AUGUSTUS - Segmentation fault error on OS X 10.9.5

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AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

Originally posted in the old forum by TuanDuong on 18.11.2014 - 14:45
Dear all,
I am having trouble with running Augustus 3.0.1 on my Mac-pro OS X 10.9.5 Mavericks. When I call augustus as: augustus --AUGUSTUS_CONFIG_PATH=/usr/local/Cellar/augustus/3.0.1/libexec/config --species=neurospora_crassa sequence.fa
The program terminated with the following message: Segmentation fault: 11
I search and found out that this bug has been fixed since the previous versions of Augustus? Does anyone know how can I solve this problem?
Thanks
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Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

by lizzy on 21.11.2014 - 11:44
Hi Tuan, I will try to find out what's going wrong. First of all did you compile Augustus yourself or did you download the binaries?
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Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

by TuanDuong on 21.11.2014 - 15:34
Hi Lizzy. Thanks for the reply. I installed Augustus via home-brew: brew install augustus.
After installation if I ran augustus without the input file (e.g. augustus --species=help) everything seem file. Just when I tried to run with the data then the problem occurred.
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Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

by katharina on 24.11.2014 - 10:31
Please install the current version of AUGUSTUS (i.e. compile it, yourself, instead of using brew). If the problem persists, please make a small test data set available to us, so that we can verify it and try to find the bug.
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Katharina
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Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

by TuanDuong on 25.11.2014 - 07:46
Hi Katharina,
I followed the advise and tried to install the lastest version of augustus (v 3.0.3) but got the following warning and errors when trying to compile the software:
../include/hints.hh:147:7: warning: equality comparison result unused [-Wunused-comparison]
name == "";
../include/hints.hh:147:7: note: use '=' to turn this equality comparison into an assignment
name == "";
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/algorithm:685:97: error: invalid operands to binary expression
('const OptionListItem' and 'const OptionListItem')
_LIBCPP_INLINE_VISIBILITY bool operator()(const _T1& __x, const _T1& __y) const {return __x < __y;}
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/algorithm:685:97: error: invalid operands to binary expression
('const GBFeature' and 'const GBFeature')
_LIBCPP_INLINE_VISIBILITY bool operator()(const _T1& __x, const _T1& __y) const {return __x < __y;}
Do you have any idea how can I fix this?
Regards,
Tuan
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Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

by katharina on 25.11.2014 - 19:13
Have you followed the compilation instructions for OS X in the Makefile:
remove -static from src/Makefile for MAC users
remove -g -gdb from CFLAGS
?
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Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

by TuanDuong on 26.11.2014 - 12:03
I did removed -g -gdb from CFLAGS. However I could not find -static from scr/Makefile so I could not remove this.
The same errors still appeared as I tried to compile augustus.
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Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

by lizzy on 26.11.2014 - 14:30
Hi Tuan, I don't have this error message when compiling with mac, so its hard to check what is happening. What g++ compiler version do you have? I'm using g++ (MacPorts gcc47 4.7.3_5) 4.7.3 (you can see it by typing "g++ --version").
If you have an older one, upgrade and try again. Let me know if that helps
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Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

by TuanDuong on 27.11.2014 - 12:09
Hi Lizzy. I have GCC 4.9.2 installed. I downgraded to GCC 4.7 and tried to compile augustus again but still the same errors occurred.
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Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

by Michael on 16.01.2015 - 21:24
Same problem fix, plus another problem
I originally had the same problem using the native Mac g++ compiler:

Code: Select all

Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin14.0.0
Thread model: posix
I removed -g and -ggdb from CFLAGS, but I too do not see a -static flag anywhere in /src/Makefile.
I downloaded g++ 4.9.2 using fink. I now get a different error:

Code: Select all

properties.cc: In function ‘std::string findLocationOfSelfBinary()’:
properties.cc:635:5: error: ‘uint32’ was not declared in this scope
     uint32 size = static_cast<uint32>(sizeof(path));
     ^
properties.cc:636:37: error: ‘size’ was not declared in this scope
     if (_NSGetExecutablePath(path, &size) == 0){
^
Any ideas? Thanks.
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Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5

Post by katharina »

by Michael on 11.02.2015 - 20:33
For those with similar problems, using g++ 4.9.2, and rolling back to augustus-3.0.1 fixed my problem.
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