[med-svn] [Git][med-team/altree][master] 9 commits: Do not require atlas
Andreas Tille
gitlab at salsa.debian.org
Wed Nov 6 13:44:53 GMT 2019
Andreas Tille pushed to branch master at Debian Med / altree
Commits:
5259faa8 by Andreas Tille at 2019-11-06T12:53:17Z
Do not require atlas
- - - - -
addfec98 by Andreas Tille at 2019-11-06T12:54:17Z
Recommends: libopenblas-base | libatlas3-base | libmkl-rt | libblas.so.3
- - - - -
9e3459f7 by Andreas Tille at 2019-11-06T12:55:43Z
debhelper-compat 12
- - - - -
64c399c1 by Andreas Tille at 2019-11-06T12:59:00Z
Standards-Version: 4.4.1
- - - - -
764e4b7b by Andreas Tille at 2019-11-06T12:59:00Z
Remove trailing whitespace in debian/changelog
- - - - -
c2dddbd2 by Andreas Tille at 2019-11-06T12:59:01Z
Trim trailing whitespace.
Fixes lintian: file-contains-trailing-whitespace
See https://lintian.debian.org/tags/file-contains-trailing-whitespace.html for more details.
- - - - -
0f88f54d by Andreas Tille at 2019-11-06T12:59:02Z
Set fields Upstream-Name in debian/copyright.
- - - - -
9f1746e9 by Andreas Tille at 2019-11-06T12:59:03Z
Remove obsolete fields Name, Contact from debian/upstream/metadata.
- - - - -
4330b5ab by Andreas Tille at 2019-11-06T13:40:31Z
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- + debian/patches/blas.patch
- debian/patches/series
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+altree (1.3.1-8) unstable; urgency=medium
+
+ [ Mo Zhou ]
+ * Do not require atlas
+ Closes: #943828
+ * Recommends: libopenblas-base | libatlas3-base | libmkl-rt | libblas.so.3
+
+ [ Andreas Tille ]
+ * debhelper-compat 12
+ * Standards-Version: 4.4.1
+ * Remove trailing whitespace in debian/changelog
+ * Trim trailing whitespace.
+ * Set fields Upstream-Name in debian/copyright.
+ * Remove obsolete fields Name, Contact from debian/upstream/metadata.
+
+ -- Andreas Tille <tille at debian.org> Wed, 06 Nov 2019 13:59:03 +0100
+
altree (1.3.1-7) unstable; urgency=medium
* Build-Depends: fig2dev
@@ -55,7 +72,7 @@ altree (1.3.1-3) unstable; urgency=medium
altree (1.3.1-2) unstable; urgency=medium
- * Fix "FTBFS with clang instead of gcc"
+ * 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
@@ -129,9 +146,9 @@ altree (1.0.1-7) unstable; urgency=low
altree (1.0.1-5) unstable; urgency=low
* Upload source package without 3.0 (quilt) autopatch leftover.
- Closes: #643045.
+ Closes: #643045.
* Corrected VCS URLs in debian/control.
- * Use Debhelper 8 (debian/control, debian/compat).
+ * 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).
@@ -241,4 +258,3 @@ 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
-
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -6,7 +6,7 @@ Uploaders: Charles Plessy <plessy at debian.org>,
Section: science
Priority: optional
Build-Depends: bash-completion,
- debhelper (>= 11~),
+ debhelper-compat (= 12),
latex-make,
ghostscript,
texlive-lang-french,
@@ -15,10 +15,10 @@ Build-Depends: bash-completion,
texlive-fonts-recommended,
libmath-tamuanova-perl,
libgsl-dev,
- libatlas-base-dev,
+ libblas-dev,
libtest-deep-perl,
fig2dev
-Standards-Version: 4.1.4
+Standards-Version: 4.4.1
Vcs-Browser: https://salsa.debian.org/med-team/altree
Vcs-Git: https://salsa.debian.org/med-team/altree.git
Homepage: https://gitlab.inria.fr/NGS/ALTree
@@ -29,6 +29,7 @@ Depends: ${shlibs:Depends},
${misc:Depends},
${perl:Depends},
libmath-tamuanova-perl
+Recommends: libopenblas-base | libatlas3-base | libmkl-rt | libblas.so.3
Suggests: altree-examples
Description: program to perform phylogeny-based association and localization analysis
ALTree was designed to perform association detection and localization of
=====================================
debian/copyright
=====================================
@@ -1,6 +1,7 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Contact: Vincent Danjean <vdanjean.ml at free.fr>
Source: https://gitlab.inria.fr/NGS/ALTree
+Upstream-Name: ALTree
Files: *
Copyright: © 2005-2008 Claire Bardel <Claire.Bardel at univ-lyon1.fr>
@@ -26,4 +27,3 @@ License: GPL-2+
.
On Debian systems, the complete text of the GNU General Public License
version 2 can be found in ‘/usr/share/common-licenses/GPL-2’.
-
=====================================
debian/patches/blas.patch
=====================================
@@ -0,0 +1,16 @@
+Author: Mo Zhou <lumin at debian.org>
+Last-Update: Wed, 30 Oct 2019 13:08:31 +0000
+Bug-Debian: https://bugs.debian.org/943828
+Description: Do not require atlas
+
+--- a/CUtils/Makefile.PL
++++ b/CUtils/Makefile.PL
+@@ -9,7 +9,7 @@ WriteMakefile(
+ ($] >= 5.005 ? ## Add these new keywords supported since 5.005
+ (ABSTRACT_FROM => 'lib/ALTree/CUtils.pm', # retrieve abstract from module
+ AUTHOR => 'Claire Bardel <Claire.Bardel at univ-lyon1.fr>') : ()),
+- LIBS => ['-lm -lpthread -lgsl -lcblas'], # e.g., '-lm'
++ LIBS => ['-lm -lpthread -lgsl -lblas'], # e.g., '-lm'
+ DEFINE => '', # e.g., '-DHAVE_SOMETHING'
+ INC => '-ggdb3 -I. -Ic_sources', # e.g., '-I. -I/usr/include/other'
+ # Un-comment this if you add C files to link with later:
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
from-upstream-no-nested-functions.patch
no-quicksort.patch
+blas.patch
=====================================
debian/upstream/metadata
=====================================
@@ -1,23 +1,21 @@
-Contact: Claire Bardel <Claire.Bardel at univ-lyon1.fr>
-Name: ALTree
Reference:
- Author: Bardel, Claire and Danjean, Vincent and Genin, Emmanuelle
- DOI: 10.1093/bioinformatics/btl131
- PMID: 16595555
- Journal: Bioinformatics
- Number: 11
- Pages: 1402-1403
- Title: >
- ALTree: association detection and localization of susceptibility sites
- using haplotype phylogenetic trees
- URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/11/1402
- eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/11/1402.pdf
- Volume: 22
- Year: 2006
+ Author: Bardel, Claire and Danjean, Vincent and Genin, Emmanuelle
+ DOI: 10.1093/bioinformatics/btl131
+ PMID: 16595555
+ Journal: Bioinformatics
+ Number: 11
+ Pages: 1402-1403
+ Title: >
+ ALTree: association detection and localization of susceptibility sites
+ using haplotype phylogenetic trees
+ URL: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/11/1402
+ eprint: http://bioinformatics.oxfordjournals.org/cgi/reprint/22/11/1402.pdf
+ Volume: 22
+ Year: 2006
Registry:
- - Name: SciCrunch
- Entry: SCR_007562
- - Name: bio.tools
- Entry: NA
- - Name: OMICtools
- Entry: OMICS_13032
+- Name: SciCrunch
+ Entry: SCR_007562
+- Name: bio.tools
+ Entry: NA
+- Name: OMICtools
+ Entry: OMICS_13032
View it on GitLab: https://salsa.debian.org/med-team/altree/compare/7d76ba7a5725209ec00b03e1705394f625e5fa69...4330b5abc34601f069d05e4dca86dbe7d2d03d4a
--
View it on GitLab: https://salsa.debian.org/med-team/altree/compare/7d76ba7a5725209ec00b03e1705394f625e5fa69...4330b5abc34601f069d05e4dca86dbe7d2d03d4a
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