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
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