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2bits / disass.txt
Created November 6, 2012 06:33
mpd-0.17.2 - crash on stop after playing iTunes m4a on OSX - disass
(gdb) disass $pc-32,$pc+32
Dump of assembler code for function decoder_stream_decode:
0x000000010000d0e0 <decoder_stream_decode+0>: push %rbp
0x000000010000d0e1 <decoder_stream_decode+1>: mov %rsp,%rbp
0x000000010000d0e4 <decoder_stream_decode+4>: push %r15
0x000000010000d0e6 <decoder_stream_decode+6>: push %r14
0x000000010000d0e8 <decoder_stream_decode+8>: push %rbx
0x000000010000d0e9 <decoder_stream_decode+9>: push %rax
0x000000010000d0ea <decoder_stream_decode+10>: mov %rdx,%r14
0x000000010000d0ed <decoder_stream_decode+13>: mov %rsi,%rbx
@2bits
2bits / bt.txt
Created November 6, 2012 06:29
mpd-0.17.2 - crash on stop after playing iTunes m4a on OSX
(gdb) bt
#0 decoder_stream_decode (plugin=0x1000655f8, decoder=0x100000000, input_stream=0x10093cd00) at decoder_thread.c:141
#1 0x000000010000cbec in decoder_run_file [inlined] () at /private/tmp/mpd-De4y/mpd-0.17.2/src/decoder_thread.c:364
#2 0x000000010000cbec in decoder_run_song [inlined] () at /private/tmp/mpd-De4y/mpd-0.17.2/src/decoder_thread.c:408
#3 0x000000010000cbec in decoder_run [inlined] () at /private/tmp/mpd-De4y/mpd-0.17.2/src/decoder_thread.c:453
#4 0x000000010000cbec in decoder_task (arg=0x1028004f0) at decoder_thread.c:141
#5 0x0000000100322503 in g_thread_proxy ()
#6 0x00007fff80db5742 in _pthread_start ()
#7 0x00007fff80da2181 in thread_start ()
@2bits
2bits / tophat206.diff
Created October 28, 2012 16:30
--- a/src/segment_juncs.cpp 2012-10-17 09:29:03.000000000 -0700
+++ b/src/segment_juncs.cpp 2012-10-27 22:24:44.000000000 -0700
@@ -4854,15 +4854,15 @@
exit(0);
}
- std::set<Junction, skip_count_lt> vseg_juncs[num_threads];
+ std::set<Junction, skip_count_lt> vseg_juncs[1];
std::set<Junction, skip_count_lt> cov_juncs;
std::set<Junction, skip_count_lt> butterfly_juncs;
@2bits
2bits / error.log
Created October 28, 2012 16:28
tophat-2.0.6 build error with clang-4.1 on OSX, non-POD variable length arrays
$ make -j1
/usr/bin/make all-recursive
Making all in src
c++ -DHAVE_CONFIG_H -I. -I. -I.. -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -DNDEBUG -pthread -I/usr/local/include -I/usr/local/include -I./SeqAn-1.3 -c -o segment_juncs.o segment_juncs.cpp
brew: superenv removed: -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized -O3 -I/usr/local/include -I/usr/local/include
segment_juncs.cpp:4857:47: error: variable length array of non-POD element type 'std::set<Junction, skip_count_lt>'
std::set<Junction, skip_count_lt> vseg_juncs[num_threads];
^
segment_juncs.cpp:4863:32: error: variable length array of non-POD element type 'std::set<Deletion>'
std::set<Deletion> vdeletions[num_threads];
@2bits
2bits / no-brew.txt
Created October 20, 2012 16:49
tmap-3.2.0 standalone install log, OSX 10.8.2 with --enable-perftools - 'rpl_malloc' undeclared
$ brew unpack tmap
==> Unpacking tmap to: /Users/nibbles/Temp/tmap-3.2.0
==> Cloning https://github.com/iontorrent/TMAP.git
git status -s
Updating /Library/Caches/Homebrew/tmap--git
git config remote.origin.url https://github.com/iontorrent/TMAP.git
git config remote.origin.fetch +refs/tags/tmap.3.2.0:refs/tags/tmap.3.2.0
git fetch origin
==> Checking out tag tmap.3.2.0
git checkout tmap.3.2.0 --
@2bits
2bits / config.log
Created October 20, 2012 16:27
tmap-3.2.0 config log, OSX 10.8.2 with --enable-perftools
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by tmap configure 3.2.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --disable-dependency-tracking --prefix=/usr/local/Cellar/tmap/3.2.0 --enable-perftools
## --------- ##
## Platform. ##
@2bits
2bits / stdout.txt
Created October 20, 2012 16:25
tmap-3.2.0 + Homebrew install log, OSX 10.8.2 with --enable-perftools - 'rpl_malloc' undeclared
$ brew install -vd --perf tmap
/usr/local/bin/brew: loading /usr/local/Library/Formula/tmap.rb
/usr/local/bin/brew: loading /usr/local/Library/Formula/automake.rb
/usr/local/bin/brew: loading /usr/local/Library/Formula/autoconf.rb
/usr/local/bin/brew: loading /usr/local/Library/Formula/libtool.rb
/usr/local/bin/brew: loading /usr/local/Library/Formula/google-perftools.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/automake.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/autoconf.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/libtool.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/google-perftools.rb
@2bits
2bits / more_nm_output.txt
Created October 17, 2012 19:05
tmap-3.2.0 nm output on OSX 10.8.2 showing undefined symbols
$ nm src/map/map2/tmap_map2_aux.o
0000000000006068 s EH_frame0
0000000000005c48 s L_.str
0000000000005c66 s L_.str1
0000000000005cb1 s L_.str2
0000000000005cc9 s L_.str3
0000000000005ce4 s L_.str4
0000000000005d04 s L_.str5
0000000000005d0a s L_.str6
0000000000005d13 s L_.str7
@2bits
2bits / config.log
Created October 17, 2012 19:01
tmap-3.2.0 config.log from OSX 10.8.2 with XCode-4.5.1+CLT
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by tmap configure 3.2.0, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ ./configure --disable-dependency-tracking --prefix=/usr/local/Cellar/tmap/3.2.0
## --------- ##
## Platform. ##
@2bits
2bits / stdout.txt
Created October 17, 2012 19:00
tmap-3.2.0 install log from OSX 10.8.2 with XCode-4.5.1+CLT showing missing symbols on link
$ brew install -vd --env=std tmap
/usr/local/bin/brew: loading /usr/local/Library/Formula/tmap.rb
/usr/local/bin/brew: loading /usr/local/Library/Formula/automake.rb
/usr/local/bin/brew: loading /usr/local/Library/Formula/autoconf.rb
/usr/local/bin/brew: loading /usr/local/Library/Formula/libtool.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/automake.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/autoconf.rb
/usr/local/Library/Formula/tmap.rb: loading /usr/local/Library/Formula/libtool.rb
==> Cloning https://github.com/iontorrent/TMAP.git
git status -s