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

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Sat Nov 6 07:34:34 EST 2004


           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 @@
+             extra_compile_args=["-fPIC"],
+            extra_compile_args=["-fPIC"],

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.

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:


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

Best regards,
Philipp Benner


------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.

More information about the Biopython-dev mailing list