Core dump

[lpalomerol]

Hello people.

I am trying to work with your awesome solution and I am experiencing a weird core dump problem. I've been debugging your code until reaching the problematic line at method XS(_wrap_chi2test_2by2table), concretely after launching chi2test_2b2table method.

chi2test_2by2table(arg1,arg2,arg3);

ST(argvi) = sv_newmortal();
{
  unpack1D((SV*)_saved[0], (void *)arg1, 'd', 0); //Core dump at this line.
}
{
  SV *tempsv;
  tempsv = SvRV(_saved[1]);
  sv_setnv(tempsv, *arg2);
}
{
  SV *tempsv;
  tempsv = SvRV(_saved[2]);
  sv_setnv(tempsv, *arg3);
}

Seems that the problem could be in the integration between c and perl. Maybe the compilation? I've performed the make with the standart options too.

Thank you for this awesome package!

Luis.

[kaichop]

were you able to re-compile the source code, before you run the program? There are a couple of reasons, but most likely it is because the old perl-C conversion code no longer works with latest version of Perl API, or no longer works with the latest version of GCC (assuming that you are using gcc4 or gcc5). I am in the process of re-organizing older files and I will check if using a newer version of swig to generate a new C code can solve this problem.

On Wed, Feb 21, 2018 at 10:06 AM, lpalomerol notifications@github.com wrote:

Hello people.

I am trying to work with your awesome solution and I am experiencing a weird core dump problem. I've been debugging your code until reaching the problematic line at method XS(_wrap_chi2test_2by2table), concretely after launching chi2test_2b2table method.

chi2test_2by2table(arg1,arg2,arg3);

ST(argvi) = sv_newmortal(); { unpack1D((SV)_saved[0], (void )arg1, 'd', 0); //Core dump at this line. } { SV tempsv; tempsv = SvRV(_saved[1]); sv_setnv(tempsv, arg2); } { SV tempsv; tempsv = SvRV(_saved[2]); sv_setnv(tempsv, arg3); }

Seems that the problem could be in the integration between c and perl. Maybe the compilation? I've performed the make with the standart options too.

Thank you for this awesome package!

Luis.

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[lpalomerol]

Hello Kai,

thank you for your early response!

My gcc version is 4.8.5 and my perl is 5.16.3.

And the problem occurs when launghing a calculate_association.pl file with this isntruction:

/home/idibell/opt/gengen/GenGen-1.0.1/calculate_association.pl -cc -plink  \

../results/20180221.perform.gwas/1.trasposed/tmpTrasposed.tfam  \

../results/20180221.perform.gwas/1.trasposed/tmpTrasposed.tped -out   \

../results/20180221.perform.gwas/2.association/out

What do you suggest? Try another gcc/perl version?, wait your fixup?

Thank you again!

[kaichop]

The easiest way is probably just install a lower version of perl, then compile again (after setting appropriate path that has the new perl ahead of old perl)

http://penncnv.openbioinformatics.org/en/latest/user-guide/install/#the-last-resort

On Fri, Feb 23, 2018 at 4:09 AM, lpalomerol notifications@github.com wrote:

Hello Kai,

thank you for your early response!

My gcc version is 4.8.5 and my perl is 5.16.3.

And the problem occurs when launghing a calculate_association.pl file with this isntruction:

/home/idibell/opt/gengen/GenGen-1.0.1/calculate_association.pl -cc -plink \

../results/20180221.perform.gwas/1.trasposed/tmpTrasposed.tfam \

../results/20180221.perform.gwas/1.trasposed/tmpTrasposed.tped -out \

../results/20180221.perform.gwas/2.association/out

What do you suggest? Try another gcc/perl version?, wait your fixup?

Thank you again!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/GenGen/issues/2#issuecomment-367951808, or mute the thread https://github.com/notifications/unsubscribe-auth/AFptuAnDZEh9KF2HASdfoF6gb3czzSnfks5tXoA8gaJpZM4SNyhn .

[lpalomerol]

Thanks! I'll try it and I'll confirm you if it has worked

2018-02-23 14:52 GMT+01:00 Kai Wang notifications@github.com:

The easiest way is probably just install a lower version of perl, then compile again (after setting appropriate path that has the new perl ahead of old perl)

http://penncnv.openbioinformatics.org/en/latest/user-guide/install/# the-last-resort

On Fri, Feb 23, 2018 at 4:09 AM, lpalomerol notifications@github.com wrote:

Hello Kai,

thank you for your early response!

My gcc version is 4.8.5 and my perl is 5.16.3.

And the problem occurs when launghing a calculate_association.pl file with this isntruction:

/home/idibell/opt/gengen/GenGen-1.0.1/calculate_association.pl -cc -plink \

../results/20180221.perform.gwas/1.trasposed/tmpTrasposed.tfam \

../results/20180221.perform.gwas/1.trasposed/tmpTrasposed.tped -out \

../results/20180221.perform.gwas/2.association/out

What do you suggest? Try another gcc/perl version?, wait your fixup?

Thank you again!

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/WGLab/GenGen/issues/2#issuecomment-367951808, or mute the thread https://github.com/notifications/unsubscribe-auth/ AFptuAnDZEh9KF2HASdfoF6gb3czzSnfks5tXoA8gaJpZM4SNyhn

.

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[lpalomerol]

Hello again,

still not working, I've tried with perl 5.14 version and gives me same error. Do you suggest any concrete version?

This is the core trace of performed process with 5.14 version (go to kext folder, make clean, make, go back and perform association test). Any help would be appreciated

`

lpalomero ~/Documentos/pipelines/8.pujana/20180219.comorbidity/bin $ cd ~/opt/gengen/GenGen-1.0.1/kext/; make clean; make; cd -;

rm -f .o .so gcc perl -MExtUtils::Embed -e ccopts -fPIC -c -o kc_wrap.o kc_wrap.c gcc perl -MExtUtils::Embed -e ccopts -fPIC -c -o kc.o kc.c gcc -shared -o kc.so kc_wrap.o kc.o perl -MExtUtils::Embed -e ldopts mkdir -p perl -MConfig -e 'print $Config{version}' mkdir -p perl -MConfig -e 'print $Config{version}'/perl -MConfig -e 'print $Config{archname}'/ mkdir -p perl -MConfig -e 'print $Config{version}'/perl -MConfig -e 'print $Config{archname}'/auto/ mv kc.so perl -MConfig -e 'print $Config{version}'/perl -MConfig -e 'print $Config{archname}'/ /home/idibell/Documentos/pipelines/8.pujana/20180219.comorbidity/bin

lpalomero ~/Documentos/pipelines/8.pujana/20180219.comorbidity/bin $ perl -v

This is perl 5, version 14, subversion 2 (v5.14.2) built for x86_64-linux-thread-multi

Copyright 1987-2011, Larry Wall

Perl may be copied only under the terms of either the Artistic License or the GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on this system using "man perl" or "perldoc perl". If you have access to the Internet, point your browser at http://www.perl.org/, the Perl Home Page.

lpalomero ~/Documentos/pipelines/8.pujana/20180219.comorbidity/bin $             
/home/idibell/opt/gengen/GenGen-1.0.1/calculate_association.pl -cc -plink 
../results/20180221.perform.gwas/1.trasposed/tmpTrasposed.tfam 
../results/20180221.perform.gwas/1.trasposed/tmpTrasposed.tped -out 
../results/20180221.perform.gwas/2.association/out

NOTICE: program notification/warning messages that appear in STDERR will be also recorded in log file ../results/20180221.perform.gwas/2.association/out.log NOTICE: detailed genotyping summary information for all markers (even if not passing quality control threshold) will be written to ../results/20180221.perform.gwas/2.association/out.minfo NOTICE: detailed genotyping summary information for all samples will be written to ../results/20180221.perform.gwas/2.association/out.sinfo NOTICE: detailed genotyping summary information for all families with Mendelian errors will be written to ../results/20180221.perform.gwas/2.association/out.finfo NOTICE: the following marker exclusion criteria is in effect: --geno 0.1 --maf 0.01 --mme 0.1 --hwe 0.001 NOTICE: the following individual exclusion criteria will NOT be used in association test However, individuals failing these criteria will be recorded for re-running program (with --remove argument): --mind 0.1 --fme 1 --ime 0.02 NOTICE: Finished reading pedigree information for 2287 individuals from header file ../results/20180221.perform.gwas/1.trasposed/tmpTrasposed.tfam NOTICE: Current pedigree contains 2287 families with 2287 individuals Sex: 0 are male, 2287 are female, 0 are of unknown sex Founder: 2287 are founders, 0 are non-founders Phenotype (binary trait): 1142 are unaffected, 1145 are affected, and 0 are unknown

Violación de segmento (core' generado)

[lpalomerol]

Hello!

Finally I could run it successfully using PERL version 5.8.9 instead of 5.14

Thank you!

[kaichop]

Thank you for the update. This is good to know that it is caused by perl version issues.

On Mon, Mar 5, 2018 at 5:31 AM, lpalomerol notifications@github.com wrote:

Hello!

Finally I could run it successfully using PERL version 5.8.9 instead of 5.14

Thank you!

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