the version you're trying to port; the following is from

Ahh, sorry.  I was basing my packaging onto BioConductor Release (2.12)
containing RSamtools version 1.12.4.  The rationale for using this version
was that I wanted to stick to BioConductor 2.12 until all needed packages
were uploaded to Debian and afterwards upgrading in one rush to the latest
BioConductor version.
 
>   https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools

Well, this requires some autorisation but may be there is no need that
I review the development trunk just for this reason.

> >Files: inst/extdata/CaffeineTxdb.sqlite
> >  I tried `grep -R CaffeineTxdb` with no hit.
> 
> stale; removed. sqlite tables derived from querying a public data
> base ('biomart.org').

I could remove this file from the original tarball or weit for a new
release without this file (in case this might be at horizon). 

Thanks for all the other explanations.  I'll include it into the
packaging and hope our ftpmaster will consider it sufficient.

Kind regards

       Andreas.


> >Files: inst/extdata/ex1.bam
> 
> ex1.sam is the text representation of ex1.bam (using
> Rsamtools::asBam at the time of file creation); ex1.bam.bai is an
> index created on ex1.bam (using Rsamtools::indexBam at the time of
> file creation). ex1.sam is derived from files originally distributed
> with 'samtools' software under an MIT license, see Rsamtools/LICENSE
> 
> >  I tried
> >
> >   $ grep -R ex1\.bam | grep -v system\.file
> >   inst/unitTests/test_BcfFile.R:        checkEquals("ex1.bam", h[["Sample"]])
> >   inst/doc/Rsamtools-Overview.Rnw:list.files(dirname(bamFile), pattern="ex1.bam(.bai)?")
> >   inst/doc/Rsamtools-Overview.R:list.files(dirname(bamFile), pattern="ex1.bam(.bai)?")
> >   src/samtools/knetfile.c:                fp = knet_open("http://www.sanger.ac.uk/Users/lh3/ex1.bam", "r");
> >
> >  None of these files is kind of documenting the origin and even worse
> >  the URL at www.sanger.ac.uk does not exist any more.
> >
> >Files: inst/extdata/ex1.bam
> >  I tried `grep -R ex1\.bcf | grep -v system\.file` with no hit
> 
> ex1.bcf is a file hand created in antiquity, and used in unit tests and man pages.
> 
> Rsamtools$ grep -lr ex1.bcf *|grep -v svn
> inst/unitTests/test_BcfFile.R
> man/BcfFile-class.Rd
> man/scanBcf.Rd
> 
> >
> >Files: inst/extdata/example\.gtf*:
> >  I tried `grep -R example\.gtf  | grep -v system\.file` with no hit
> 
> example.gtf.gz is gz-compressed text file used in unit tests and man
> pages, hand curated from public data sources, the .tbi variant is an
> index (Rsamtools::indexTabix)
> 
> Rsamtools$ grep -lr example.gtf.gz *|grep -v svn
> inst/unitTests/test_TabixFile.R
> man/headerTabix.Rd
> man/seqnamesTabix.Rd
> man/TabixFile-class.Rd
> 
> >
> >Files: inst/extdata/example_from_SAM_Spec*:
> >  These files are neither documented nor used since not even
> >    grep -R example_from_SAM_Spec
> >  shows any hit
> 
> This is a file useful to the developer, hand-curated from the SAM spec at
> 
>   http://samtools.sourceforge.net/SAMv1.pdf
> 
> although SAM.pdf did not historically include version numbers so the
> precise origin is unknown.
> 
> >
> >Files: inst/extdata/olaps.Rda
> >  This file is mentioned in a load statement in
> >   inst/doc/Rsamtools-Overview.R
> >  but no hint to its origin.
> 
> The script for creating this file is in the vignette Rsamtools-Overiew.Rnw
> 
> <<readGAlignmentsFromBam, eval=FALSE>>=
> library(parallel)
> options(srapply_fapply="parallel", mc.cores=detectCores())
> olaps <- readGAlignmentsFromBam(bv)
> @
> 
> >
> >Files: inst/unitTests/cases/ex1.sam.gz
> >  Except of the first two lines this is a copy of file
> >   inst/extdata/ex1.sam
> >
> >Files: inst/unitTests/cases/ex1_*.bam*
> >  Seems these files are derived from file
> >   inst/extdata/ex1.sam
> >  and just used for verification of the correctness of
> >  Rsamtools.  Please confirm this suspicion.
> >
> >Files: inst/unitTests/cases/plp_refskip.bam*
> >  I tried `grep -R plp_refskip | grep -v system\.file` with no hit
> 
> This is a hand-crafted file used in a unit test
> 
> Rsamtools$ grep -lr plp_refskip *|grep -v svn
> inst/unitTests/test_applyPileups.R
> 
> >
> >
> >It would be really helpful if you could clarify the origin of these
> >files since otherwise Debian ftpmasters will consider the package
> >as non-free which will prevent it from inclusion into main Debian
> >distribution and in turn we also could not get cummeRbund updated.
> >
> >Kind regards and thanks for your cooperation
> >
> >       Andreas.
> >
> 
> 
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