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
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Rsamtools
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').
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.
--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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