[Debian-med-packaging] Bug#965073: macs: shared library is not properly linked with libm

[Aurelien Jarno]

Package: macs
Version: 2.2.7.1-2
Severity: serious
Tags: patch

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

The attached patch fixes that.
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--- macs-2.2.7.1.orig/setup.py
+++ macs-2.2.7.1/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),
     ]