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

[Andreas Tille]

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:

Files: inst/extdata/CaffeineTxdb.sqlite
 I tried `grep -R CaffeineTxdb` with no hit.

Files: inst/extdata/ex1.bam
 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

Files: inst/extdata/example\.gtf*:
 I tried `grep -R example\.gtf  | grep -v system\.file` with no hit

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

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.

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


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.

-- 
http://fam-tille.de