From gabrielle_doan at gmx.net Tue Jun 24 11:39:14 2008 From: gabrielle_doan at gmx.net (Gabrielle Doan) Date: Tue, 24 Jun 2008 17:39:14 +0200 Subject: [BioSQL-l] Problems when trying to persist a sequence in my BioSQL database using BioPerl Message-ID: <20080624153914.49760@gmx.net> Hi all, I am new to BioPerl and BioSQL so please excuse me if my question is a bit simple. I followed the installation files in the current version of BioPerl very strictly (I used the Bioperl 1.5.2, Developer Release from the bioperl website). After successful installation I tried to persist a genbank file in my BioSQL database, which runs on a database server and is accessible using the mysql command shell. When using bioperl I receive the following error message: ================ $ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb --dbuser myuser --dbpass mypasswd --namespace GenBank /home/doan/db-data/ref_chr1.gbk Loading /local/doan/db-daten/ref_chr1.gbk ... Bio::SeqIO: genbank cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::genbank. Weak references are not implemented in the version of perl at /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91 BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91. Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172. BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172. Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm line 425. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:427 STACK: Bio::SeqIO::_load_format_module /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:555 STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:376 STACK: /usr/bin/bp_load_seqdatabase.pl:541 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at /usr/bin/bp_load_seqdatabase.pl line 565. ================ Unfortunately, even Google does not provide any hints when searching for the particular message. It seems that for some reason the path to the Bio::SeqIO::genbank module cannot be found. I am greateful for any hint! Cheers, Gabrielle -- GMX startet ShortView.de. Hier findest Du Leute mit Deinen Interessen! Jetzt dabei sein: http://www.shortview.de/?mc=sv_ext_mf at gmx From gabrielle_doan at gmx.net Tue Jun 24 11:49:38 2008 From: gabrielle_doan at gmx.net (Gabrielle Doan) Date: Tue, 24 Jun 2008 17:49:38 +0200 Subject: [BioSQL-l] Problems when trying to persist a sequence in my BioSQL database using, BioPerl Message-ID: <48611792.2060906@gmx.net> Hi all, I am new to BioPerl and BioSQL so please excuse me if my question is a bit simple. I followed the installation files in the current version of BioPerl very strictly (I used the Bioperl 1.5.2, Developer Release from the bioperl website). After successful installation I tried to persist a genbank file in my BioSQL database, which runs on a database server and is accessible using the mysql command shell. When using bioperl I receive the following error message: ================ $ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb --dbuser myuser --dbpass mypasswd --namespace GenBank /home/doan/db-data/ref_chr1.gbk Loading /local/doan/db-daten/ref_chr1.gbk ... Bio::SeqIO: genbank cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::genbank. Weak references are not implemented in the version of perl at /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91 BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91. Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172. BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172. Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm line 425. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:427 STACK: Bio::SeqIO::_load_format_module /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:555 STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:376 STACK: /usr/bin/bp_load_seqdatabase.pl:541 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at /usr/bin/bp_load_seqdatabase.pl line 565. ================ Unfortunately, even Google does not provide any hints when searching for the particular message. It seems that for some reason the path to the Bio::SeqIO::genbank module cannot be found. I am greateful for any hint! Cheers, Gabrielle From hlapp at gmx.net Wed Jun 25 18:07:09 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 25 Jun 2008 18:07:09 -0400 Subject: [BioSQL-l] Problems when trying to persist a sequence in my BioSQL database using, BioPerl In-Reply-To: <48611792.2060906@gmx.net> References: <48611792.2060906@gmx.net> Message-ID: <1DB86640-D4D5-4081-8DE5-E3181DD9D6A3@gmx.net> Hi Gabrielle, (note that I have changed the mailing list to bioperl - whoever replies please cut biosql from the cc list, assuming that this indeed isn't BioSQL's fault) given the error message below, Bio::SeqIO::genbank can be found, but it fails to load because it requires Bio::Species, which in turn imports support for weak references from Scalar::Util. The last step fails, causing loading Bio::Species to fail, which in turn causes Bio::SeqIO::genbank to fail to load. The real question is why your version of Perl doesn't seem to have support for weak references (the reason for Scalar::Util failing to load). Could you give details on your OS version and your version of Perl (output of 'perl -V'). The question for BioPerl is whether there is a fall-back mechanism we might want to support if weak references aren't supported, rather than rendering the genbank parser unusable. Sendu or Chris - any thoughts on this? -hilmar On Jun 24, 2008, at 10:49 AM, Gabrielle Doan wrote: > Hi all, > > I am new to BioPerl and BioSQL so please excuse me if my question is > a bit simple. I followed the installation files in the current > version of BioPerl very strictly (I used the Bioperl 1.5.2, > Developer Release from the bioperl website). After successful > installation I tried to persist a genbank file in my BioSQL > database, which runs on a database server and is accessible using > the mysql command shell. When using bioperl I receive the following > error message: > > ================ > > $ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb -- > dbuser myuser --dbpass mypasswd --namespace GenBank /home/doan/db- > data/ref_chr1.gbk > Loading /local/doan/db-daten/ref_chr1.gbk ... > Bio::SeqIO: genbank cannot be found > Exception ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::genbank. Weak references are > not implemented in the version of perl at /usr/lib/perl5/site_perl/ > 5.8.8/Bio/Species.pm line 91 > BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/ > Bio/Species.pm line 91. > Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/ > SeqIO/genbank.pm line 172. > BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/ > Bio/SeqIO/genbank.pm line 172. > Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/ > Root/Root.pm line 425. > > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ > Root/Root.pm:359 > STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/ > Bio/Root/Root.pm:427 > STACK: Bio::SeqIO::_load_format_module /usr/lib/perl5/site_perl/ > 5.8.8/Bio/SeqIO.pm:555 > STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:376 > STACK: /usr/bin/bp_load_seqdatabase.pl:541 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run > time > Can't call method "next_seq" on an undefined value at /usr/bin/ > bp_load_seqdatabase.pl line 565. > > ================ > > Unfortunately, even Google does not provide any hints when searching > for the particular message. It seems that for some reason the path > to the Bio::SeqIO::genbank module cannot be found. I am greateful > for any hint! > > Cheers, > Gabrielle > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From gabrielle_doan at gmx.net Tue Jun 24 15:39:14 2008 From: gabrielle_doan at gmx.net (Gabrielle Doan) Date: Tue, 24 Jun 2008 17:39:14 +0200 Subject: [BioSQL-l] Problems when trying to persist a sequence in my BioSQL database using BioPerl Message-ID: <20080624153914.49760@gmx.net> Hi all, I am new to BioPerl and BioSQL so please excuse me if my question is a bit simple. I followed the installation files in the current version of BioPerl very strictly (I used the Bioperl 1.5.2, Developer Release from the bioperl website). After successful installation I tried to persist a genbank file in my BioSQL database, which runs on a database server and is accessible using the mysql command shell. When using bioperl I receive the following error message: ================ $ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb --dbuser myuser --dbpass mypasswd --namespace GenBank /home/doan/db-data/ref_chr1.gbk Loading /local/doan/db-daten/ref_chr1.gbk ... Bio::SeqIO: genbank cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::genbank. Weak references are not implemented in the version of perl at /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91 BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91. Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172. BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172. Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm line 425. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:427 STACK: Bio::SeqIO::_load_format_module /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:555 STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:376 STACK: /usr/bin/bp_load_seqdatabase.pl:541 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at /usr/bin/bp_load_seqdatabase.pl line 565. ================ Unfortunately, even Google does not provide any hints when searching for the particular message. It seems that for some reason the path to the Bio::SeqIO::genbank module cannot be found. I am greateful for any hint! Cheers, Gabrielle -- GMX startet ShortView.de. Hier findest Du Leute mit Deinen Interessen! Jetzt dabei sein: http://www.shortview.de/?mc=sv_ext_mf at gmx From gabrielle_doan at gmx.net Tue Jun 24 15:49:38 2008 From: gabrielle_doan at gmx.net (Gabrielle Doan) Date: Tue, 24 Jun 2008 17:49:38 +0200 Subject: [BioSQL-l] Problems when trying to persist a sequence in my BioSQL database using, BioPerl Message-ID: <48611792.2060906@gmx.net> Hi all, I am new to BioPerl and BioSQL so please excuse me if my question is a bit simple. I followed the installation files in the current version of BioPerl very strictly (I used the Bioperl 1.5.2, Developer Release from the bioperl website). After successful installation I tried to persist a genbank file in my BioSQL database, which runs on a database server and is accessible using the mysql command shell. When using bioperl I receive the following error message: ================ $ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb --dbuser myuser --dbpass mypasswd --namespace GenBank /home/doan/db-data/ref_chr1.gbk Loading /local/doan/db-daten/ref_chr1.gbk ... Bio::SeqIO: genbank cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Failed to load module Bio::SeqIO::genbank. Weak references are not implemented in the version of perl at /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91 BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/Species.pm line 91. Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172. BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO/genbank.pm line 172. Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm line 425. STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:359 STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:427 STACK: Bio::SeqIO::_load_format_module /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:555 STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:376 STACK: /usr/bin/bp_load_seqdatabase.pl:541 ----------------------------------------------------------- For more information about the SeqIO system please see the SeqIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_seq" on an undefined value at /usr/bin/bp_load_seqdatabase.pl line 565. ================ Unfortunately, even Google does not provide any hints when searching for the particular message. It seems that for some reason the path to the Bio::SeqIO::genbank module cannot be found. I am greateful for any hint! Cheers, Gabrielle From hlapp at gmx.net Wed Jun 25 22:07:09 2008 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 25 Jun 2008 18:07:09 -0400 Subject: [BioSQL-l] Problems when trying to persist a sequence in my BioSQL database using, BioPerl In-Reply-To: <48611792.2060906@gmx.net> References: <48611792.2060906@gmx.net> Message-ID: <1DB86640-D4D5-4081-8DE5-E3181DD9D6A3@gmx.net> Hi Gabrielle, (note that I have changed the mailing list to bioperl - whoever replies please cut biosql from the cc list, assuming that this indeed isn't BioSQL's fault) given the error message below, Bio::SeqIO::genbank can be found, but it fails to load because it requires Bio::Species, which in turn imports support for weak references from Scalar::Util. The last step fails, causing loading Bio::Species to fail, which in turn causes Bio::SeqIO::genbank to fail to load. The real question is why your version of Perl doesn't seem to have support for weak references (the reason for Scalar::Util failing to load). Could you give details on your OS version and your version of Perl (output of 'perl -V'). The question for BioPerl is whether there is a fall-back mechanism we might want to support if weak references aren't supported, rather than rendering the genbank parser unusable. Sendu or Chris - any thoughts on this? -hilmar On Jun 24, 2008, at 10:49 AM, Gabrielle Doan wrote: > Hi all, > > I am new to BioPerl and BioSQL so please excuse me if my question is > a bit simple. I followed the installation files in the current > version of BioPerl very strictly (I used the Bioperl 1.5.2, > Developer Release from the bioperl website). After successful > installation I tried to persist a genbank file in my BioSQL > database, which runs on a database server and is accessible using > the mysql command shell. When using bioperl I receive the following > error message: > > ================ > > $ /usr/bin/bp_load_seqdatabase.pl --host radb --dbname bioseqdb -- > dbuser myuser --dbpass mypasswd --namespace GenBank /home/doan/db- > data/ref_chr1.gbk > Loading /local/doan/db-daten/ref_chr1.gbk ... > Bio::SeqIO: genbank cannot be found > Exception ------------- EXCEPTION: Bio::Root::Exception ------------- > MSG: Failed to load module Bio::SeqIO::genbank. Weak references are > not implemented in the version of perl at /usr/lib/perl5/site_perl/ > 5.8.8/Bio/Species.pm line 91 > BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/ > Bio/Species.pm line 91. > Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/ > SeqIO/genbank.pm line 172. > BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/ > Bio/SeqIO/genbank.pm line 172. > Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Bio/ > Root/Root.pm line 425. > > STACK: Error::throw > STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/ > Root/Root.pm:359 > STACK: Bio::Root::Root::_load_module /usr/lib/perl5/site_perl/5.8.8/ > Bio/Root/Root.pm:427 > STACK: Bio::SeqIO::_load_format_module /usr/lib/perl5/site_perl/ > 5.8.8/Bio/SeqIO.pm:555 > STACK: Bio::SeqIO::new /usr/lib/perl5/site_perl/5.8.8/Bio/SeqIO.pm:376 > STACK: /usr/bin/bp_load_seqdatabase.pl:541 > ----------------------------------------------------------- > > For more information about the SeqIO system please see the SeqIO docs. > This includes ways of checking for formats at compile time, not run > time > Can't call method "next_seq" on an undefined value at /usr/bin/ > bp_load_seqdatabase.pl line 565. > > ================ > > Unfortunately, even Google does not provide any hints when searching > for the particular message. It seems that for some reason the path > to the Bio::SeqIO::genbank module cannot be found. I am greateful > for any hint! > > Cheers, > Gabrielle > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : ===========================================================