[med-svn] [Git][med-team/ghmm][master] 5 commits: Do not build-depends on atlas

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / ghmm


Commits:
01f86ba2 by Andreas Tille at 2024-01-11T17:07:06+01:00
Do not build-depends on atlas

- - - - -
b32b9a03 by Andreas Tille at 2024-01-11T17:07:25+01:00
routine-update: Standards-Version: 4.6.2

- - - - -
c3368687 by Andreas Tille at 2024-01-11T17:07:42+01:00
Avoid explicitly specifying -Wl,--as-needed linker flag.

Changes-By: lintian-brush
Fixes: lintian: debian-rules-uses-as-needed-linker-flag
See-also: https://lintian.debian.org/tags/debian-rules-uses-as-needed-linker-flag.html

- - - - -
a5f0b10f by Andreas Tille at 2024-01-11T17:10:30+01:00
Typo

- - - - -
b3e5f923 by Andreas Tille at 2024-01-11T17:30:52+01:00
First attempt to use LAPACKE instead of ATLAS

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/lapacke.patch
- debian/patches/series
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+ghmm (0.9~rc3-5) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Do not build-depends on atlas
+    Closes: #1056673
+  * Standards-Version: 4.6.2 (routine-update)
+  * Avoid explicitly specifying -Wl,--as-needed linker flag.
+
+ -- Andreas Tille <tille at debian.org>  Thu, 11 Jan 2024 17:06:32 +0100
+
 ghmm (0.9~rc3-4) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -9,11 +9,11 @@ Build-Depends: debhelper-compat (= 13),
                pkg-config,
                libxml2-dev,
                libgsl-dev,
-               libatlas-base-dev,
-               liblapack-dev,
+               libblas-dev | libblas.so,
+               liblapacke-dev,
                zlib1g-dev,
                swig
-Standards-Version: 4.5.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/ghmm
 Vcs-Git: https://salsa.debian.org/med-team/ghmm.git
 Homepage: https://sourceforge.net/p/ghmm/wiki/Home/
@@ -25,6 +25,7 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          python3,
          libghmm1
+Recommends: libopenblas0 | libblis4
 Description: General Hidden-Markov-Model library - tools
  The General Hidden Markov Model Library (GHMM) is a C library with
  additional Python3 bindings implementing a wide range of types of


=====================================
debian/patches/lapacke.patch
=====================================
@@ -0,0 +1,46 @@
+Description: Use LAPACKE instead of ATLAS
+Bug-Debian: https://bugs.debian.org/1056673
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 11 Jan 2024 17:06:32 +0100
+FIXME: This is not sufficient and needs more changes inside the code
+
+--- a/configure.in
++++ b/configure.in
+@@ -226,7 +226,7 @@ AC_ARG_ENABLE(atlas,
+ 
+         dnl checking for clapack_dgetrf
+         AC_MSG_CHECKING([for clapack_dgetrf in -llapack])
+-        AC_TRY_COMPILE([#include <clapack.h>],
++        AC_TRY_COMPILE([#include <lapacke.h>],
+         [
+                 double a;
+                 int ipiv;
+@@ -239,7 +239,7 @@ AC_ARG_ENABLE(atlas,
+ 
+         dnl checking for clapack_dgetri
+         AC_MSG_CHECKING([for clapack_dgetri in -llapack])
+-        AC_TRY_COMPILE([#include <clapack.h>],
++        AC_TRY_COMPILE([#include <lapacke.h>],
+         [
+                 double a;
+                 int ipiv;
+@@ -252,7 +252,7 @@ AC_ARG_ENABLE(atlas,
+ 
+         dnl checking for clapack_dpotrf
+         AC_MSG_CHECKING([for clapack_dpotrf in -llapack])
+-        AC_TRY_COMPILE([#include <clapack.h>],
++        AC_TRY_COMPILE([#include <lapacke.h>],
+         [
+                 double a;
+                 int x = clapack_dpotrf(0, 0, 0, &a, 0);
+--- a/ghmm/matrixop.c
++++ b/ghmm/matrixop.c
+@@ -45,7 +45,7 @@
+ #endif
+ 
+ #ifdef DO_WITH_ATLAS
+-#include <clapack.h>
++#include <lapacke.h>
+ #endif
+ 
+ /*============================================================================*/


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ pythonpaths.patch
 fix_libxml2_config.patch
 2to3.patch
 python3_build_system.patch
+lapacke.patch


=====================================
debian/rules
=====================================
@@ -3,8 +3,6 @@
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
-export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed
-
 %:
 	dh $@
 



View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/d1a2418dac35111ee2b48dc873d421537791d7eb...b3e5f923ccd894bb550404fefe4a893512b61ec3

-- 
View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/compare/d1a2418dac35111ee2b48dc873d421537791d7eb...b3e5f923ccd894bb550404fefe4a893512b61ec3
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