Doesn't compile on OS X 10.8 (or clang)

[GoogleCodeExporter]

Due to inlining grammar in C99, clang cannot export some symbols defined inline 
in samtools' ksort.h header.

What steps will reproduce the problem?
1. build pysam with clang (os x 10.8)
2. install 
3. run

What is the expected output? What do you see instead?
>>> import pysam
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "pysam/__init__.py", line 1, in <module>
    from csamtools import *
ImportError: 
dlopen(/Library/Python/2.7/site-packages/pysam-0.6-py2.7-macosx-10.8-intel.egg/c
samtools.so, 2): Symbol not found: ___ks_insertsort_heap
  Referenced from: /Library/Python/2.7/site-packages/pysam-0.6-py2.7-macosx-10.8-intel.egg/csamtools.so
  Expected in: flat namespace
 in /Library/Python/2.7/site-packages/pysam-0.6-py2.7-macosx-10.8-intel.egg/csamtools.so

What version of the product are you using? On what operating system?
I'm using latest pysam code (change set add4ce397e78), python2.7 

Please provide any additional information below.
A correct patch (also submitted to samtools project) is to make the inlined 
static:

diff -r add4ce397e78 samtools/ksort.h
--- a/samtools/ksort.h  Mon Oct 08 16:09:33 2012 +0100
+++ b/samtools/ksort.h  Wed Oct 17 11:16:01 2012 +0200
@@ -141,7 +141,7 @@
            tmp = *l; *l = l[i]; l[i] = tmp; ks_heapadjust_##name(0, i, l); \
        }                                                               \
    }                                                                   \
-   inline void __ks_insertsort_##name(type_t *s, type_t *t)            \
+   static inline void __ks_insertsort_##name(type_t *s, type_t *t)         \
    {                                                                   \
        type_t *i, *j, swap_tmp;                                        \
        for (i = s + 1; i < t; ++i)                                     \

see here http://clang.llvm.org/compatibility.html#inline

Original issue reported on code.google.com by daweonline on 17 Oct 2012 at 9:19

[GoogleCodeExporter]

Thanks, i have applied this patch manually.

Note that unless it is fixed in samtools, it will re-appear.

Best wishes,
Andreas

Original comment by andreas....@gmail.com on 21 Nov 2012 at 3:23

• Changed state: Accepted

[GoogleCodeExporter]

Original comment by andreas....@gmail.com on 21 Nov 2012 at 3:24

• Changed state: Fixed