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.
--- 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),
]
