AUGUSTUS - Segmentation fault error on OS X 10.9.5
Moderator: bioinf
AUGUSTUS - Segmentation fault error on OS X 10.9.5
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
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
Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5
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?
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?
Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5
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.
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.
Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5
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.
Best regards,
Katharina
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.
Best regards,
Katharina
Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5
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
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
Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5
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
?
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
?
Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5
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.
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.
Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5
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
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
Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5
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.
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.
Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5
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:
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:
^
Any ideas? Thanks.
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 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.
Re: AUGUSTUS - Segmentation fault error on OS X 10.9.5
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.
For those with similar problems, using g++ 4.9.2, and rolling back to augustus-3.0.1 fixed my problem.