Your message dated Thu, 9 Jun 2011 15:51:28 +0200
with message-id <20110609135128.ga9...@jwilk.net>
and subject line Re: [Debichem-devel] Bug#628826: pdb2pqr: FTBFS on i386:
collect2: ld terminated with signal 6
has caused the Debian Bug report #628826,
regarding pdb2pqr: FTBFS on i386: collect2: ld terminated with signal 6
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
628826: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=628826
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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=\"ba...@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
--- End Message ---
--- Begin Message ---
* Manuel Prinz <man...@debian.org>, 2011-06-09, 15:36:
I can build pdb2pqr without problems in i386 unstable chroots on two
different amd64 host. Can you please give details on your build setup?
I can't reproduce the bug any more. This must have been a transient
toolchain bug. Sorry for the noise - and closing the bug.
--
Jakub Wilk
--- End Message ---
