[med-svn] [Git][med-team/macs][master] 4 commits: Link properly with libm

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / macs


Commits:
9742008b by Andreas Tille at 2020-07-15T22:28:45+02:00
Link properly with libm

- - - - -
2fe45674 by Andreas Tille at 2020-07-15T22:29:05+02:00
routine-update: debhelper-compat 13

- - - - -
77773514 by Andreas Tille at 2020-07-15T23:27:16+02:00
Do not require pip

- - - - -
7094a0e3 by Andreas Tille at 2020-07-15T23:33:20+02:00
Upload to unstable

- - - - -


5 changed files:

- debian/changelog
- debian/control
- + debian/patches/link-libm.patch
- + debian/patches/no-pip.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+macs (2.2.7.1-3) unstable; urgency=medium
+
+  * Link properly with libm
+    Closes: #965073
+  * debhelper-compat 13 (routine-update)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 15 Jul 2020 23:27:39 +0200
+
 macs (2.2.7.1-2) unstable; urgency=medium
 
   * Ensure that debian/rules clean always suceeds. Closes #958109


=====================================
debian/control
=====================================
@@ -4,7 +4,7 @@ Uploaders: Michael R. Crusoe <crusoe at debian.org>,
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                dh-python,
                python3-all-dev,
                python3-numpy,


=====================================
debian/patches/link-libm.patch
=====================================
@@ -0,0 +1,24 @@
+Date: Wed, 15 Jul 2020 18:16:54 +0200
+From: Aurelien Jarno <aurel32 at debian.org>
+Bug-Debian: https://bugs.debian.org/965073
+Description: macs use the log() math function, but doesn't link link with libm.so.
+ This causes the non-versioned __log_finite symbol to be used, which in
+ turn causes issues when glibc version is upgraded:
+ .
+ https://ci.debian.net/data/autopkgtest/testing/amd64/m/macs/6261687/log.gz
+ .
+ This patches is fixing this.
+
+--- a/setup.py
++++ b/setup.py
+@@ -59,8 +59,8 @@ def main():
+                    Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+                    Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+                    Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=extra_c_args),
+-                   Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
+-                   Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
++                   Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
++                   Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
+                    #Extension("MACS2.Statistics", ["MACS2/Statistics.pyx"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
+     ]
+ 


=====================================
debian/patches/no-pip.patch
=====================================
@@ -0,0 +1,28 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 15 Jul 2020 22:28:05 +0200
+Description: Do not require pip
+
+--- a/setup.py
++++ b/setup.py
+@@ -27,21 +27,6 @@ def main():
+     cwd = os.path.abspath(os.path.dirname(__file__))
+ 
+     # install required numpy
+-    p = subprocess.call([sys.executable, "-m", 'pip', 'install', f'numpy{numpy_requires}'],cwd=cwd)
+-    if p != 0:
+-        # Could be due to a too old pip version and build isolation, check that
+-        try:
+-            # Note, pip may not be installed or not have been used
+-            import pip
+-            if LooseVersion(pip.__version__) < LooseVersion('18.0.0'):
+-                raise RuntimeError("Installing requirements failed. Possibly due "
+-                                   "to `pip` being too old, found version {}, "
+-                                   "needed is >= 18.0.0.".format(pip.__version__))
+-            else:
+-                raise RuntimeError("Installing requirements failed!")
+-        except ImportError:
+-            raise RuntimeError("Installing requirement failed! `pip` has to be installed!")
+-        
+     from numpy import get_include as numpy_get_include
+     numpy_include_dir = [numpy_get_include()]
+         


=====================================
debian/patches/series
=====================================
@@ -1,2 +1,4 @@
 spelling
 keep_debug
+link-libm.patch
+no-pip.patch



View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/6300ff53c5f264986c035d77a248117fe5d6339f...7094a0e3d3d54a6ca55bdb579793939672d3e742

-- 
View it on GitLab: https://salsa.debian.org/med-team/macs/-/compare/6300ff53c5f264986c035d77a248117fe5d6339f...7094a0e3d3d54a6ca55bdb579793939672d3e742
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