debian/changelog

+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@debian.org>  Wed, 06 Nov 2019 13:59:03 +0100
+
 altree (1.3.1-7) unstable; urgency=medium
 
   * Build-Depends: fig2dev
@@ -241,4 +258,3 @@ alphy (0.9.1c-1) unstable; urgency=low
   * Initial release
 
  -- Vincent Danjean <Vincent.Danjean@ens-lyon.org>  Mon, 25 Jul 2005 22:22:50 +0200
-

debian/compat

-11

debian/control

@@ -6,7 +6,7 @@ Uploaders: Charles Plessy <plessy@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

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Contact: Vincent Danjean <vdanjean.ml@free.fr>
 Source: https://gitlab.inria.fr/NGS/ALTree
+Upstream-Name: ALTree
 
 Files: *
 Copyright: © 2005-2008 Claire Bardel <Claire.Bardel@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

+Author: Mo Zhou <lumin@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@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

 from-upstream-no-nested-functions.patch
 no-quicksort.patch
+blas.patch

debian/upstream/metadata

-Contact: Claire Bardel <Claire.Bardel@univ-lyon1.fr>
-Name: ALTree
 Reference:
   Author: Bardel, Claire and Danjean, Vincent and Genin, Emmanuelle
   DOI: 10.1093/bioinformatics/btl131