Bug#721801: [devteam-bioc] Precomputed results in GenomicRanges [Was: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED]
Hi,
The objects in precomputed_results can be generated by running the
code in the OverlapEncodings.Rnw vignette. However running this code
takes a long time and would make 'R CMD check' take too much time to
complete, making the maintenance of the package very impractical.
So the trick is to have some of the more time-consuming code chunks
in the vignette set to eval=FALSE, and to load the precomputed results
instead. The loading is performed in a hidden code chunk and it also
performs some sanity checks to verify that the precomputed object that
was just loaded is in sync with other objects generated earlier in the
vignette.
HTH,
H.
On 10/12/2013 02:59 AM, Maintainer wrote:
Hi,
the Debian Med team tries to package several parts of BioConductor.
When trying to upload GenomicRanges our ftpmaster criticised that the
source contains some precomputed results inside the documentation which
is in conflict with our policy which requires the source for all binary
data. There could be different solutions for this:
1. If you consider the files
GenomicRanges/inst/doc/precomputed_results/*.rda
as not very important for the user documentation and it might be
sufficient to download the files from somewhere else.
2. Provide a recipe to reprodce the precomputed results we could
use in the package building process to recreate the data.
May be there are other solutions but these come to my mind for the
moment.
Any hint what we should do?
Kind regards and thanks for providing BioConductor as Free Software
Andreas.
----- Forwarded message from Paul Richards Tagliamonte <ftpmaster@ftp-master.debian.org> -----
Date: Sat, 21 Sep 2013 04:00:52 +0000
From: Paul Richards Tagliamonte <ftpmaster@ftp-master.debian.org>
To: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>, Andreas Tille <tille@debian.org>
Subject: r-bioc-genomicranges_1.12.4-1_amd64.changes REJECTED
Howdy R-folks,
As per the recent mail, there are precomputed results in
./GenomicRanges/inst/doc/precomputed_results but no way to reproduce
this (as far as I can see).
I don't see you rebuilding these in d/rules.
Please point me to how these can be rebuilt with what's currently
in the source tarball.
Thanks!
Paul
===
Please feel free to respond to this email if you don't understand why
your files were rejected, or if you upload new files which address our
concerns.
_______________________________________________
Debian-med-packaging mailing list
Debian-med-packaging@lists.alioth.debian.org
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging
----- End forwarded message -----
--
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@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
Reply to: