[Debichem-devel] Bug#628826: pdb2pqr: FTBFS on i386: collect2: ld terminated with signal 6

[Jakub Wilk]

Source: pdb2pqr
Version: 1.7-1
Severity: serious
Justification: fails to build from source

pdb2pqr fails to build from source on i386:
| g++ -DPACKAGE_NAME=\"PDB2PQR\" -DPACKAGE_TARNAME=\"pdb2pqr\" -DPACKAGE_VERSION=\"1.7\" -DPACKAGE_STRING=\"PDB2PQR\ 1.7\" -DPACKAGE_BUGREPORT=\"baker at biochem.wustl.edu\" -DPACKAGE=\"PDB2PQR\" -DVERSION=\"1.7\" -I.    -I/usr/include/python2.6 -I/usr/numpy/lib/python2.6/site-packages/numpy/core/include/numpy  -g -O2 -c -o Algorithms.o Algorithms.cpp
| In file included from /usr/include/python2.6/Python.h:8:0,
|                  from Algorithms.cpp:40:
| /usr/include/python2.6/pyconfig.h:1031:0: warning: "_POSIX_C_SOURCE" redefined [enabled by default]
| /usr/include/features.h:163:0: note: this is the location of the previous definition
| /usr/include/python2.6/pyconfig.h:1040:0: warning: "_XOPEN_SOURCE" redefined [enabled by default]
| /usr/include/features.h:165:0: note: this is the location of the previous definition
| g++ -o Algorithms.so -shared Algorithms.o
| collect2: ld terminated with signal 6 [Aborted]
| *** glibc detected *** /usr/bin/ld: double free or corruption (!prev): 0x09e0a9c8 ***
| ======= Backtrace: =========
| /lib/libc.so.6(+0x6a81a)[0x556f381a]
| /lib/libc.so.6(+0x6c078)[0x556f5078]
| /lib/libc.so.6(cfree+0x6d)[0x556f817d]
| /usr/lib/libbfd-2.21.51-system.20110523.so(objalloc_free+0x2c)[0x55639e0c]
| ======= Memory map: ========
| 08048000-080f4000 r-xp 00000000 00:68 8547                               /usr/bin/ld.bfd
| 080f4000-080f5000 rw-p 000ac000 00:68 8547                               /usr/bin/ld.bfd
| 080f5000-080f6000 rw-p 00000000 00:00 0
| 09aad000-09e8a000 rw-p 00000000 00:00 0                                  [heap]
| 55555000-55570000 r-xp 00000000 00:68 30                                 /lib/ld-2.13.so
| 55570000-55571000 r--p 0001b000 00:68 30                                 /lib/ld-2.13.so
| 55571000-55572000 rw-p 0001c000 00:68 30                                 /lib/ld-2.13.so
| 55572000-55573000 r-xp 00000000 00:00 0                                  [vdso]
| 55573000-55578000 rw-p 00000000 00:00 0
| 55578000-55660000 r-xp 00000000 00:68 6721                               /usr/lib/libbfd-2.21.51-system.20110523.so
| 55660000-5566c000 rw-p 000e8000 00:68 6721                               /usr/lib/libbfd-2.21.51-system.20110523.so
| 5566c000-55670000 rw-p 00000000 00:00 0
| 55670000-55683000 r-xp 00000000 00:68 199                                /usr/lib/libz.so.1.2.3.4
| 55683000-55684000 rw-p 00013000 00:68 199                                /usr/lib/libz.so.1.2.3.4
| 55684000-55685000 rw-p 00000000 00:00 0
| 55685000-55687000 r-xp 00000000 00:68 60                                 /lib/libdl-2.13.so
| 55687000-55688000 r--p 00001000 00:68 60                                 /lib/libdl-2.13.so
| 55688000-55689000 rw-p 00002000 00:68 60                                 /lib/libdl-2.13.so
| 55689000-557c7000 r-xp 00000000 00:68 33                                 /lib/libc-2.13.so
| 557c7000-557c8000 ---p 0013e000 00:68 33                                 /lib/libc-2.13.so
| 557c8000-557ca000 r--p 0013e000 00:68 33                                 /lib/libc-2.13.so
| 557ca000-557cb000 rw-p 00140000 00:68 33                                 /lib/libc-2.13.so
| 557cb000-557f7000 rw-p 00000000 00:00 0
| 557f8000-557fe000 rw-p 00000000 00:00 0
| 55800000-55821000 rw-p 00000000 00:00 0
| 55821000-55900000 ---p 00000000 00:00 0
| 55903000-5591f000 r-xp 00000000 00:68 239                                /lib/libgcc_s.so.1
| 5591f000-55920000 rw-p 0001b000 00:68 239                                /lib/libgcc_s.so.1
| ffc8e000-ffcaf000 rw-p 00000000 00:00 0                                  [stack]
| make[3]: *** [Algorithms.so] Error 1

-- 
Jakub Wilk