Re: Bug#611008: does not run with current version of R in squeeze
Hi release heros,
while the bug would be fixed in unstable after a simple rebuild it
concerns the Squeeze release. I prepared a fixed version of the package
(see debdiff).
Notes to the debdiff besides fixing (rebuilding against the R version in
Squeeze):
- Updated Standards-Version to keep lintian silent (should not break
anything because no changes were needed)
- Added watch file (should not break anything)
- Added upstream-metadata.yaml to the source (should not break anything
but helps in maintaining references in Debian Med and Debian Science
+ if you agree I would be in big favour of bumping debhelper compat to
7 but I hesitated to put it into the changelog without your confirmation
Please tell me whether I should upload to testing-proposed-updates (with
or without the debhelper bump).
Kind regards and thanks for your work as release team
Andreas.
On Mon, Jan 24, 2011 at 09:05:40PM +0100, Steffen Moeller wrote:
> Package: r-other-mott-happy
> Version: 2.1-4+b1
> Severity: grave
> Tags: squeeze sid
>
> The current -4 package was built with a version of R < 2.10 and is hence incompatible. The current version should not be shipped with squeeze.
>
> -- System Information:
> Debian Release: 6.0
> APT prefers unstable
> APT policy: (500, 'unstable'), (500, 'testing'), (1, 'experimental')
> Architecture: amd64 (x86_64)
>
> Kernel: Linux 2.6.37-rc5-amd64 (SMP w/2 CPU cores)
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
>
> Versions of packages r-other-mott-happy depends on:
> ii libc6 2.11.2-9 Embedded GNU C Library: Shared lib
> ii r-base-core 2.12.1-1 GNU R core of statistical computat
> ii r-cran-g.data 2.0-2 GNU R package for delayed-data
> ii r-cran-mass [r-cran-vr] 7.3-9-1 GNU R package of Venables and Ripl
>
> r-other-mott-happy recommends no packages.
>
> r-other-mott-happy suggests no packages.
>
> -- no debconf information
>
>
>
--
http://fam-tille.de
diff -u r-other-mott-happy-2.1/debian/control r-other-mott-happy-2.1/debian/control
--- r-other-mott-happy-2.1/debian/control
+++ r-other-mott-happy-2.1/debian/control
@@ -1,17 +1,18 @@
Source: r-other-mott-happy
Section: gnu-r
Priority: optional
-Maintainer: Debian-Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
-Uploaders: Steffen Moeller <moeller@debian.org>
-Build-Depends: debhelper (>= 5.0.0), cdbs, r-base-dev, r-cran-g.data, r-cran-vr, quilt
-Standards-Version: 3.8.3
+Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller@debian.org>,
+ Andreas Tille <tille@debian.org>
+Build-Depends: debhelper (>= 5.0.0), cdbs, r-base-dev (>= 2.10), r-cran-g.data, r-cran-vr, quilt
+Standards-Version: 3.9.1
Homepage: http://www.well.ox.ac.uk/happy/happyR.shtml
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/R/r-other-mott-happy/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/R/r-other-mott-happy/trunk/
Package: r-other-mott-happy
Architecture: any
-Depends: ${shlibs:Depends}, r-base-core, r-cran-g.data, r-cran-vr
+Depends: ${shlibs:Depends}, r-base-core (>= 2.10), r-cran-g.data, r-cran-vr
Description: GNU R package for fine-mapping complex diseases
Most phenotypes of medical importance can be measured quantitatively,
and in many cases the genetic contribution is substantial, accounting
diff -u r-other-mott-happy-2.1/debian/changelog r-other-mott-happy-2.1/debian/changelog
--- r-other-mott-happy-2.1/debian/changelog
+++ r-other-mott-happy-2.1/debian/changelog
@@ -1,3 +1,20 @@
+r-other-mott-happy (2.1-5) testing-proposed-updates; urgency=low
+
+ [Andreas Tille]
+ * debian/control:
+ - Build-Depends r-base-dev (>= 2.10), Depends r-core (2.10) and
+ rebuild on current Squeeze system
+ Closes: #611008
+ - Added myself to uploaders
+ - Standards-Version: 3.9.1 (no changes needed)
+ - Fixed name of Debian Med team
+ * Added watch file
+
+ [Charles Plessy]
+ * Added upstream-metadata.yaml
+
+ -- Andreas Tille <tille@debian.org> Tue, 25 Jan 2011 08:17:57 +0100
+
r-other-mott-happy (2.1-4) unstable; urgency=low
* Fixed build dependency on MASS library (packaged
only in patch2:
unchanged:
--- r-other-mott-happy-2.1.orig/debian/watch
+++ r-other-mott-happy-2.1/debian/watch
@@ -0,0 +1,2 @@
+version=3
+http://www.well.ox.ac.uk/happy/happyR.shtml happy.*_([\d\.]+).tar.gz
only in patch2:
unchanged:
--- r-other-mott-happy-2.1.orig/debian/upstream-metadata.yaml
+++ r-other-mott-happy-2.1/debian/upstream-metadata.yaml
@@ -0,0 +1,15 @@
+Contact: Richard Mott <Richard.Mott@well.ox.ac.uk>
+DOI: 10.1073/pnas.230304397
+Homepage: http://www.well.ox.ac.uk/happy/happyR
+Name: HAPPY
+PMID: 11050180
+Reference:
+ author: Mott, Richard and Talbot, Christopher J. and Turri, Maria G. and Collins, Allan C. and Flint, Jonathan
+ title: A method for fine mapping quantitative trait loci in outbred animal stocks
+ journal: Proc Natl Acad Sci U S A
+ volume: 97
+ number: 23
+ pages: 12649-12654
+ year: 2000
+ URL: http://www.pnas.org/content/97/23/12649.abstract
+ eprint: http://www.pnas.org/content/97/23/12649.full.pdf+html
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