[med-svn] r20703 - in trunk/packages/altree/tags: . 1.3.1-4 1.3.1-4/debian 1.3.1-4/debian/patches
Vincent Danjean
vdanjean at moszumanska.debian.org
Wed Dec 9 22:44:56 UTC 2015
Author: vdanjean
Date: 2015-12-09 22:44:55 +0000 (Wed, 09 Dec 2015)
New Revision: 20703
Added:
trunk/packages/altree/tags/1.3.1-4/
trunk/packages/altree/tags/1.3.1-4/debian/
trunk/packages/altree/tags/1.3.1-4/debian/altree.install
trunk/packages/altree/tags/1.3.1-4/debian/changelog
trunk/packages/altree/tags/1.3.1-4/debian/control
trunk/packages/altree/tags/1.3.1-4/debian/patches/from-upstream-no-nested-functions.patch
trunk/packages/altree/tags/1.3.1-4/debian/rules
Removed:
trunk/packages/altree/tags/1.3.1-4/debian/
trunk/packages/altree/tags/1.3.1-4/debian/changelog
trunk/packages/altree/tags/1.3.1-4/debian/control
trunk/packages/altree/tags/1.3.1-4/debian/patches/from-upstream-no-nested-functions.patch
trunk/packages/altree/tags/1.3.1-4/debian/rules
Log:
[svn-buildpackage] Tagging altree 1.3.1-4
Copied: trunk/packages/altree/tags/1.3.1-4/debian/altree.install (from rev 20702, trunk/packages/altree/trunk/debian/altree.install)
===================================================================
--- trunk/packages/altree/tags/1.3.1-4/debian/altree.install (rev 0)
+++ trunk/packages/altree/tags/1.3.1-4/debian/altree.install 2015-12-09 22:44:55 UTC (rev 20703)
@@ -0,0 +1 @@
+/usr
Deleted: trunk/packages/altree/tags/1.3.1-4/debian/changelog
===================================================================
--- trunk/packages/altree/trunk/debian/changelog 2015-12-09 15:09:20 UTC (rev 20698)
+++ trunk/packages/altree/tags/1.3.1-4/debian/changelog 2015-12-09 22:44:55 UTC (rev 20703)
@@ -1,199 +0,0 @@
-altree (1.3.1-3) unstable; urgency=medium
-
- * [debian/control] Update build dependencies for GSL 2, change libgsl0-dev to
- libgsl-dev. Thanks Bas Couwenberg <sebastic at debian.org> (Closes: #807173)
- * Fix "FTBFS with perl 5.22 in experimental (MakeMaker changes)" by removing
- manual (wrong) call to "make install PREFIX=..." (Closes: #807423)
- * [debian/control] Bump Standards-Version (no changes needed)
-
- -- Vincent Danjean <vdanjean at debian.org> Tue, 08 Dec 2015 20:47:26 +0100
-
-altree (1.3.1-2) unstable; urgency=medium
-
- * Fix "FTBFS with clang instead of gcc"
- clang does not support nested functions so removing them.
- Instead of inlining the nested function as proposed in the submitted
- patch (thanks Arthur <arthur at info9.net>), use a external function
- with an explicit context (Closes: #742843)
- * bump standard-version (no change needed)
-
- -- Vincent Danjean <vdanjean at debian.org> Sun, 30 Mar 2014 23:43:51 +0200
-
-altree (1.3.1-1) unstable; urgency=low
-
- * New upstream release
- + fix a SEGV when ALTREE_PARALLEL is used with more processors
- than requested permutations (-r program parameter)
- + Fix "FTBFS with perl 5.12.0-1: long doubles" (Closes: #578550)
- * debian/control:
- Add B-D on libtest-deep-perl (required when fixing 578550)
-
- -- Vincent Danjean <vdanjean at debian.org> Fri, 13 Dec 2013 23:27:04 +0100
-
-altree (1.3.0-1) unstable; urgency=low
-
- * New upstream release
- + Mostly performance improvment
- * debian/control:
- + bump Standard-Version (no change needed)
- + put canonical vcs fields
- + remove outdated DM-Upload-Allowed field
- + improve altree-examples long description
- + add libgsl0-dev and libatlas-base-dev as new build-dependency
- + remove libpdl-stats-perl as (build-)dependency
-
- -- Vincent Danjean <vdanjean at debian.org> Fri, 22 Nov 2013 23:57:43 +0100
-
-altree (1.2.1-1) unstable; urgency=low
-
- [ Andreas Tille ]
- * debian/upstream: Add eprint
- * debian/reference: Removed in favour of debian/upstream
-
- [ Vincent Danjean ]
- * New (stable) upstream release 1.2.1
- * debian/{README.Debian,watch}: No need to skip old last version 1.1.1
- * debian/patches/*: latex bug fixed upstream
-
- -- Vincent Danjean <vdanjean at debian.org> Sat, 09 Jun 2012 22:45:06 +0200
-
-altree (1.0.1-7) unstable; urgency=low
-
- [ Thorsten Alteholz ]
- * debian/rules: target get-orig-source added
-
- [ Charles Plessy ]
- * Renamed debian/upstream-metadata.yaml to debian/upstream
-
- [ Andreas Tille ]
- * debian/upstream: Single Reference field instead of Reference-*
- * debian/watch: Do not download version 1.1.1 as the author has
- asked for in
- http://lists.debian.org/debian-med/2009/08/msg00104.html
- * debian/README.Debian: Document the "do not package new version"
- issue
- * debian/control: Standards-Version: 3.9.3 (no changes needed)
- * debian/changelog: Verified DEP5 using
- cme fix dpkg-copyright
- * debian/patches/build-with-recent-tetex.patch: Drop dvips option
- Closes: #669551
- * debhelper 9 (control+compat)
-
- -- Andreas Tille <tille at debian.org> Sun, 22 Apr 2012 08:40:48 +0200
-
-altree (1.0.1-5) unstable; urgency=low
-
- * Upload source package without 3.0 (quilt) autopatch leftover.
- Closes: #643045.
- * Corrected VCS URLs in debian/control.
- * Use Debhelper 8 (debian/control, debian/compat).
- * Converted debian/copyright to machine-readable format 1.0 (DEP 5).
- * Compress binary packages with xz (debian/rules).
- * Conforms with Policy 3.9.2 (debian/control, no other changes needed).
-
- -- Charles Plessy <plessy at debian.org> Tue, 27 Sep 2011 08:31:14 +0900
-
-altree (1.0.1-4) unstable; urgency=low
-
- [ Charles Plessy ]
- * Depends on libtamuanova-perl (debian/control).
- * Added a BibTeX reference in debian/reference and install it through
- debian/altree.docs.
- * Refreshed debian/copyright.
- * Using debhelper 7 (debian/compat, debian/control).
- * Incremented Standards-Version to reflect conformance to Policy 3.8.1
- (no changes needed).
- * Bash completion:
- - Build-depend on bash-completion >= 1:1 in debian/control.
- - Install the altree completion file using dh_bash-completion.
- * Added information about Upstream in debian/upstream-metadata.yaml.
-
- [ David Paleino ]
- * debian/control:
- - removed unneeded Build-Dependencies
- - added ${misc:Depends} dependency to altree-examples
- - removed myself from Uploaders
- * debian/rules:
- - removing unneeded included Makefile
-
- [Andreas Tille]
- * use short debhelper instead of cdbs because the install target
- did not worked properly any more
- * debian/source/format: 3.0 (quilt)
- * debian/control:
- - Standards-Version: 3.9.1
- - Added myself to Uploaders
- - Added Build-Depends: ghostscript to avoid errors in LaTeX run
- Closes: #614538
- - Removed libtamuanova-perl from Depends again because it has no
- installation candidate
-
- -- Andreas Tille <tille at debian.org> Tue, 22 Feb 2011 14:37:21 +0100
-
-altree (1.0.1-3) unstable; urgency=low
-
- [ Charles Plessy ]
- * Initial release for Debian (Closes: #461506)
- * debian/copyright: converted to machine-readable format.
- * debian/control:
- - Added texlive-lang-french, texlive-latex-base, texlive-latex-recommended
- and texlive-latex-extra as build dependencies.
- - Updated my email address.
-
- [ David Paleino ]
- * Added debian/watch
- * debian/compat and debhelper dependency updated
- * debian/control:
- - added myself in Uploaders
- - Standards-Version is now 3.7.3
-
- [ Vincent Danjean ]
- * remove unused debian/control.in file
- * Fix copyright (and update email addresses)
- * Fix build-depends:
- + remove debian part of version (thanks lintian)
- + change latex-utils to latex-make (always present with this name in
- Debian)
- * Fix depends: add ${perl:Depends}
- * remove empty dir in package (/usr/sbin)
- => package lintian clean now
-
- -- Vincent Danjean <vdanjean at debian.org> Mon, 12 May 2008 08:19:31 +0200
-
-altree (1.0.1-1) unstable; urgency=low
-
- * New upstream release
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Fri, 13 Jan 2006 15:46:52 +0100
-
-altree (1.0.0-1) unstable; urgency=low
-
- * New upstream release
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Fri, 13 Jan 2006 09:40:02 +0100
-
-altree (0.9.2-2) unstable; urgency=low
-
- * Update FSF address in copyright file
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Sat, 10 Sep 2005 10:25:23 +0200
-
-altree (0.9.2-1) unstable; urgency=low
-
- * New upstream release
- * New upstream name
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Tue, 2 Aug 2005 19:52:19 +0200
-
-alphy (0.9.1d-1) unstable; urgency=low
-
- * New upstream release
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Tue, 26 Jul 2005 00:08:40 +0200
-
-alphy (0.9.1c-1) unstable; urgency=low
-
- * Initial release
-
- -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Mon, 25 Jul 2005 22:22:50 +0200
-
Copied: trunk/packages/altree/tags/1.3.1-4/debian/changelog (from rev 20700, trunk/packages/altree/trunk/debian/changelog)
===================================================================
--- trunk/packages/altree/tags/1.3.1-4/debian/changelog (rev 0)
+++ trunk/packages/altree/tags/1.3.1-4/debian/changelog 2015-12-09 22:44:55 UTC (rev 20703)
@@ -0,0 +1,212 @@
+altree (1.3.1-4) unstable; urgency=medium
+
+ [ Andreas Tille ]
+ * cme fix dpkg-control (dropped Replace/Provides/Conflicts of non-existing
+ packages alphy, libcutils-perl)
+ * xz compression is default and does not need to be enforced
+
+ [ Vincent Danjean ]
+ * Fix "Produces empty binary package" by adding debian/altree.install
+ (Closes: #807493)
+
+ -- Vincent Danjean <vdanjean at debian.org> Wed, 09 Dec 2015 22:37:46 +0100
+
+altree (1.3.1-3) unstable; urgency=medium
+
+ * [debian/control] Update build dependencies for GSL 2, change libgsl0-dev to
+ libgsl-dev. Thanks Bas Couwenberg <sebastic at debian.org> (Closes: #807173)
+ * Fix "FTBFS with perl 5.22 in experimental (MakeMaker changes)" by removing
+ manual (wrong) call to "make install PREFIX=..." (Closes: #807423)
+ * [debian/control] Bump Standards-Version (no changes needed)
+
+ -- Vincent Danjean <vdanjean at debian.org> Tue, 08 Dec 2015 20:47:26 +0100
+
+altree (1.3.1-2) unstable; urgency=medium
+
+ * Fix "FTBFS with clang instead of gcc"
+ clang does not support nested functions so removing them.
+ Instead of inlining the nested function as proposed in the submitted
+ patch (thanks Arthur <arthur at info9.net>), use a external function
+ with an explicit context (Closes: #742843)
+ * bump standard-version (no change needed)
+
+ -- Vincent Danjean <vdanjean at debian.org> Sun, 30 Mar 2014 23:43:51 +0200
+
+altree (1.3.1-1) unstable; urgency=low
+
+ * New upstream release
+ + fix a SEGV when ALTREE_PARALLEL is used with more processors
+ than requested permutations (-r program parameter)
+ + Fix "FTBFS with perl 5.12.0-1: long doubles" (Closes: #578550)
+ * debian/control:
+ Add B-D on libtest-deep-perl (required when fixing 578550)
+
+ -- Vincent Danjean <vdanjean at debian.org> Fri, 13 Dec 2013 23:27:04 +0100
+
+altree (1.3.0-1) unstable; urgency=low
+
+ * New upstream release
+ + Mostly performance improvment
+ * debian/control:
+ + bump Standard-Version (no change needed)
+ + put canonical vcs fields
+ + remove outdated DM-Upload-Allowed field
+ + improve altree-examples long description
+ + add libgsl0-dev and libatlas-base-dev as new build-dependency
+ + remove libpdl-stats-perl as (build-)dependency
+
+ -- Vincent Danjean <vdanjean at debian.org> Fri, 22 Nov 2013 23:57:43 +0100
+
+altree (1.2.1-1) unstable; urgency=low
+
+ [ Andreas Tille ]
+ * debian/upstream: Add eprint
+ * debian/reference: Removed in favour of debian/upstream
+
+ [ Vincent Danjean ]
+ * New (stable) upstream release 1.2.1
+ * debian/{README.Debian,watch}: No need to skip old last version 1.1.1
+ * debian/patches/*: latex bug fixed upstream
+
+ -- Vincent Danjean <vdanjean at debian.org> Sat, 09 Jun 2012 22:45:06 +0200
+
+altree (1.0.1-7) unstable; urgency=low
+
+ [ Thorsten Alteholz ]
+ * debian/rules: target get-orig-source added
+
+ [ Charles Plessy ]
+ * Renamed debian/upstream-metadata.yaml to debian/upstream
+
+ [ Andreas Tille ]
+ * debian/upstream: Single Reference field instead of Reference-*
+ * debian/watch: Do not download version 1.1.1 as the author has
+ asked for in
+ http://lists.debian.org/debian-med/2009/08/msg00104.html
+ * debian/README.Debian: Document the "do not package new version"
+ issue
+ * debian/control: Standards-Version: 3.9.3 (no changes needed)
+ * debian/changelog: Verified DEP5 using
+ cme fix dpkg-copyright
+ * debian/patches/build-with-recent-tetex.patch: Drop dvips option
+ Closes: #669551
+ * debhelper 9 (control+compat)
+
+ -- Andreas Tille <tille at debian.org> Sun, 22 Apr 2012 08:40:48 +0200
+
+altree (1.0.1-5) unstable; urgency=low
+
+ * Upload source package without 3.0 (quilt) autopatch leftover.
+ Closes: #643045.
+ * Corrected VCS URLs in debian/control.
+ * Use Debhelper 8 (debian/control, debian/compat).
+ * Converted debian/copyright to machine-readable format 1.0 (DEP 5).
+ * Compress binary packages with xz (debian/rules).
+ * Conforms with Policy 3.9.2 (debian/control, no other changes needed).
+
+ -- Charles Plessy <plessy at debian.org> Tue, 27 Sep 2011 08:31:14 +0900
+
+altree (1.0.1-4) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * Depends on libtamuanova-perl (debian/control).
+ * Added a BibTeX reference in debian/reference and install it through
+ debian/altree.docs.
+ * Refreshed debian/copyright.
+ * Using debhelper 7 (debian/compat, debian/control).
+ * Incremented Standards-Version to reflect conformance to Policy 3.8.1
+ (no changes needed).
+ * Bash completion:
+ - Build-depend on bash-completion >= 1:1 in debian/control.
+ - Install the altree completion file using dh_bash-completion.
+ * Added information about Upstream in debian/upstream-metadata.yaml.
+
+ [ David Paleino ]
+ * debian/control:
+ - removed unneeded Build-Dependencies
+ - added ${misc:Depends} dependency to altree-examples
+ - removed myself from Uploaders
+ * debian/rules:
+ - removing unneeded included Makefile
+
+ [Andreas Tille]
+ * use short debhelper instead of cdbs because the install target
+ did not worked properly any more
+ * debian/source/format: 3.0 (quilt)
+ * debian/control:
+ - Standards-Version: 3.9.1
+ - Added myself to Uploaders
+ - Added Build-Depends: ghostscript to avoid errors in LaTeX run
+ Closes: #614538
+ - Removed libtamuanova-perl from Depends again because it has no
+ installation candidate
+
+ -- Andreas Tille <tille at debian.org> Tue, 22 Feb 2011 14:37:21 +0100
+
+altree (1.0.1-3) unstable; urgency=low
+
+ [ Charles Plessy ]
+ * Initial release for Debian (Closes: #461506)
+ * debian/copyright: converted to machine-readable format.
+ * debian/control:
+ - Added texlive-lang-french, texlive-latex-base, texlive-latex-recommended
+ and texlive-latex-extra as build dependencies.
+ - Updated my email address.
+
+ [ David Paleino ]
+ * Added debian/watch
+ * debian/compat and debhelper dependency updated
+ * debian/control:
+ - added myself in Uploaders
+ - Standards-Version is now 3.7.3
+
+ [ Vincent Danjean ]
+ * remove unused debian/control.in file
+ * Fix copyright (and update email addresses)
+ * Fix build-depends:
+ + remove debian part of version (thanks lintian)
+ + change latex-utils to latex-make (always present with this name in
+ Debian)
+ * Fix depends: add ${perl:Depends}
+ * remove empty dir in package (/usr/sbin)
+ => package lintian clean now
+
+ -- Vincent Danjean <vdanjean at debian.org> Mon, 12 May 2008 08:19:31 +0200
+
+altree (1.0.1-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Fri, 13 Jan 2006 15:46:52 +0100
+
+altree (1.0.0-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Fri, 13 Jan 2006 09:40:02 +0100
+
+altree (0.9.2-2) unstable; urgency=low
+
+ * Update FSF address in copyright file
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Sat, 10 Sep 2005 10:25:23 +0200
+
+altree (0.9.2-1) unstable; urgency=low
+
+ * New upstream release
+ * New upstream name
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Tue, 2 Aug 2005 19:52:19 +0200
+
+alphy (0.9.1d-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Tue, 26 Jul 2005 00:08:40 +0200
+
+alphy (0.9.1c-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Vincent Danjean <Vincent.Danjean at ens-lyon.org> Mon, 25 Jul 2005 22:22:50 +0200
+
Deleted: trunk/packages/altree/tags/1.3.1-4/debian/control
===================================================================
--- trunk/packages/altree/trunk/debian/control 2015-12-09 15:09:20 UTC (rev 20698)
+++ trunk/packages/altree/tags/1.3.1-4/debian/control 2015-12-09 22:44:55 UTC (rev 20703)
@@ -1,43 +0,0 @@
-Source: altree
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Vincent Danjean <vdanjean at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: bash-completion, debhelper (>= 9), latex-make, ghostscript,
- texlive-lang-french, texlive-latex-extra, texlive-latex-recommended,
- texlive-fonts-recommended,
- libmath-tamuanova-perl, libgsl-dev, libatlas-base-dev,
- libtest-deep-perl
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/altree/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/altree/trunk/
-Homepage: http://claire.bardel.free.fr/software.html
-
-Package: altree
-Architecture: any
-Conflicts: libcutils-perl, alphy
-Replaces: libcutils-perl, alphy
-Provides: libcutils-perl, alphy
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends},
- libmath-tamuanova-perl
-Suggests: altree-examples
-Description: program to perform phylogeny-based association and localization analysis
- ALTree was designed to perform association detection and localization of
- susceptibility sites using haplotype phylogenetic trees: first, it allows the
- detection of an association between a candidate gene and a disease, and second,
- it enables to make hypothesis about the susceptibility loci.
-
-Package: altree-examples
-Architecture: all
-Recommends: altree (= ${binary:Version})
-Depends: ${misc:Depends}
-Description: example files for ALTree
- ALTree was designed to perform association detection and localization of
- susceptibility sites using haplotype phylogenetic trees: first, it allows the
- detection of an association between a candidate gene and a disease, and second,
- it enables to make hypothesis about the susceptibility loci.
- .
- This package contains the example files for the ALTree package discussed in
- its PDF manual.
Copied: trunk/packages/altree/tags/1.3.1-4/debian/control (from rev 20699, trunk/packages/altree/trunk/debian/control)
===================================================================
--- trunk/packages/altree/tags/1.3.1-4/debian/control (rev 0)
+++ trunk/packages/altree/tags/1.3.1-4/debian/control 2015-12-09 22:44:55 UTC (rev 20703)
@@ -0,0 +1,49 @@
+Source: altree
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Charles Plessy <plessy at debian.org>,
+ Vincent Danjean <vdanjean at debian.org>,
+ Andreas Tille <tille at debian.org>
+Section: science
+Priority: optional
+Build-Depends: bash-completion,
+ debhelper (>= 9),
+ latex-make,
+ ghostscript,
+ texlive-lang-french,
+ texlive-latex-extra,
+ texlive-latex-recommended,
+ texlive-fonts-recommended,
+ libmath-tamuanova-perl,
+ libgsl-dev,
+ libatlas-base-dev,
+ libtest-deep-perl
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/altree/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/altree/trunk/
+Homepage: http://claire.bardel.free.fr/software.html
+
+Package: altree
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${perl:Depends},
+ libmath-tamuanova-perl
+Suggests: altree-examples
+Description: program to perform phylogeny-based association and localization analysis
+ ALTree was designed to perform association detection and localization of
+ susceptibility sites using haplotype phylogenetic trees: first, it allows the
+ detection of an association between a candidate gene and a disease, and second,
+ it enables to make hypothesis about the susceptibility loci.
+
+Package: altree-examples
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: altree (= ${binary:Version})
+Description: example files for ALTree
+ ALTree was designed to perform association detection and localization of
+ susceptibility sites using haplotype phylogenetic trees: first, it allows the
+ detection of an association between a candidate gene and a disease, and second,
+ it enables to make hypothesis about the susceptibility loci.
+ .
+ This package contains the example files for the ALTree package discussed in
+ its PDF manual.
Deleted: trunk/packages/altree/tags/1.3.1-4/debian/patches/from-upstream-no-nested-functions.patch
===================================================================
--- trunk/packages/altree/trunk/debian/patches/from-upstream-no-nested-functions.patch 2015-12-09 15:09:20 UTC (rev 20698)
+++ trunk/packages/altree/tags/1.3.1-4/debian/patches/from-upstream-no-nested-functions.patch 2015-12-09 22:44:55 UTC (rev 20703)
@@ -1,105 +0,0 @@
-Avoid nested C functions
---- a/CUtils/c_sources/rhyper.c
-+++ b/CUtils/c_sources/rhyper.c
-@@ -52,55 +52,61 @@
- * If (i > 7), use Stirling's approximation, otherwise use table lookup.
- */
-
--static double afc(int i)
--{
-- static int computed=10;
-- static double al[1756] =
-- {
-- 0.0,
-- 0,/*ln(0!)*/
-- 0,/*ln(1!)*/
-- 0.693147180559945309,/*ln(2!)*/
-- 1.791759469228055,/*ln(3!)*/
-- 3.17805383034794562,/*ln(4!)*/
-- 4.78749174278204599,/*ln(5!)*/
-- 6.579251212010101,/*ln(6!)*/
-- 8.5251613610654143,/*ln(7!)*/
-- 10.6046029027452502,/*ln(8!)*/
-- 12.8018274800814696,/*ln(9!)*/
-- 15.1044125730755153,/*ln(10!)*/
-- };
-- double compute(int n) {
-- static long double cur=3628800;
-- static int i=11;
-- static volatile int mutex=0;
--
-- while (__sync_lock_test_and_set(&mutex, 1)) {
-- /* Internal loop with only read to avoid cache line ping-pong
-- on multi-processors */
-- while(mutex) {
-- /* spinlock */
-- }
-- }
-+struct afc_data {
-+ int computed;
-+ double al[1756];
-+};
-+
-+double compute(int n, struct afc_data * __restrict__ data) {
-+ static long double cur=3628800;
-+ static int i=11;
-+ static volatile int mutex=0;
-
-- for(; i<=n; i++) {
-- cur*=i;
-- al[i+1]=logl(cur);
-+ while (__sync_lock_test_and_set(&mutex, 1)) {
-+ /* Internal loop with only read to avoid cache line ping-pong
-+ on multi-processors */
-+ while(mutex) {
-+ /* spinlock */
- }
-- computed=n;
-- __sync_lock_release(&mutex);
-- return al[i];
-- };
-+ }
-
-+ for(; i<=n; i++) {
-+ cur*=i;
-+ data->al[i+1]=logl(cur);
-+ }
-+ data->computed=n;
-+ __sync_lock_release(&mutex);
-+ return data->al[i];
-+};
-+
-+static double afc(int i)
-+{
- double di, value;
-+ static struct afc_data data = {
-+ .computed = 10,
-+ .al = {
-+ 0.0,
-+ 0,/*ln(0!)*/
-+ 0,/*ln(1!)*/
-+ 0.693147180559945309,/*ln(2!)*/
-+ 1.791759469228055,/*ln(3!)*/
-+ 3.17805383034794562,/*ln(4!)*/
-+ 4.78749174278204599,/*ln(5!)*/
-+ 6.579251212010101,/*ln(6!)*/
-+ 8.5251613610654143,/*ln(7!)*/
-+ 10.6046029027452502,/*ln(8!)*/
-+ 12.8018274800814696,/*ln(9!)*/
-+ 15.1044125730755153,/*ln(10!)*/
-+ }
-+ };
-
- if (i < 0) {
- fprintf(stderr, "rhyper.c: afc(i), i=%d < 0 -- SHOULD NOT HAPPEN!\n", i);
- exit(1);
-- } else if (i <= computed) {
-- value = al[i + 1];
-+ } else if (i <= data.computed) {
-+ value = data.al[i + 1];
- } else if (i <= 1754) {
-- value = compute(i);
-+ value = compute(i, &data);
- } else {
- di = i;
- value = (di + 0.5) * log(di) - di + 0.08333333333333 / di
Copied: trunk/packages/altree/tags/1.3.1-4/debian/patches/from-upstream-no-nested-functions.patch (from rev 20699, trunk/packages/altree/trunk/debian/patches/from-upstream-no-nested-functions.patch)
===================================================================
--- trunk/packages/altree/tags/1.3.1-4/debian/patches/from-upstream-no-nested-functions.patch (rev 0)
+++ trunk/packages/altree/tags/1.3.1-4/debian/patches/from-upstream-no-nested-functions.patch 2015-12-09 22:44:55 UTC (rev 20703)
@@ -0,0 +1,105 @@
+Description: From upstream, avoid nested C functions
+--- a/CUtils/c_sources/rhyper.c
++++ b/CUtils/c_sources/rhyper.c
+@@ -52,55 +52,61 @@
+ * If (i > 7), use Stirling's approximation, otherwise use table lookup.
+ */
+
+-static double afc(int i)
+-{
+- static int computed=10;
+- static double al[1756] =
+- {
+- 0.0,
+- 0,/*ln(0!)*/
+- 0,/*ln(1!)*/
+- 0.693147180559945309,/*ln(2!)*/
+- 1.791759469228055,/*ln(3!)*/
+- 3.17805383034794562,/*ln(4!)*/
+- 4.78749174278204599,/*ln(5!)*/
+- 6.579251212010101,/*ln(6!)*/
+- 8.5251613610654143,/*ln(7!)*/
+- 10.6046029027452502,/*ln(8!)*/
+- 12.8018274800814696,/*ln(9!)*/
+- 15.1044125730755153,/*ln(10!)*/
+- };
+- double compute(int n) {
+- static long double cur=3628800;
+- static int i=11;
+- static volatile int mutex=0;
+-
+- while (__sync_lock_test_and_set(&mutex, 1)) {
+- /* Internal loop with only read to avoid cache line ping-pong
+- on multi-processors */
+- while(mutex) {
+- /* spinlock */
+- }
+- }
++struct afc_data {
++ int computed;
++ double al[1756];
++};
++
++double compute(int n, struct afc_data * __restrict__ data) {
++ static long double cur=3628800;
++ static int i=11;
++ static volatile int mutex=0;
+
+- for(; i<=n; i++) {
+- cur*=i;
+- al[i+1]=logl(cur);
++ while (__sync_lock_test_and_set(&mutex, 1)) {
++ /* Internal loop with only read to avoid cache line ping-pong
++ on multi-processors */
++ while(mutex) {
++ /* spinlock */
+ }
+- computed=n;
+- __sync_lock_release(&mutex);
+- return al[i];
+- };
++ }
+
++ for(; i<=n; i++) {
++ cur*=i;
++ data->al[i+1]=logl(cur);
++ }
++ data->computed=n;
++ __sync_lock_release(&mutex);
++ return data->al[i];
++};
++
++static double afc(int i)
++{
+ double di, value;
++ static struct afc_data data = {
++ .computed = 10,
++ .al = {
++ 0.0,
++ 0,/*ln(0!)*/
++ 0,/*ln(1!)*/
++ 0.693147180559945309,/*ln(2!)*/
++ 1.791759469228055,/*ln(3!)*/
++ 3.17805383034794562,/*ln(4!)*/
++ 4.78749174278204599,/*ln(5!)*/
++ 6.579251212010101,/*ln(6!)*/
++ 8.5251613610654143,/*ln(7!)*/
++ 10.6046029027452502,/*ln(8!)*/
++ 12.8018274800814696,/*ln(9!)*/
++ 15.1044125730755153,/*ln(10!)*/
++ }
++ };
+
+ if (i < 0) {
+ fprintf(stderr, "rhyper.c: afc(i), i=%d < 0 -- SHOULD NOT HAPPEN!\n", i);
+ exit(1);
+- } else if (i <= computed) {
+- value = al[i + 1];
++ } else if (i <= data.computed) {
++ value = data.al[i + 1];
+ } else if (i <= 1754) {
+- value = compute(i);
++ value = compute(i, &data);
+ } else {
+ di = i;
+ value = (di + 0.5) * log(di) - di + 0.08333333333333 / di
Deleted: trunk/packages/altree/tags/1.3.1-4/debian/rules
===================================================================
--- trunk/packages/altree/trunk/debian/rules 2015-12-09 15:09:20 UTC (rev 20698)
+++ trunk/packages/altree/tags/1.3.1-4/debian/rules 2015-12-09 22:44:55 UTC (rev 20703)
@@ -1,27 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-# debian/rules file for altree
-# Andreas Tille <tille at debian.org>
-# GPL
-
-%:
- dh $@
-
-override_dh_auto_clean:
- $(MAKE) -C Documentation distclean
- dh_auto_clean
-
-override_dh_auto_build:
- $(MAKE) -C Documentation pdf
- dh_auto_build
-
-override_dh_compress:
- dh_compress --exclude=.pdf
-
-override_dh_builddeb:
- dh_builddeb -- -Z xz
-
-get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --destdir=../tarballs
-
Copied: trunk/packages/altree/tags/1.3.1-4/debian/rules (from rev 20699, trunk/packages/altree/trunk/debian/rules)
===================================================================
--- trunk/packages/altree/tags/1.3.1-4/debian/rules (rev 0)
+++ trunk/packages/altree/tags/1.3.1-4/debian/rules 2015-12-09 22:44:55 UTC (rev 20703)
@@ -0,0 +1,24 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# debian/rules file for altree
+# Andreas Tille <tille at debian.org>
+# GPL
+
+%:
+ dh $@
+
+override_dh_auto_clean:
+ $(MAKE) -C Documentation distclean
+ dh_auto_clean
+
+override_dh_auto_build:
+ $(MAKE) -C Documentation pdf
+ dh_auto_build
+
+override_dh_compress:
+ dh_compress --exclude=.pdf
+
+get-orig-source:
+ mkdir -p ../tarballs
+ uscan --verbose --force-download --destdir=../tarballs
+
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