[Biopython-dev] [Bug 1709] New: Not using -fPIC to build shared lib.

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=1709

           Summary: Not using -fPIC to build shared lib.
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mail at philipp-benner.de


Biopython is now part of the Debian distribution, but we had to fix
some bugs before submitting.
The most recent is that "-fPIC" is not used to compile KDTree and
Affy. Therefore compilation failes at some arches.
See http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=278959

I fixed this bug as follows:

--- python-biopython-1.30.orig/setup.py
+++ python-biopython-1.30/setup.py
@@ -448,10 +448,12 @@
               ["Bio/KDTree/KDTree.cpp",
                "Bio/KDTree/KDTree.swig.cpp"],
               libraries=["stdc++"],
+             extra_compile_args=["-fPIC"],
               language="c++"
               ),
     CplusplusExtension('Bio.Affy._cel',
              ['Bio/Affy/celmodule.cc'],
+            extra_compile_args=["-fPIC"],
              language="c++"
              ),
 ]


Apart from this bug I had to change the following:

1. /usr/lib/python*/site-packages/Bio/EUtils/DTDs/*dtd
These files should have mode 644 as permission.
(http://www.debian.org/doc/debian-policy/ch-files.html#s10.9)

2. Many site-package modules include a special first-line
comment (script magic) after installation. I had to remove all of these.

3. The following files were not deleted after cleaning the
source tree:

MANIFEST
Makefile
Martel/*.pyc
build

The clean target must undo any effects that the build target may have had.

Best regards,
Philipp Benner

---------
http://packages.qa.debian.org/p/python-biopython.html



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