From hlapp at drycafe.net Thu Jan 7 10:49:39 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Thu, 7 Jan 2010 10:49:39 -0500 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: References: Message-ID: <1919B039-6F77-412B-8984-9B8EC956BABD@drycafe.net> Hi Amy, this looks like a problem with installing DBD::mysql, not BioSQL. I don't know how you built DBD::mysql and DBI, and I haven't encountered this error (but maybe someone else on the BioSQL list has come across this?), so your best avenue for getting help is probably the DBD::mysql mailing list. Cheers, -hilmar On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: > Dear Hilmar, > > Happy New Year! I hope you had enjoyable holidays. So, my sys admin > colleague and I are trying to get BioSQL (with a BioPerl language > binding) > up and running ASAP. > > We have successfully installed MySQL and BioPerl. We are having > trouble, > however, getting the DBD::mysql module installed (on a Macbook Pro > running > OS X 10.6.1) to finish the last steps of BioSQL installation. The > error > message for our attempt is pasted below. We have also attempted a > manual > install, and get the same result (i.e., croaking at the make test > step)-failed installation. > > Would you please guide us through the necessary final steps in getting > BioSQL up and running? Any help you can provide would be greatly > appreciated. Thanks very much and I look forward to hearing from you. > Sincerely, AJP > > > [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] > > cpan[1]> install Bundle::DBD::mysql > CPAN: Storable loaded ok (v2.21) > Going to read '/var/root/.cpan/Metadata' > Database was generated on Wed, 06 Jan 2010 09:01:01 GMT > CPAN: YAML loaded ok (v0.70) > Going to read 52 yaml files from /var/root/.cpan/build/ > CPAN: Time::HiRes loaded ok (v1.9711) > DONE > Restored the state of none (in 1.1851 secs) > Has already been unwrapped into directory > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > DBI is up to date (1.609). > Running install for module 'DBD::mysql' > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > Has already been unwrapped into directory > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > Has already been made > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/00base.t .................. 1/6 > # Failed test 'use DBD::mysql;' > # at t/00base.t line 21. > # Tried to use 'DBD::mysql'. > # Error: Can't load > '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ > DBD/mys > ql/mysql.bundle' for module DBD::mysql: > dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ > arch/auto/D > BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix > # Referenced from: > /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ > DBD/mysq > l/mysql.bundle > # Expected in: flat namespace > # in > /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ > DBD/mysq > l/mysql.bundle at > /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm > line > 207. > # at (eval 7) line 2 > # Compilation failed in require at (eval 7) line 2. > # BEGIN failed--compilation aborted at (eval 7) line 2. > Bailout called. Further testing stopped: Unable to load DBD::mysql > FAILED--Further testing stopped: Unable to load DBD::mysql > make: *** [test_dynamic] Error 255 > CAPTTOFU/DBD-mysql-4.013.tar.gz > make test -- NOT OK > //hint// to see the cpan-testers results for installing this module, > try: > reports CAPTTOFU/DBD-mysql-4.013.tar.gz > Running make install > make test had returned bad status, won't install without force > Failed during this command: > CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From maj at fortinbras.us Thu Jan 7 11:08:20 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 7 Jan 2010 11:08:20 -0500 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: <1919B039-6F77-412B-8984-9B8EC956BABD@drycafe.net> References: <1919B039-6F77-412B-8984-9B8EC956BABD@drycafe.net> Message-ID: <9F6B6EB3FA7E4C0C8F9471F17F249A09@NewLife> This portion > Running install for module 'DBD::mysql' > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > Has already been unwrapped into directory > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > Has already been made > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/00base.t .................. 1/6 > # Failed test 'use DBD::mysql;' > # at t/00base.t line 21. > # Tried to use 'DBD::mysql'. > # Error: Can't load suggests that, though DBD::mysql was made, the module can't be found by perl (is not in @INC). You could try installing from scratch again cpan> fforce install DBD::mysql The other issue may be that your mysql installation can't be found or encounters an error when DBD::mysql is loaded. Try at the command line $ perl -MDBD::mysql -e 1 and see if any more helpful errors ensue. MAJ ----- Original Message ----- From: "Hilmar Lapp" To: "Powell Phd, Amy Jo" Cc: "biosql-l" ; "Bolin,Samuel" Sent: Thursday, January 07, 2010 10:49 AM Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies > Hi Amy, > > this looks like a problem with installing DBD::mysql, not BioSQL. I don't > know how you built DBD::mysql and DBI, and I haven't encountered this error > (but maybe someone else on the BioSQL list has come across this?), so your > best avenue for getting help is probably the DBD::mysql mailing list. > > Cheers, > > -hilmar > > On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: > >> Dear Hilmar, >> >> Happy New Year! I hope you had enjoyable holidays. So, my sys admin >> colleague and I are trying to get BioSQL (with a BioPerl language binding) >> up and running ASAP. >> >> We have successfully installed MySQL and BioPerl. We are having trouble, >> however, getting the DBD::mysql module installed (on a Macbook Pro running >> OS X 10.6.1) to finish the last steps of BioSQL installation. The error >> message for our attempt is pasted below. We have also attempted a manual >> install, and get the same result (i.e., croaking at the make test >> step)-failed installation. >> >> Would you please guide us through the necessary final steps in getting >> BioSQL up and running? Any help you can provide would be greatly >> appreciated. Thanks very much and I look forward to hearing from you. >> Sincerely, AJP >> >> >> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] >> >> cpan[1]> install Bundle::DBD::mysql >> CPAN: Storable loaded ok (v2.21) >> Going to read '/var/root/.cpan/Metadata' >> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT >> CPAN: YAML loaded ok (v0.70) >> Going to read 52 yaml files from /var/root/.cpan/build/ >> CPAN: Time::HiRes loaded ok (v1.9711) >> DONE >> Restored the state of none (in 1.1851 secs) >> Has already been unwrapped into directory >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >> DBI is up to date (1.609). >> Running install for module 'DBD::mysql' >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> Has already been unwrapped into directory >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >> Has already been made >> Running make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/00base.t .................. 1/6 >> # Failed test 'use DBD::mysql;' >> # at t/00base.t line 21. >> # Tried to use 'DBD::mysql'. >> # Error: Can't load >> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ DBD/mys >> ql/mysql.bundle' for module DBD::mysql: >> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ arch/auto/D >> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix >> # Referenced from: >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ DBD/mysq >> l/mysql.bundle >> # Expected in: flat namespace >> # in >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ DBD/mysq >> l/mysql.bundle at >> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm line >> 207. >> # at (eval 7) line 2 >> # Compilation failed in require at (eval 7) line 2. >> # BEGIN failed--compilation aborted at (eval 7) line 2. >> Bailout called. Further testing stopped: Unable to load DBD::mysql >> FAILED--Further testing stopped: Unable to load DBD::mysql >> make: *** [test_dynamic] Error 255 >> CAPTTOFU/DBD-mysql-4.013.tar.gz >> make test -- NOT OK >> //hint// to see the cpan-testers results for installing this module, try: >> reports CAPTTOFU/DBD-mysql-4.013.tar.gz >> Running make install >> make test had returned bad status, won't install without force >> Failed during this command: >> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO >> >> > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > > From biopython at maubp.freeserve.co.uk Wed Jan 13 06:37:59 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 13 Jan 2010 11:37:59 +0000 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> Message-ID: <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com> On Thu, Dec 10, 2009 at 3:03 PM, Peter wrote: > > Brad and I are hoping to include BioSQL on SQLite support in the > imminent release of Biopython 1.53, although we will stress in the > release notes that this (and the schema) is still experimental. > > For this initial release, the user probably still have to manually > create the SQLite database - this is something I hope we can make > much more user friendly in the subsequent releases of Biopython > (taking advantage of the fact the SQLite is included with Python 2.5 > onwards, so we can do this without any external dependencies). > > Peter > > See also: > http://bugzilla.open-bio.org/show_bug.cgi?id=2870 > http://bugzilla.open-bio.org/show_bug.cgi?id=2866 > To keep you guys informed, we released Biopython 1.53 at the end of 2009, and this did include BioSQL on SQLite support based on the draft schema: http://news.open-bio.org/news/2009/12/biopython-release-153/ Even if a BioSQL v1.0.2 release isn't imminent, could the draft SQLite schema be checked into BioSQL's SVN repository please? Repository link to see the file (currently no revisions): http://github.com/biopython/biopython/blob/master/Tests/BioSQL/biosqldb-sqlite.sql Alternatively you can grab the file here: http://biopython.open-bio.org/SRC/biopython/Tests/BioSQL/biosqldb-sqlite.sql (updated hourly, not that we have any revisions planned) As I said before, we'd like to make using BioSQL on SQLite from within Biopython much easier (because unlike the other database back ends, it is *very* simple to create or delete a new SQLite database). This would require us to install a copy of the schema as part of Biopython (currently we just include a copy used for unit tests), so the sooner the schema becomes "official", the better. Regards, Peter From sabolin at sandia.gov Wed Jan 13 11:22:03 2010 From: sabolin at sandia.gov (Bolin, Samuel) Date: Wed, 13 Jan 2010 09:22:03 -0700 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: References: <9F6B6EB3FA7E4C0C8F9471F17F249A09@NewLife> Message-ID: <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> Mark and Hilmar I am working with Amy Powell on getting BioSQL up and running Decided to take a different tact and am now using Fedora Was able to get MySQL BioPerl installed along with getting past the DBD and DBI issues However I have read thru the documentation and have been unable to figure out how BioSQL ties in must less get it installed Any guidance? Sammy From: Powell Phd, Amy Jo Sent: Thursday, January 07, 2010 10:29 AM To: Mark A. Jensen; Hilmar Lapp Cc: biosql-l; Bolin, Samuel Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies Hi there- Thanks very much for your suggestion. We?ll give it a try and see what happens. Sincerely, AJP On 1/7/10 9:08 AM, "Mark A. Jensen" wrote: This portion > Running install for module 'DBD::mysql' > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > Has already been unwrapped into directory > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > Has already been made > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/00base.t .................. 1/6 > # Failed test 'use DBD::mysql;' > # at t/00base.t line 21. > # Tried to use 'DBD::mysql'. > # Error: Can't load suggests that, though DBD::mysql was made, the module can't be found by perl (is not in @INC). You could try installing from scratch again cpan> fforce install DBD::mysql The other issue may be that your mysql installation can't be found or encounters an error when DBD::mysql is loaded. Try at the command line $ perl -MDBD::mysql -e 1 and see if any more helpful errors ensue. MAJ ----- Original Message ----- From: "Hilmar Lapp" To: "Powell Phd, Amy Jo" Cc: "biosql-l" ; "Bolin,Samuel" Sent: Thursday, January 07, 2010 10:49 AM Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies > Hi Amy, > > this looks like a problem with installing DBD::mysql, not BioSQL. I don't > know how you built DBD::mysql and DBI, and I haven't encountered this error > (but maybe someone else on the BioSQL list has come across this?), so your > best avenue for getting help is probably the DBD::mysql mailing list. > > Cheers, > > -hilmar > > On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: > >> Dear Hilmar, >> >> Happy New Year! I hope you had enjoyable holidays. So, my sys admin >> colleague and I are trying to get BioSQL (with a BioPerl language binding) >> up and running ASAP. >> >> We have successfully installed MySQL and BioPerl. We are having trouble, >> however, getting the DBD::mysql module installed (on a Macbook Pro running >> OS X 10.6.1) to finish the last steps of BioSQL installation. The error >> message for our attempt is pasted below. We have also attempted a manual >> install, and get the same result (i.e., croaking at the make test >> step)-failed installation. >> >> Would you please guide us through the necessary final steps in getting >> BioSQL up and running? Any help you can provide would be greatly >> appreciated. Thanks very much and I look forward to hearing from you. >> Sincerely, AJP >> >> >> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] >> >> cpan[1]> install Bundle::DBD::mysql >> CPAN: Storable loaded ok (v2.21) >> Going to read '/var/root/.cpan/Metadata' >> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT >> CPAN: YAML loaded ok (v0.70) >> Going to read 52 yaml files from /var/root/.cpan/build/ >> CPAN: Time::HiRes loaded ok (v1.9711) >> DONE >> Restored the state of none (in 1.1851 secs) >> Has already been unwrapped into directory >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >> DBI is up to date (1.609). >> Running install for module 'DBD::mysql' >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> Has already been unwrapped into directory >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >> Has already been made >> Running make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/00base.t .................. 1/6 >> # Failed test 'use DBD::mysql;' >> # at t/00base.t line 21. >> # Tried to use 'DBD::mysql'. >> # Error: Can't load >> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ auto/ DBD/mys >> ql/mysql.bundle' for module DBD::mysql: >> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ arch/auto/D >> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix >> # Referenced from: >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ auto/ DBD/mysq >> l/mysql.bundle >> # Expected in: flat namespace >> # in >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ auto/ DBD/mysq >> l/mysql.bundle at >> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/ DynaLoader.pm line >> 207. >> # at (eval 7) line 2 >> # Compilation failed in require at (eval 7) line 2. >> # BEGIN failed--compilation aborted at (eval 7) line 2. >> Bailout called. Further testing stopped: Unable to load DBD::mysql >> FAILED--Further testing stopped: Unable to load DBD::mysql >> make: *** [test_dynamic] Error 255 >> CAPTTOFU/DBD-mysql-4.013.tar.gz >> make test -- NOT OK >> //hint// to see the cpan-testers results for installing this module, try: >> reports CAPTTOFU/DBD-mysql-4.013.tar.gz >> Running make install >> make test had returned bad status, won't install without force >> Failed during this command: >> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO >> >> > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > > From hlapp at drycafe.net Wed Jan 13 12:03:06 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 13 Jan 2010 12:03:06 -0500 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> References: <9F6B6EB3FA7E4C0C8F9471F17F249A09@NewLife> <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> Message-ID: <1DD26F99-82AE-4279-A0D7-D3CD5A1352D7@drycafe.net> Hi Sammy, please always On Jan 13, 2010, at 11:22 AM, Bolin, Samuel wrote: > Mark and Hilmar > > I am working with Amy Powell on getting BioSQL up and running > Decided to take a different tact and am now using Fedora > Was able to get MySQL BioPerl installed along with getting past the > DBD and DBI issues > However I have read thru the documentation and have been unable to > figure out how BioSQL ties in must less get it installed > Any guidance? > > Sammy > > From: Powell Phd, Amy Jo > Sent: Thursday, January 07, 2010 10:29 AM > To: Mark A. Jensen; Hilmar Lapp > Cc: biosql-l; Bolin, Samuel > Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) > dependencies > > Hi there- > > Thanks very much for your suggestion. We?ll give it a try and see > what happens. Sincerely, AJP > > > On 1/7/10 9:08 AM, "Mark A. Jensen" wrote: > > This portion > > > Running install for module 'DBD::mysql' > > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > > Has already been unwrapped into directory > > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > > Has already been made > > Running make test > > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > > t/00base.t .................. 1/6 > > # Failed test 'use DBD::mysql;' > > # at t/00base.t line 21. > > # Tried to use 'DBD::mysql'. > > # Error: Can't load > > suggests that, though DBD::mysql was made, the module can't be > found by perl (is not in @INC). You could try installing from scratch > again > > cpan> fforce install DBD::mysql > > The other issue may be that your mysql installation can't be found > or encounters > an error when > DBD::mysql is loaded. Try at the command line > > $ perl -MDBD::mysql -e 1 > > and see if any more helpful errors ensue. > > MAJ > > ----- Original Message ----- > From: "Hilmar Lapp" > To: "Powell Phd, Amy Jo" > Cc: "biosql-l" ; "Bolin,Samuel" > > Sent: Thursday, January 07, 2010 10:49 AM > Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) > dependencies > > > > Hi Amy, > > > > this looks like a problem with installing DBD::mysql, not BioSQL. > I don't > > know how you built DBD::mysql and DBI, and I haven't encountered > this error > > (but maybe someone else on the BioSQL list has come across > this?), so your > > best avenue for getting help is probably the DBD::mysql mailing > list. > > > > Cheers, > > > > -hilmar > > > > On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: > > > >> Dear Hilmar, > >> > >> Happy New Year! I hope you had enjoyable holidays. So, my sys > admin > >> colleague and I are trying to get BioSQL (with a BioPerl > language binding) > >> up and running ASAP. > >> > >> We have successfully installed MySQL and BioPerl. We are having > trouble, > >> however, getting the DBD::mysql module installed (on a Macbook > Pro running > >> OS X 10.6.1) to finish the last steps of BioSQL installation. > The error > >> message for our attempt is pasted below. We have also attempted > a manual > >> install, and get the same result (i.e., croaking at the make test > >> step)-failed installation. > >> > >> Would you please guide us through the necessary final steps in > getting > >> BioSQL up and running? Any help you can provide would be greatly > >> appreciated. Thanks very much and I look forward to hearing from > you. > >> Sincerely, AJP > >> > >> > >> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] > >> > >> cpan[1]> install Bundle::DBD::mysql > >> CPAN: Storable loaded ok (v2.21) > >> Going to read '/var/root/.cpan/Metadata' > >> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT > >> CPAN: YAML loaded ok (v0.70) > >> Going to read 52 yaml files from /var/root/.cpan/build/ > >> CPAN: Time::HiRes loaded ok (v1.9711) > >> DONE > >> Restored the state of none (in 1.1851 secs) > >> Has already been unwrapped into directory > >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > >> DBI is up to date (1.609). > >> Running install for module 'DBD::mysql' > >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > >> Has already been unwrapped into directory > >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > >> Has already been made > >> Running make test > >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > >> t/00base.t .................. 1/6 > >> # Failed test 'use DBD::mysql;' > >> # at t/00base.t line 21. > >> # Tried to use 'DBD::mysql'. > >> # Error: Can't load > >> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mys > >> ql/mysql.bundle' for module DBD::mysql: > >> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ > arch/auto/D > >> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix > >> # Referenced from: > >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mysq > >> l/mysql.bundle > >> # Expected in: flat namespace > >> # in > >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mysq > >> l/mysql.bundle at > >> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/ > DynaLoader.pm line > >> 207. > >> # at (eval 7) line 2 > >> # Compilation failed in require at (eval 7) line 2. > >> # BEGIN failed--compilation aborted at (eval 7) line 2. > >> Bailout called. Further testing stopped: Unable to load > DBD::mysql > >> FAILED--Further testing stopped: Unable to load DBD::mysql > >> make: *** [test_dynamic] Error 255 > >> CAPTTOFU/DBD-mysql-4.013.tar.gz > >> make test -- NOT OK > >> //hint// to see the cpan-testers results for installing this > module, try: > >> reports CAPTTOFU/DBD-mysql-4.013.tar.gz > >> Running make install > >> make test had returned bad status, won't install without force > >> Failed during this command: > >> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO > >> > >> > > > > -- > > =========================================================== > > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > > =========================================================== > > > > > > > > > > _______________________________________________ > > 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 drycafe dot net : =========================================================== From hlapp at drycafe.net Wed Jan 13 12:04:48 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 13 Jan 2010 12:04:48 -0500 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> References: <9F6B6EB3FA7E4C0C8F9471F17F249A09@NewLife> <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> Message-ID: <686C367C-A9E3-44E9-BC71-EA18A1C84CBD@drycafe.net> (hit send erroneously ...) Hi Sammy, please always direct your questions to the mailing list. There are many more people there who can help you out. Have you looked at the INSTALL file that comes with BioSQL and tried to follow the instructions therein? If yes, what did you find not to work? -hilmar On Jan 13, 2010, at 11:22 AM, Bolin, Samuel wrote: > Mark and Hilmar > > I am working with Amy Powell on getting BioSQL up and running > Decided to take a different tact and am now using Fedora > Was able to get MySQL BioPerl installed along with getting past the > DBD and DBI issues > However I have read thru the documentation and have been unable to > figure out how BioSQL ties in must less get it installed > Any guidance? > > Sammy > > From: Powell Phd, Amy Jo > Sent: Thursday, January 07, 2010 10:29 AM > To: Mark A. Jensen; Hilmar Lapp > Cc: biosql-l; Bolin, Samuel > Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) > dependencies > > Hi there- > > Thanks very much for your suggestion. We?ll give it a try and see > what happens. Sincerely, AJP > > > On 1/7/10 9:08 AM, "Mark A. Jensen" wrote: > > This portion > > > Running install for module 'DBD::mysql' > > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > > Has already been unwrapped into directory > > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > > Has already been made > > Running make test > > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > > t/00base.t .................. 1/6 > > # Failed test 'use DBD::mysql;' > > # at t/00base.t line 21. > > # Tried to use 'DBD::mysql'. > > # Error: Can't load > > suggests that, though DBD::mysql was made, the module can't be > found by perl (is not in @INC). You could try installing from scratch > again > > cpan> fforce install DBD::mysql > > The other issue may be that your mysql installation can't be found > or encounters > an error when > DBD::mysql is loaded. Try at the command line > > $ perl -MDBD::mysql -e 1 > > and see if any more helpful errors ensue. > > MAJ > > ----- Original Message ----- > From: "Hilmar Lapp" > To: "Powell Phd, Amy Jo" > Cc: "biosql-l" ; "Bolin,Samuel" > > Sent: Thursday, January 07, 2010 10:49 AM > Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) > dependencies > > > > Hi Amy, > > > > this looks like a problem with installing DBD::mysql, not BioSQL. > I don't > > know how you built DBD::mysql and DBI, and I haven't encountered > this error > > (but maybe someone else on the BioSQL list has come across > this?), so your > > best avenue for getting help is probably the DBD::mysql mailing > list. > > > > Cheers, > > > > -hilmar > > > > On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: > > > >> Dear Hilmar, > >> > >> Happy New Year! I hope you had enjoyable holidays. So, my sys > admin > >> colleague and I are trying to get BioSQL (with a BioPerl > language binding) > >> up and running ASAP. > >> > >> We have successfully installed MySQL and BioPerl. We are having > trouble, > >> however, getting the DBD::mysql module installed (on a Macbook > Pro running > >> OS X 10.6.1) to finish the last steps of BioSQL installation. > The error > >> message for our attempt is pasted below. We have also attempted > a manual > >> install, and get the same result (i.e., croaking at the make test > >> step)-failed installation. > >> > >> Would you please guide us through the necessary final steps in > getting > >> BioSQL up and running? Any help you can provide would be greatly > >> appreciated. Thanks very much and I look forward to hearing from > you. > >> Sincerely, AJP > >> > >> > >> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] > >> > >> cpan[1]> install Bundle::DBD::mysql > >> CPAN: Storable loaded ok (v2.21) > >> Going to read '/var/root/.cpan/Metadata' > >> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT > >> CPAN: YAML loaded ok (v0.70) > >> Going to read 52 yaml files from /var/root/.cpan/build/ > >> CPAN: Time::HiRes loaded ok (v1.9711) > >> DONE > >> Restored the state of none (in 1.1851 secs) > >> Has already been unwrapped into directory > >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > >> DBI is up to date (1.609). > >> Running install for module 'DBD::mysql' > >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > >> Has already been unwrapped into directory > >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > >> Has already been made > >> Running make test > >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > >> t/00base.t .................. 1/6 > >> # Failed test 'use DBD::mysql;' > >> # at t/00base.t line 21. > >> # Tried to use 'DBD::mysql'. > >> # Error: Can't load > >> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mys > >> ql/mysql.bundle' for module DBD::mysql: > >> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ > arch/auto/D > >> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix > >> # Referenced from: > >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mysq > >> l/mysql.bundle > >> # Expected in: flat namespace > >> # in > >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mysq > >> l/mysql.bundle at > >> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/ > DynaLoader.pm line > >> 207. > >> # at (eval 7) line 2 > >> # Compilation failed in require at (eval 7) line 2. > >> # BEGIN failed--compilation aborted at (eval 7) line 2. > >> Bailout called. Further testing stopped: Unable to load > DBD::mysql > >> FAILED--Further testing stopped: Unable to load DBD::mysql > >> make: *** [test_dynamic] Error 255 > >> CAPTTOFU/DBD-mysql-4.013.tar.gz > >> make test -- NOT OK > >> //hint// to see the cpan-testers results for installing this > module, try: > >> reports CAPTTOFU/DBD-mysql-4.013.tar.gz > >> Running make install > >> make test had returned bad status, won't install without force > >> Failed during this command: > >> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO > >> > >> > > > > -- > > =========================================================== > > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > > =========================================================== > > > > > > > > > > _______________________________________________ > > 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 drycafe dot net : =========================================================== From hlapp at drycafe.net Wed Jan 13 12:21:13 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 13 Jan 2010 12:21:13 -0500 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: <51677525E6912B4FA646302AD6D1D78C80F9810C17@ES03SNLNT.srn.sandia.gov> References: <9F6B6EB3FA7E4C0C8F9471F17F249A09@NewLife> <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> <686C367C-A9E3-44E9-BC71-EA18A1C84CBD@drycafe.net> <51677525E6912B4FA646302AD6D1D78C80F9810C17@ES03SNLNT.srn.sandia.gov> Message-ID: Sammy - please always keep the list copied. Links to and documentation for downloads are at http://biosql.org. Specifically look for the section titled 'Downloads'. -hilmar On Jan 13, 2010, at 12:09 PM, Bolin, Samuel wrote: > I have not looked at the install file as I am unable to find a > biosql package/rpm/tar etc > Could you point me in the direction of that, I am working off of > instructions given to me by amy > > -----Original Message----- > From: Hilmar Lapp [mailto:hlapp at drycafe.net] > Sent: Wednesday, January 13, 2010 10:05 AM > To: Bolin, Samuel > Cc: Mark A. Jensen; biosql-l > Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) > dependencies > > (hit send erroneously ...) > > Hi Sammy, > > please always direct your questions to the mailing list. There are > many more people there who can help you out. > > Have you looked at the INSTALL file that comes with BioSQL and tried > to follow the instructions therein? If yes, what did you find not to > work? > > -hilmar > > On Jan 13, 2010, at 11:22 AM, Bolin, Samuel wrote: > >> Mark and Hilmar >> >> I am working with Amy Powell on getting BioSQL up and running >> Decided to take a different tact and am now using Fedora >> Was able to get MySQL BioPerl installed along with getting past the >> DBD and DBI issues >> However I have read thru the documentation and have been unable to >> figure out how BioSQL ties in must less get it installed >> Any guidance? >> >> Sammy >> >> From: Powell Phd, Amy Jo >> Sent: Thursday, January 07, 2010 10:29 AM >> To: Mark A. Jensen; Hilmar Lapp >> Cc: biosql-l; Bolin, Samuel >> Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) >> dependencies >> >> Hi there- >> >> Thanks very much for your suggestion. We'll give it a try and see >> what happens. Sincerely, AJP >> >> >> On 1/7/10 9:08 AM, "Mark A. Jensen" wrote: >> >> This portion >> >>> Running install for module 'DBD::mysql' >>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> Has already been unwrapped into directory >>> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >>> Has already been made >>> Running make test >>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >>> t/00base.t .................. 1/6 >>> # Failed test 'use DBD::mysql;' >>> # at t/00base.t line 21. >>> # Tried to use 'DBD::mysql'. >>> # Error: Can't load >> >> suggests that, though DBD::mysql was made, the module can't be >> found by perl (is not in @INC). You could try installing from scratch >> again >> >> cpan> fforce install DBD::mysql >> >> The other issue may be that your mysql installation can't be found >> or encounters >> an error when >> DBD::mysql is loaded. Try at the command line >> >> $ perl -MDBD::mysql -e 1 >> >> and see if any more helpful errors ensue. >> >> MAJ >> >> ----- Original Message ----- >> From: "Hilmar Lapp" >> To: "Powell Phd, Amy Jo" >> Cc: "biosql-l" ; "Bolin,Samuel" >> >> Sent: Thursday, January 07, 2010 10:49 AM >> Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) >> dependencies >> >> >>> Hi Amy, >>> >>> this looks like a problem with installing DBD::mysql, not BioSQL. >> I don't >>> know how you built DBD::mysql and DBI, and I haven't encountered >> this error >>> (but maybe someone else on the BioSQL list has come across >> this?), so your >>> best avenue for getting help is probably the DBD::mysql mailing >> list. >>> >>> Cheers, >>> >>> -hilmar >>> >>> On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: >>> >>>> Dear Hilmar, >>>> >>>> Happy New Year! I hope you had enjoyable holidays. So, my sys >> admin >>>> colleague and I are trying to get BioSQL (with a BioPerl >> language binding) >>>> up and running ASAP. >>>> >>>> We have successfully installed MySQL and BioPerl. We are having >> trouble, >>>> however, getting the DBD::mysql module installed (on a Macbook >> Pro running >>>> OS X 10.6.1) to finish the last steps of BioSQL installation. >> The error >>>> message for our attempt is pasted below. We have also attempted >> a manual >>>> install, and get the same result (i.e., croaking at the make test >>>> step)-failed installation. >>>> >>>> Would you please guide us through the necessary final steps in >> getting >>>> BioSQL up and running? Any help you can provide would be greatly >>>> appreciated. Thanks very much and I look forward to hearing from >> you. >>>> Sincerely, AJP >>>> >>>> >>>> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] >>>> >>>> cpan[1]> install Bundle::DBD::mysql >>>> CPAN: Storable loaded ok (v2.21) >>>> Going to read '/var/root/.cpan/Metadata' >>>> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT >>>> CPAN: YAML loaded ok (v0.70) >>>> Going to read 52 yaml files from /var/root/.cpan/build/ >>>> CPAN: Time::HiRes loaded ok (v1.9711) >>>> DONE >>>> Restored the state of none (in 1.1851 secs) >>>> Has already been unwrapped into directory >>>> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >>>> DBI is up to date (1.609). >>>> Running install for module 'DBD::mysql' >>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> Has already been unwrapped into directory >>>> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >>>> Has already been made >>>> Running make test >>>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >>>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >>>> t/00base.t .................. 1/6 >>>> # Failed test 'use DBD::mysql;' >>>> # at t/00base.t line 21. >>>> # Tried to use 'DBD::mysql'. >>>> # Error: Can't load >>>> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ >> auto/ DBD/mys >>>> ql/mysql.bundle' for module DBD::mysql: >>>> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ >> arch/auto/D >>>> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix >>>> # Referenced from: >>>> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ >> auto/ DBD/mysq >>>> l/mysql.bundle >>>> # Expected in: flat namespace >>>> # in >>>> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ >> auto/ DBD/mysq >>>> l/mysql.bundle at >>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/ >> DynaLoader.pm line >>>> 207. >>>> # at (eval 7) line 2 >>>> # Compilation failed in require at (eval 7) line 2. >>>> # BEGIN failed--compilation aborted at (eval 7) line 2. >>>> Bailout called. Further testing stopped: Unable to load >> DBD::mysql >>>> FAILED--Further testing stopped: Unable to load DBD::mysql >>>> make: *** [test_dynamic] Error 255 >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> make test -- NOT OK >>>> //hint// to see the cpan-testers results for installing this >> module, try: >>>> reports CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> Running make install >>>> make test had returned bad status, won't install without force >>>> Failed during this command: >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO >>>> >>>> >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : >>> =========================================================== >>> >>> >>> >>> >>> _______________________________________________ >>> 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 drycafe dot net : > =========================================================== > > > > > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From hlapp at gmx.net Wed Jan 13 12:06:39 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Jan 2010 12:06:39 -0500 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com> Message-ID: Hi Peter, yes, I know I'm remiss on doing that. Will do shortly. Please don't stop pestering if I seem to have forgotten :-) -hilmar On Jan 13, 2010, at 6:37 AM, Peter wrote: > On Thu, Dec 10, 2009 at 3:03 PM, Peter > wrote: >> >> Brad and I are hoping to include BioSQL on SQLite support in the >> imminent release of Biopython 1.53, although we will stress in the >> release notes that this (and the schema) is still experimental. >> >> For this initial release, the user probably still have to manually >> create the SQLite database - this is something I hope we can make >> much more user friendly in the subsequent releases of Biopython >> (taking advantage of the fact the SQLite is included with Python 2.5 >> onwards, so we can do this without any external dependencies). >> >> Peter >> >> See also: >> http://bugzilla.open-bio.org/show_bug.cgi?id=2870 >> http://bugzilla.open-bio.org/show_bug.cgi?id=2866 >> > > To keep you guys informed, we released Biopython 1.53 at the > end of 2009, and this did include BioSQL on SQLite support > based on the draft schema: > http://news.open-bio.org/news/2009/12/biopython-release-153/ > > Even if a BioSQL v1.0.2 release isn't imminent, could the draft > SQLite schema be checked into BioSQL's SVN repository please? > > Repository link to see the file (currently no revisions): > http://github.com/biopython/biopython/blob/master/Tests/BioSQL/biosqldb-sqlite.sql > > Alternatively you can grab the file here: > http://biopython.open-bio.org/SRC/biopython/Tests/BioSQL/biosqldb-sqlite.sql > (updated hourly, not that we have any revisions planned) > > As I said before, we'd like to make using BioSQL on SQLite > from within Biopython much easier (because unlike the other > database back ends, it is *very* simple to create or delete a > new SQLite database). This would require us to install a > copy of the schema as part of Biopython (currently we just > include a copy used for unit tests), so the sooner the schema > becomes "official", the better. > > Regards, > > Peter > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From piotrborowiec at g.pl Mon Jan 18 12:54:45 2010 From: piotrborowiec at g.pl (Piotr Borowiec) Date: Mon, 18 Jan 2010 18:54:45 +0100 Subject: [BioSQL-l] Problems with installation Biosql Message-ID: <1c828cb91001180954r43b01287pc5f4258065d024e4@mail.gmail.com> Hi, I have problems with installation Biosql. Everything is progressing well to running a script load_ncbi_taxonomy.pl stage. Displays the message: Access denied for user 'Peter' @ 'localhost' (using password: NO) at load_ncbi_taxonomy.pl line 311 Please advice. Peter From biopython at maubp.freeserve.co.uk Mon Jan 18 16:10:55 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Mon, 18 Jan 2010 21:10:55 +0000 Subject: [BioSQL-l] Problems with installation Biosql In-Reply-To: <1c828cb91001180954r43b01287pc5f4258065d024e4@mail.gmail.com> References: <1c828cb91001180954r43b01287pc5f4258065d024e4@mail.gmail.com> Message-ID: <320fb6e01001181310n2be4889cked47da5d609c4223@mail.gmail.com> On Mon, Jan 18, 2010 at 5:54 PM, Piotr Borowiec wrote: > > Hi, > I have problems with installation Biosql. Everything is progressing > well to running a script load_ncbi_taxonomy.pl stage. Displays the > message: Access denied for user 'Peter' @ 'localhost' (using password: > NO) at load_ncbi_taxonomy.pl line 311 > Please advice. > > Peter You have to give the script a database username and password (which you should know or be able to create if it was you that setup the BioSQL database) via its optional command line options. Peter C From biopython at maubp.freeserve.co.uk Tue Jan 19 05:11:51 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 19 Jan 2010 10:11:51 +0000 Subject: [BioSQL-l] Problems with installation Biosql In-Reply-To: <1c828cb91001190142h11aca5a4o153e3c614a6a2fe2@mail.gmail.com> References: <1c828cb91001180954r43b01287pc5f4258065d024e4@mail.gmail.com> <320fb6e01001181310n2be4889cked47da5d609c4223@mail.gmail.com> <1c828cb91001190142h11aca5a4o153e3c614a6a2fe2@mail.gmail.com> Message-ID: <320fb6e01001190211u2905e1fbu36c0ceacba11bb86@mail.gmail.com> Hi, Don't forget to CC the mailing list on replies ;) On Tue, Jan 19, 2010 at 9:42 AM, Piotr Borowiec wrote: > > Thanks for advice. I gave the script all parameters and next there was > a message: > > Loading NCBI taxon database in taxdata: > ? ? ? ?... retrieving all taxon nodes in the database > ? ? ? ?... reading in taxon nodes from nodes.dmp > Couldn't open data file taxdata/nodes.dmp: No such file or directory > rollback ineffective with AutoCommit enabled at load_ncbi_taxonomy.pl line 841. > Use of uninitialized value in concatenation (.) or string at > load_ncbi_taxonomy.pl line 843. The script has an option to download the taxonomy file from the NCBI (--download true), or to use an existing copy (e.g. from a previous run). I suspect that you have a partial copy from an aborted run which is confusing the script. I would try again explicitly asking for a fresh download. I would also try removing the taxdata directory (if present) and any (partial) taxdata archive file - then try again. Peter From biopython at maubp.freeserve.co.uk Thu Jan 21 07:33:53 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 21 Jan 2010 12:33:53 +0000 Subject: [BioSQL-l] SwissProt DE lines and UniProt XML / TagTree as XML in BioSQL Message-ID: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> Hi all, This is cross posted to try and ensure relevant people see it. I suggest we continue the discussion on the BioSQL list (for how to serialise structured annotation to BioSQL), and/or the OpenBio list (for things like file format naming conventions). I am hoping we (Bio*) can be consistent in how we parse and load into BioSQL the SwissProt DE lines (known as "swiss" format in both BioPerl and Biopython's SeqIO, and by EMBOSS) or the equivalent UniProt XML tags (which we are tentatively going to call the "uniprot" format in Biopython's SeqIO - comments?). Like BioPerl (etc), Biopython can parse plain text SwissProt ("swiss") files and load them into BioSQL. Biopython currently treats the DE comment lines as a long string, as BioPerl used to: http://lists.open-bio.org/pipermail/bioperl-l/2009-May/030041.html http://lists.open-bio.org/pipermail/biosql-l/2009-May/001514.html I understand that BioPerl now turns the SwissProt DE lines into a TagTree, and for storing this in BioSQL this gets serialised as XML. I would like Biopython to handle this the same way (although rather than a Perl TagTree, we'd use a Python structure of course), and would appreciate clarification of what exactly was implemented (e.g. which bit of the BioPerl source code should be look at, and could you show a worked example?). Andrea Pierlenoin (CC'd - not sure if he is on the BioSQL or Open-Bio lists yet) has started work on parsing UniProt XML files for Biopython. Here the DE comment lines are already provided broken up with XML markup. Hopefully their nested structure matches what BioPerl was doing with the SwissProt DE lines. Regards, Peter From cjfields at illinois.edu Thu Jan 21 08:34:12 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 21 Jan 2010 07:34:12 -0600 Subject: [BioSQL-l] [Open-bio-l] SwissProt DE lines and UniProt XML / TagTree as XML in BioSQL In-Reply-To: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> References: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> Message-ID: Peter, The relevant code is in Bio::Annotation::TagTree in bioperl-live, which is a decorator for Data::Stag: http://search.cpan.org/~cmungall/Data-Stag-0.11/Data/Stag.pm This is where the text output is derived from. It's a bit of a heavyweight solution to the problem, but it's capable of round-tripping the DE data and parses out the data in a way that's approachable. We could probably abstract out the serialization backend there and allow a pure bioperl solution (or the current solution) as a fallback. If the plain-text DE info is represented in a hierarchy already in UniProt XML, we should probably conform as closely as possible to that (using a standard format like XML, JSON, etc.). chris On Jan 21, 2010, at 6:33 AM, Peter wrote: > Hi all, > > This is cross posted to try and ensure relevant people see it. > I suggest we continue the discussion on the BioSQL list > (for how to serialise structured annotation to BioSQL), and/or > the OpenBio list (for things like file format naming conventions). > > I am hoping we (Bio*) can be consistent in how we parse and load > into BioSQL the SwissProt DE lines (known as "swiss" format in > both BioPerl and Biopython's SeqIO, and by EMBOSS) or the > equivalent UniProt XML tags (which we are tentatively going to > call the "uniprot" format in Biopython's SeqIO - comments?). > > Like BioPerl (etc), Biopython can parse plain text SwissProt ("swiss") > files and load them into BioSQL. Biopython currently treats the DE > comment lines as a long string, as BioPerl used to: > > http://lists.open-bio.org/pipermail/bioperl-l/2009-May/030041.html > http://lists.open-bio.org/pipermail/biosql-l/2009-May/001514.html > > I understand that BioPerl now turns the SwissProt DE lines into a > TagTree, and for storing this in BioSQL this gets serialised as XML. > I would like Biopython to handle this the same way (although rather > than a Perl TagTree, we'd use a Python structure of course), and > would appreciate clarification of what exactly was implemented > (e.g. which bit of the BioPerl source code should be look at, > and could you show a worked example?). > > Andrea Pierlenoin (CC'd - not sure if he is on the BioSQL or > Open-Bio lists yet) has started work on parsing UniProt XML > files for Biopython. Here the DE comment lines are already > provided broken up with XML markup. Hopefully their nested > structure matches what BioPerl was doing with the SwissProt > DE lines. > > Regards, > > Peter From holland at eaglegenomics.com Fri Jan 22 05:51:52 2010 From: holland at eaglegenomics.com (Richard Holland) Date: Fri, 22 Jan 2010 10:51:52 +0000 Subject: [BioSQL-l] SwissProt DE lines and UniProt XML / TagTree as XML in BioSQL In-Reply-To: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> References: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> Message-ID: <8FECCBDE-2DE1-40EE-B5A4-73BDAC893E2D@eaglegenomics.com> Nice idea. Currently, BioJava just stores the complete section as a string without parsing it, but it provides a parser module for converting it into useful tag/value format within a user's program (but not to be stored in BioSQL). On 21 Jan 2010, at 12:33, Peter wrote: > Hi all, > > This is cross posted to try and ensure relevant people see it. > I suggest we continue the discussion on the BioSQL list > (for how to serialise structured annotation to BioSQL), and/or > the OpenBio list (for things like file format naming conventions). > > I am hoping we (Bio*) can be consistent in how we parse and load > into BioSQL the SwissProt DE lines (known as "swiss" format in > both BioPerl and Biopython's SeqIO, and by EMBOSS) or the > equivalent UniProt XML tags (which we are tentatively going to > call the "uniprot" format in Biopython's SeqIO - comments?). > > Like BioPerl (etc), Biopython can parse plain text SwissProt ("swiss") > files and load them into BioSQL. Biopython currently treats the DE > comment lines as a long string, as BioPerl used to: > > http://lists.open-bio.org/pipermail/bioperl-l/2009-May/030041.html > http://lists.open-bio.org/pipermail/biosql-l/2009-May/001514.html > > I understand that BioPerl now turns the SwissProt DE lines into a > TagTree, and for storing this in BioSQL this gets serialised as XML. > I would like Biopython to handle this the same way (although rather > than a Perl TagTree, we'd use a Python structure of course), and > would appreciate clarification of what exactly was implemented > (e.g. which bit of the BioPerl source code should be look at, > and could you show a worked example?). > > Andrea Pierlenoin (CC'd - not sure if he is on the BioSQL or > Open-Bio lists yet) has started work on parsing UniProt XML > files for Biopython. Here the DE comment lines are already > provided broken up with XML markup. Hopefully their nested > structure matches what BioPerl was doing with the SwissProt > DE lines. > > Regards, > > Peter > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andrea at biocomp.unibo.it Fri Jan 22 07:18:32 2010 From: andrea at biocomp.unibo.it (Andrea Pierleoni) Date: Fri, 22 Jan 2010 13:18:32 +0100 (CET) Subject: [BioSQL-l] SwissProt DE lines and UniProt XML / TagTree as XML in BioSQL In-Reply-To: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> References: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> Message-ID: <2b6e30c4628585042366646a7b46386e.squirrel@lipid.biocomp.unibo.it> I think that the point here can be a little broader, since not only the swissprot DE lines carry complex and structured data. To define a common, language-independent way to store structured data into the comment and *_qualifier_value tables of the actual BioSQL schema could be very useful. XML looks like a good candidate to me, and the UniprotXML format can be used as reference or as a template to start from. Each Bio* project will then parse and report this structured data in its own programming language data structure. Andrea > Hi all, > > This is cross posted to try and ensure relevant people see it. > I suggest we continue the discussion on the BioSQL list > (for how to serialise structured annotation to BioSQL), and/or > the OpenBio list (for things like file format naming conventions). > > I am hoping we (Bio*) can be consistent in how we parse and load > into BioSQL the SwissProt DE lines (known as "swiss" format in > both BioPerl and Biopython's SeqIO, and by EMBOSS) or the > equivalent UniProt XML tags (which we are tentatively going to > call the "uniprot" format in Biopython's SeqIO - comments?). > > Like BioPerl (etc), Biopython can parse plain text SwissProt ("swiss") > files and load them into BioSQL. Biopython currently treats the DE > comment lines as a long string, as BioPerl used to: > > http://lists.open-bio.org/pipermail/bioperl-l/2009-May/030041.html > http://lists.open-bio.org/pipermail/biosql-l/2009-May/001514.html > > I understand that BioPerl now turns the SwissProt DE lines into a > TagTree, and for storing this in BioSQL this gets serialised as XML. > I would like Biopython to handle this the same way (although rather > than a Perl TagTree, we'd use a Python structure of course), and > would appreciate clarification of what exactly was implemented > (e.g. which bit of the BioPerl source code should be look at, > and could you show a worked example?). > > Andrea Pierlenoin (CC'd - not sure if he is on the BioSQL or > Open-Bio lists yet) has started work on parsing UniProt XML > files for Biopython. Here the DE comment lines are already > provided broken up with XML markup. Hopefully their nested > structure matches what BioPerl was doing with the SwissProt > DE lines. > > Regards, > > Peter > From chapmanb at 50mail.com Thu Jan 28 15:35:05 2010 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 28 Jan 2010 15:35:05 -0500 Subject: [BioSQL-l] OpenBio solution challenge: Project updates at BOSC 2010 Message-ID: <20100128203505.GG40046@sobchak.mgh.harvard.edu> Hello all; The BOSC 2010 organizing committee is hard at work getting prepared for this July's meeting in Boston: http://www.open-bio.org/wiki/BOSC_2010 One of the items we've traditionally had at the conference is a project update from each of the OpenBio affiliated groups. This year, we're thinking about organizing these talks around a central theme: the OpenBio solution challenge. We start with a biological question of general interest, and each of the project talks would focus around how you would solve that problem using your toolkit and programming language. This is meant to provide a challenge for OpenBio contributors, a nice tutorial style overview of various projects and approaches for other programmers, and a fun opportunity to compete and learn from other projects. Conference attendees will vote on their favorite solution, with the winner receiving fame and fortune (warning: fortune not guaranteed). For this to be successful, it of course requires interest and enthusiasm from y'all fine folks involved with the projects. Specifically: - Is there interest from your group in participating in the challenge? You'll want at least a few people to work on it, and someone to give a presentation at BOSC. - Do you have suggestions on a good theme or specific biological problem to tackle? We'll hope to pick something in a sweet spot that is challenging enough to be of interest, yet reasonable for presentation and preparation. Let's discuss ideas and get this together. Since the schedule for BOSC is developing rapidly, please give us an idea if you're interested by February 12th, and copy responses to the BOSC mailing list as a central place for discussion. bosc at open-bio.org Thanks, Brad, Michael, and the BOSC organizing committee From markw at illuminae.com Thu Jan 28 16:17:44 2010 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 28 Jan 2010 13:17:44 -0800 Subject: [BioSQL-l] [MOBY-dev] OpenBio solution challenge: Project updates at BOSC 2010 In-Reply-To: <20100128203505.GG40046@sobchak.mgh.harvard.edu> References: <20100128203505.GG40046@sobchak.mgh.harvard.edu> Message-ID: Brad, this sounds exciting! One thing strikes me, though - by asking for the sub-projects to propose the "grand challenge" themselves the one thing you can guarantee is that the "grand challenge" is solvable (or more likely, already solved!) Other "grand challenge" kinds of meetings have an independent third party pose the problem that has to be solved, and then all groups work toward a solution and compare their results. This would, IMO, be more revealing of the "state of the art" in each Open-Bio project, and point out where the weaknesses are that we should be focusing on... Someone (for example, you!) could act as the moderator to ensure that the "grand challenge" was at least a reasonable one, within the scope of what an Open-Bio project *should* be able to solve... Just my CAD $0.02 Mark On Thu, 28 Jan 2010 12:35:05 -0800, Brad Chapman wrote: > Hello all; > The BOSC 2010 organizing committee is hard at work getting prepared for > this > July's meeting in Boston: > > http://www.open-bio.org/wiki/BOSC_2010 > > One of the items we've traditionally had at the conference is a project > update from each of the OpenBio affiliated groups. This year, we're > thinking > about organizing these talks around a central theme: the OpenBio solution > challenge. We start with a biological question of general interest, and > each > of the project talks would focus around how you would solve that problem > using your toolkit and programming language. > > This is meant to provide a challenge for OpenBio contributors, a nice > tutorial > style overview of various projects and approaches for other programmers, > and a > fun opportunity to compete and learn from other projects. Conference > attendees > will vote on their favorite solution, with the winner receiving fame and > fortune (warning: fortune not guaranteed). > > For this to be successful, it of course requires interest and enthusiasm > from > y'all fine folks involved with the projects. Specifically: > > - Is there interest from your group in participating in the challenge? > You'll > want at least a few people to work on it, and someone to give a > presentation > at BOSC. > > - Do you have suggestions on a good theme or specific biological problem > to > tackle? We'll hope to pick something in a sweet spot that is > challenging > enough to be of interest, yet reasonable for presentation and > preparation. > > Let's discuss ideas and get this together. Since the schedule for BOSC is > developing rapidly, please give us an idea if you're interested by > February 12th, and copy responses to the BOSC mailing list as a central > place for discussion. > > bosc at open-bio.org > > Thanks, > Brad, Michael, and the BOSC organizing committee > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From HWillis at scripps.edu Thu Jan 28 20:03:10 2010 From: HWillis at scripps.edu (Scooter Willis) Date: Thu, 28 Jan 2010 20:03:10 -0500 Subject: [BioSQL-l] [Biojava-dev] [MOBY-dev] OpenBio solution challenge: Project updates at BOSC 2010 In-Reply-To: References: <20100128203505.GG40046@sobchak.mgh.harvard.edu> Message-ID: <716E205A-5196-409F-A7BC-EF0F52AA997A@scripps.edu> Brad I agree with Mark that a particular problem may be biased towards a toolkit/language. Another approach would be to list a collection of problems and each group would then pick a problem to present. Could be a little more interesting to the audience as you are exposed to different problems and the various strengths of each toolkit. This could also help guide future development in the other toolkits as you would benefit from learning about the api and/or programming language. Each group would register a problem that they are going to present. From the group of problems not picked that becomes the surprise challenge where each group has 24 hours to either put together a presentation or an actual solution. Scooter On Jan 28, 2010, at 4:17 PM, Mark Wilkinson wrote: > > Brad, this sounds exciting! > > One thing strikes me, though - by asking for the sub-projects to propose > the "grand challenge" themselves the one thing you can guarantee is that > the "grand challenge" is solvable (or more likely, already solved!) > > Other "grand challenge" kinds of meetings have an independent third party > pose the problem that has to be solved, and then all groups work toward a > solution and compare their results. This would, IMO, be more revealing of > the "state of the art" in each Open-Bio project, and point out where the > weaknesses are that we should be focusing on... Someone (for example, > you!) could act as the moderator to ensure that the "grand challenge" was > at least a reasonable one, within the scope of what an Open-Bio project > *should* be able to solve... > > Just my CAD $0.02 > > Mark > > > > On Thu, 28 Jan 2010 12:35:05 -0800, Brad Chapman > wrote: > >> Hello all; >> The BOSC 2010 organizing committee is hard at work getting prepared for >> this >> July's meeting in Boston: >> >> http://www.open-bio.org/wiki/BOSC_2010 >> >> One of the items we've traditionally had at the conference is a project >> update from each of the OpenBio affiliated groups. This year, we're >> thinking >> about organizing these talks around a central theme: the OpenBio solution >> challenge. We start with a biological question of general interest, and >> each >> of the project talks would focus around how you would solve that problem >> using your toolkit and programming language. >> >> This is meant to provide a challenge for OpenBio contributors, a nice >> tutorial >> style overview of various projects and approaches for other programmers, >> and a >> fun opportunity to compete and learn from other projects. Conference >> attendees >> will vote on their favorite solution, with the winner receiving fame and >> fortune (warning: fortune not guaranteed). >> >> For this to be successful, it of course requires interest and enthusiasm >> from >> y'all fine folks involved with the projects. Specifically: >> >> - Is there interest from your group in participating in the challenge? >> You'll >> want at least a few people to work on it, and someone to give a >> presentation >> at BOSC. >> >> - Do you have suggestions on a good theme or specific biological problem >> to >> tackle? We'll hope to pick something in a sweet spot that is >> challenging >> enough to be of interest, yet reasonable for presentation and >> preparation. >> >> Let's discuss ideas and get this together. Since the schedule for BOSC is >> developing rapidly, please give us an idea if you're interested by >> February 12th, and copy responses to the BOSC mailing list as a central >> place for discussion. >> >> bosc at open-bio.org >> >> Thanks, >> Brad, Michael, and the BOSC organizing committee >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > -- > Mark D Wilkinson, PI Bioinformatics > Assistant Professor, Medical Genetics > The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research > Providence Heart + Lung Institute > University of British Columbia - St. Paul's Hospital > Vancouver, BC, Canada > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev From biopython at maubp.freeserve.co.uk Fri Jan 29 05:36:40 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 29 Jan 2010 10:36:40 +0000 Subject: [BioSQL-l] [Bioperl-l] [MOBY-dev] OpenBio solution challenge: Project updates at BOSC 2010 In-Reply-To: References: <20100128203505.GG40046@sobchak.mgh.harvard.edu> Message-ID: <320fb6e01001290236l1ad02515w403a19f94dbb6d15@mail.gmail.com> Hi all, This is a great topic but should be continue it on just the one mailing list? Is there a suitable BOSC list, or how about the general Open Bio list? On Thu, Jan 28, 2010 at 9:17 PM, Mark Wilkinson wrote: > > Brad, this sounds exciting! > > One thing strikes me, though - by asking for the sub-projects to propose > the "grand challenge" themselves the one thing you can guarantee is that > the "grand challenge" is solvable (or more likely, already solved!) > > Other "grand challenge" kinds of meetings have an independent third party > pose the problem that has to be solved, and then all groups work toward a > solution and compare their results. ?This would, IMO, be more revealing of > the "state of the art" in each Open-Bio project, and point out where the > weaknesses are that we should be focusing on... ?Someone (for example, > you!) could act as the moderator to ensure that the "grand challenge" was > at least a reasonable one, within the scope of what an Open-Bio project > *should* be able to solve... > > Just my CAD $0.02 > > Mark One possible problem with having Brad act as moderator is his ties to Biopython (plus it would be a shame if we'd be one man down for trying to solve the challenges - grin). Having a project representative "sign off" on the challenge might work - or simply the whole of the BOSC committee which is quite balanced. Alternatively some kind of panel of challenges does seem a good way to reduce individual project bias (as suggest by Scooter), but there will still need to be a judging committee. I'm curious what kind of challenges the BOSC committee had in mind - would something like taking a newly sequence bacteria and producing an automated annotation as a GenBank, EMBL, or GFF file be too ambitious for example? There are already several major projects to do this e.g. RAST http://rast.nmpdr.org/ Peter (@Biopython) From hlapp at drycafe.net Thu Jan 7 15:49:39 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Thu, 7 Jan 2010 10:49:39 -0500 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: References: Message-ID: <1919B039-6F77-412B-8984-9B8EC956BABD@drycafe.net> Hi Amy, this looks like a problem with installing DBD::mysql, not BioSQL. I don't know how you built DBD::mysql and DBI, and I haven't encountered this error (but maybe someone else on the BioSQL list has come across this?), so your best avenue for getting help is probably the DBD::mysql mailing list. Cheers, -hilmar On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: > Dear Hilmar, > > Happy New Year! I hope you had enjoyable holidays. So, my sys admin > colleague and I are trying to get BioSQL (with a BioPerl language > binding) > up and running ASAP. > > We have successfully installed MySQL and BioPerl. We are having > trouble, > however, getting the DBD::mysql module installed (on a Macbook Pro > running > OS X 10.6.1) to finish the last steps of BioSQL installation. The > error > message for our attempt is pasted below. We have also attempted a > manual > install, and get the same result (i.e., croaking at the make test > step)-failed installation. > > Would you please guide us through the necessary final steps in getting > BioSQL up and running? Any help you can provide would be greatly > appreciated. Thanks very much and I look forward to hearing from you. > Sincerely, AJP > > > [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] > > cpan[1]> install Bundle::DBD::mysql > CPAN: Storable loaded ok (v2.21) > Going to read '/var/root/.cpan/Metadata' > Database was generated on Wed, 06 Jan 2010 09:01:01 GMT > CPAN: YAML loaded ok (v0.70) > Going to read 52 yaml files from /var/root/.cpan/build/ > CPAN: Time::HiRes loaded ok (v1.9711) > DONE > Restored the state of none (in 1.1851 secs) > Has already been unwrapped into directory > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > DBI is up to date (1.609). > Running install for module 'DBD::mysql' > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > Has already been unwrapped into directory > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > Has already been made > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/00base.t .................. 1/6 > # Failed test 'use DBD::mysql;' > # at t/00base.t line 21. > # Tried to use 'DBD::mysql'. > # Error: Can't load > '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ > DBD/mys > ql/mysql.bundle' for module DBD::mysql: > dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ > arch/auto/D > BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix > # Referenced from: > /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ > DBD/mysq > l/mysql.bundle > # Expected in: flat namespace > # in > /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ > DBD/mysq > l/mysql.bundle at > /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm > line > 207. > # at (eval 7) line 2 > # Compilation failed in require at (eval 7) line 2. > # BEGIN failed--compilation aborted at (eval 7) line 2. > Bailout called. Further testing stopped: Unable to load DBD::mysql > FAILED--Further testing stopped: Unable to load DBD::mysql > make: *** [test_dynamic] Error 255 > CAPTTOFU/DBD-mysql-4.013.tar.gz > make test -- NOT OK > //hint// to see the cpan-testers results for installing this module, > try: > reports CAPTTOFU/DBD-mysql-4.013.tar.gz > Running make install > make test had returned bad status, won't install without force > Failed during this command: > CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From maj at fortinbras.us Thu Jan 7 16:08:20 2010 From: maj at fortinbras.us (Mark A. Jensen) Date: Thu, 7 Jan 2010 11:08:20 -0500 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: <1919B039-6F77-412B-8984-9B8EC956BABD@drycafe.net> References: <1919B039-6F77-412B-8984-9B8EC956BABD@drycafe.net> Message-ID: <9F6B6EB3FA7E4C0C8F9471F17F249A09@NewLife> This portion > Running install for module 'DBD::mysql' > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > Has already been unwrapped into directory > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > Has already been made > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/00base.t .................. 1/6 > # Failed test 'use DBD::mysql;' > # at t/00base.t line 21. > # Tried to use 'DBD::mysql'. > # Error: Can't load suggests that, though DBD::mysql was made, the module can't be found by perl (is not in @INC). You could try installing from scratch again cpan> fforce install DBD::mysql The other issue may be that your mysql installation can't be found or encounters an error when DBD::mysql is loaded. Try at the command line $ perl -MDBD::mysql -e 1 and see if any more helpful errors ensue. MAJ ----- Original Message ----- From: "Hilmar Lapp" To: "Powell Phd, Amy Jo" Cc: "biosql-l" ; "Bolin,Samuel" Sent: Thursday, January 07, 2010 10:49 AM Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies > Hi Amy, > > this looks like a problem with installing DBD::mysql, not BioSQL. I don't > know how you built DBD::mysql and DBI, and I haven't encountered this error > (but maybe someone else on the BioSQL list has come across this?), so your > best avenue for getting help is probably the DBD::mysql mailing list. > > Cheers, > > -hilmar > > On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: > >> Dear Hilmar, >> >> Happy New Year! I hope you had enjoyable holidays. So, my sys admin >> colleague and I are trying to get BioSQL (with a BioPerl language binding) >> up and running ASAP. >> >> We have successfully installed MySQL and BioPerl. We are having trouble, >> however, getting the DBD::mysql module installed (on a Macbook Pro running >> OS X 10.6.1) to finish the last steps of BioSQL installation. The error >> message for our attempt is pasted below. We have also attempted a manual >> install, and get the same result (i.e., croaking at the make test >> step)-failed installation. >> >> Would you please guide us through the necessary final steps in getting >> BioSQL up and running? Any help you can provide would be greatly >> appreciated. Thanks very much and I look forward to hearing from you. >> Sincerely, AJP >> >> >> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] >> >> cpan[1]> install Bundle::DBD::mysql >> CPAN: Storable loaded ok (v2.21) >> Going to read '/var/root/.cpan/Metadata' >> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT >> CPAN: YAML loaded ok (v0.70) >> Going to read 52 yaml files from /var/root/.cpan/build/ >> CPAN: Time::HiRes loaded ok (v1.9711) >> DONE >> Restored the state of none (in 1.1851 secs) >> Has already been unwrapped into directory >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >> DBI is up to date (1.609). >> Running install for module 'DBD::mysql' >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> Has already been unwrapped into directory >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >> Has already been made >> Running make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/00base.t .................. 1/6 >> # Failed test 'use DBD::mysql;' >> # at t/00base.t line 21. >> # Tried to use 'DBD::mysql'. >> # Error: Can't load >> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ DBD/mys >> ql/mysql.bundle' for module DBD::mysql: >> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ arch/auto/D >> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix >> # Referenced from: >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ DBD/mysq >> l/mysql.bundle >> # Expected in: flat namespace >> # in >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/auto/ DBD/mysq >> l/mysql.bundle at >> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/DynaLoader.pm line >> 207. >> # at (eval 7) line 2 >> # Compilation failed in require at (eval 7) line 2. >> # BEGIN failed--compilation aborted at (eval 7) line 2. >> Bailout called. Further testing stopped: Unable to load DBD::mysql >> FAILED--Further testing stopped: Unable to load DBD::mysql >> make: *** [test_dynamic] Error 255 >> CAPTTOFU/DBD-mysql-4.013.tar.gz >> make test -- NOT OK >> //hint// to see the cpan-testers results for installing this module, try: >> reports CAPTTOFU/DBD-mysql-4.013.tar.gz >> Running make install >> make test had returned bad status, won't install without force >> Failed during this command: >> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO >> >> > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > > From biopython at maubp.freeserve.co.uk Wed Jan 13 11:37:59 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 13 Jan 2010 11:37:59 +0000 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> Message-ID: <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com> On Thu, Dec 10, 2009 at 3:03 PM, Peter wrote: > > Brad and I are hoping to include BioSQL on SQLite support in the > imminent release of Biopython 1.53, although we will stress in the > release notes that this (and the schema) is still experimental. > > For this initial release, the user probably still have to manually > create the SQLite database - this is something I hope we can make > much more user friendly in the subsequent releases of Biopython > (taking advantage of the fact the SQLite is included with Python 2.5 > onwards, so we can do this without any external dependencies). > > Peter > > See also: > http://bugzilla.open-bio.org/show_bug.cgi?id=2870 > http://bugzilla.open-bio.org/show_bug.cgi?id=2866 > To keep you guys informed, we released Biopython 1.53 at the end of 2009, and this did include BioSQL on SQLite support based on the draft schema: http://news.open-bio.org/news/2009/12/biopython-release-153/ Even if a BioSQL v1.0.2 release isn't imminent, could the draft SQLite schema be checked into BioSQL's SVN repository please? Repository link to see the file (currently no revisions): http://github.com/biopython/biopython/blob/master/Tests/BioSQL/biosqldb-sqlite.sql Alternatively you can grab the file here: http://biopython.open-bio.org/SRC/biopython/Tests/BioSQL/biosqldb-sqlite.sql (updated hourly, not that we have any revisions planned) As I said before, we'd like to make using BioSQL on SQLite from within Biopython much easier (because unlike the other database back ends, it is *very* simple to create or delete a new SQLite database). This would require us to install a copy of the schema as part of Biopython (currently we just include a copy used for unit tests), so the sooner the schema becomes "official", the better. Regards, Peter From sabolin at sandia.gov Wed Jan 13 16:22:03 2010 From: sabolin at sandia.gov (Bolin, Samuel) Date: Wed, 13 Jan 2010 09:22:03 -0700 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: References: <9F6B6EB3FA7E4C0C8F9471F17F249A09@NewLife> Message-ID: <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> Mark and Hilmar I am working with Amy Powell on getting BioSQL up and running Decided to take a different tact and am now using Fedora Was able to get MySQL BioPerl installed along with getting past the DBD and DBI issues However I have read thru the documentation and have been unable to figure out how BioSQL ties in must less get it installed Any guidance? Sammy From: Powell Phd, Amy Jo Sent: Thursday, January 07, 2010 10:29 AM To: Mark A. Jensen; Hilmar Lapp Cc: biosql-l; Bolin, Samuel Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies Hi there- Thanks very much for your suggestion. We?ll give it a try and see what happens. Sincerely, AJP On 1/7/10 9:08 AM, "Mark A. Jensen" wrote: This portion > Running install for module 'DBD::mysql' > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > Has already been unwrapped into directory > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > Has already been made > Running make test > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > t/00base.t .................. 1/6 > # Failed test 'use DBD::mysql;' > # at t/00base.t line 21. > # Tried to use 'DBD::mysql'. > # Error: Can't load suggests that, though DBD::mysql was made, the module can't be found by perl (is not in @INC). You could try installing from scratch again cpan> fforce install DBD::mysql The other issue may be that your mysql installation can't be found or encounters an error when DBD::mysql is loaded. Try at the command line $ perl -MDBD::mysql -e 1 and see if any more helpful errors ensue. MAJ ----- Original Message ----- From: "Hilmar Lapp" To: "Powell Phd, Amy Jo" Cc: "biosql-l" ; "Bolin,Samuel" Sent: Thursday, January 07, 2010 10:49 AM Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies > Hi Amy, > > this looks like a problem with installing DBD::mysql, not BioSQL. I don't > know how you built DBD::mysql and DBI, and I haven't encountered this error > (but maybe someone else on the BioSQL list has come across this?), so your > best avenue for getting help is probably the DBD::mysql mailing list. > > Cheers, > > -hilmar > > On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: > >> Dear Hilmar, >> >> Happy New Year! I hope you had enjoyable holidays. So, my sys admin >> colleague and I are trying to get BioSQL (with a BioPerl language binding) >> up and running ASAP. >> >> We have successfully installed MySQL and BioPerl. We are having trouble, >> however, getting the DBD::mysql module installed (on a Macbook Pro running >> OS X 10.6.1) to finish the last steps of BioSQL installation. The error >> message for our attempt is pasted below. We have also attempted a manual >> install, and get the same result (i.e., croaking at the make test >> step)-failed installation. >> >> Would you please guide us through the necessary final steps in getting >> BioSQL up and running? Any help you can provide would be greatly >> appreciated. Thanks very much and I look forward to hearing from you. >> Sincerely, AJP >> >> >> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] >> >> cpan[1]> install Bundle::DBD::mysql >> CPAN: Storable loaded ok (v2.21) >> Going to read '/var/root/.cpan/Metadata' >> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT >> CPAN: YAML loaded ok (v0.70) >> Going to read 52 yaml files from /var/root/.cpan/build/ >> CPAN: Time::HiRes loaded ok (v1.9711) >> DONE >> Restored the state of none (in 1.1851 secs) >> Has already been unwrapped into directory >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >> DBI is up to date (1.609). >> Running install for module 'DBD::mysql' >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> Has already been unwrapped into directory >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >> Has already been made >> Running make test >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >> t/00base.t .................. 1/6 >> # Failed test 'use DBD::mysql;' >> # at t/00base.t line 21. >> # Tried to use 'DBD::mysql'. >> # Error: Can't load >> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ auto/ DBD/mys >> ql/mysql.bundle' for module DBD::mysql: >> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ arch/auto/D >> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix >> # Referenced from: >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ auto/ DBD/mysq >> l/mysql.bundle >> # Expected in: flat namespace >> # in >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ auto/ DBD/mysq >> l/mysql.bundle at >> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/ DynaLoader.pm line >> 207. >> # at (eval 7) line 2 >> # Compilation failed in require at (eval 7) line 2. >> # BEGIN failed--compilation aborted at (eval 7) line 2. >> Bailout called. Further testing stopped: Unable to load DBD::mysql >> FAILED--Further testing stopped: Unable to load DBD::mysql >> make: *** [test_dynamic] Error 255 >> CAPTTOFU/DBD-mysql-4.013.tar.gz >> make test -- NOT OK >> //hint// to see the cpan-testers results for installing this module, try: >> reports CAPTTOFU/DBD-mysql-4.013.tar.gz >> Running make install >> make test had returned bad status, won't install without force >> Failed during this command: >> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO >> >> > > -- > =========================================================== > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > =========================================================== > > > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l > > From hlapp at drycafe.net Wed Jan 13 17:03:06 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 13 Jan 2010 12:03:06 -0500 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> References: <9F6B6EB3FA7E4C0C8F9471F17F249A09@NewLife> <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> Message-ID: <1DD26F99-82AE-4279-A0D7-D3CD5A1352D7@drycafe.net> Hi Sammy, please always On Jan 13, 2010, at 11:22 AM, Bolin, Samuel wrote: > Mark and Hilmar > > I am working with Amy Powell on getting BioSQL up and running > Decided to take a different tact and am now using Fedora > Was able to get MySQL BioPerl installed along with getting past the > DBD and DBI issues > However I have read thru the documentation and have been unable to > figure out how BioSQL ties in must less get it installed > Any guidance? > > Sammy > > From: Powell Phd, Amy Jo > Sent: Thursday, January 07, 2010 10:29 AM > To: Mark A. Jensen; Hilmar Lapp > Cc: biosql-l; Bolin, Samuel > Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) > dependencies > > Hi there- > > Thanks very much for your suggestion. We?ll give it a try and see > what happens. Sincerely, AJP > > > On 1/7/10 9:08 AM, "Mark A. Jensen" wrote: > > This portion > > > Running install for module 'DBD::mysql' > > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > > Has already been unwrapped into directory > > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > > Has already been made > > Running make test > > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > > t/00base.t .................. 1/6 > > # Failed test 'use DBD::mysql;' > > # at t/00base.t line 21. > > # Tried to use 'DBD::mysql'. > > # Error: Can't load > > suggests that, though DBD::mysql was made, the module can't be > found by perl (is not in @INC). You could try installing from scratch > again > > cpan> fforce install DBD::mysql > > The other issue may be that your mysql installation can't be found > or encounters > an error when > DBD::mysql is loaded. Try at the command line > > $ perl -MDBD::mysql -e 1 > > and see if any more helpful errors ensue. > > MAJ > > ----- Original Message ----- > From: "Hilmar Lapp" > To: "Powell Phd, Amy Jo" > Cc: "biosql-l" ; "Bolin,Samuel" > > Sent: Thursday, January 07, 2010 10:49 AM > Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) > dependencies > > > > Hi Amy, > > > > this looks like a problem with installing DBD::mysql, not BioSQL. > I don't > > know how you built DBD::mysql and DBI, and I haven't encountered > this error > > (but maybe someone else on the BioSQL list has come across > this?), so your > > best avenue for getting help is probably the DBD::mysql mailing > list. > > > > Cheers, > > > > -hilmar > > > > On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: > > > >> Dear Hilmar, > >> > >> Happy New Year! I hope you had enjoyable holidays. So, my sys > admin > >> colleague and I are trying to get BioSQL (with a BioPerl > language binding) > >> up and running ASAP. > >> > >> We have successfully installed MySQL and BioPerl. We are having > trouble, > >> however, getting the DBD::mysql module installed (on a Macbook > Pro running > >> OS X 10.6.1) to finish the last steps of BioSQL installation. > The error > >> message for our attempt is pasted below. We have also attempted > a manual > >> install, and get the same result (i.e., croaking at the make test > >> step)-failed installation. > >> > >> Would you please guide us through the necessary final steps in > getting > >> BioSQL up and running? Any help you can provide would be greatly > >> appreciated. Thanks very much and I look forward to hearing from > you. > >> Sincerely, AJP > >> > >> > >> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] > >> > >> cpan[1]> install Bundle::DBD::mysql > >> CPAN: Storable loaded ok (v2.21) > >> Going to read '/var/root/.cpan/Metadata' > >> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT > >> CPAN: YAML loaded ok (v0.70) > >> Going to read 52 yaml files from /var/root/.cpan/build/ > >> CPAN: Time::HiRes loaded ok (v1.9711) > >> DONE > >> Restored the state of none (in 1.1851 secs) > >> Has already been unwrapped into directory > >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > >> DBI is up to date (1.609). > >> Running install for module 'DBD::mysql' > >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > >> Has already been unwrapped into directory > >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > >> Has already been made > >> Running make test > >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > >> t/00base.t .................. 1/6 > >> # Failed test 'use DBD::mysql;' > >> # at t/00base.t line 21. > >> # Tried to use 'DBD::mysql'. > >> # Error: Can't load > >> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mys > >> ql/mysql.bundle' for module DBD::mysql: > >> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ > arch/auto/D > >> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix > >> # Referenced from: > >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mysq > >> l/mysql.bundle > >> # Expected in: flat namespace > >> # in > >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mysq > >> l/mysql.bundle at > >> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/ > DynaLoader.pm line > >> 207. > >> # at (eval 7) line 2 > >> # Compilation failed in require at (eval 7) line 2. > >> # BEGIN failed--compilation aborted at (eval 7) line 2. > >> Bailout called. Further testing stopped: Unable to load > DBD::mysql > >> FAILED--Further testing stopped: Unable to load DBD::mysql > >> make: *** [test_dynamic] Error 255 > >> CAPTTOFU/DBD-mysql-4.013.tar.gz > >> make test -- NOT OK > >> //hint// to see the cpan-testers results for installing this > module, try: > >> reports CAPTTOFU/DBD-mysql-4.013.tar.gz > >> Running make install > >> make test had returned bad status, won't install without force > >> Failed during this command: > >> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO > >> > >> > > > > -- > > =========================================================== > > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > > =========================================================== > > > > > > > > > > _______________________________________________ > > 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 drycafe dot net : =========================================================== From hlapp at drycafe.net Wed Jan 13 17:04:48 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 13 Jan 2010 12:04:48 -0500 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> References: <9F6B6EB3FA7E4C0C8F9471F17F249A09@NewLife> <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> Message-ID: <686C367C-A9E3-44E9-BC71-EA18A1C84CBD@drycafe.net> (hit send erroneously ...) Hi Sammy, please always direct your questions to the mailing list. There are many more people there who can help you out. Have you looked at the INSTALL file that comes with BioSQL and tried to follow the instructions therein? If yes, what did you find not to work? -hilmar On Jan 13, 2010, at 11:22 AM, Bolin, Samuel wrote: > Mark and Hilmar > > I am working with Amy Powell on getting BioSQL up and running > Decided to take a different tact and am now using Fedora > Was able to get MySQL BioPerl installed along with getting past the > DBD and DBI issues > However I have read thru the documentation and have been unable to > figure out how BioSQL ties in must less get it installed > Any guidance? > > Sammy > > From: Powell Phd, Amy Jo > Sent: Thursday, January 07, 2010 10:29 AM > To: Mark A. Jensen; Hilmar Lapp > Cc: biosql-l; Bolin, Samuel > Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) > dependencies > > Hi there- > > Thanks very much for your suggestion. We?ll give it a try and see > what happens. Sincerely, AJP > > > On 1/7/10 9:08 AM, "Mark A. Jensen" wrote: > > This portion > > > Running install for module 'DBD::mysql' > > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > > Has already been unwrapped into directory > > /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > > Has already been made > > Running make test > > PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > > "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > > t/00base.t .................. 1/6 > > # Failed test 'use DBD::mysql;' > > # at t/00base.t line 21. > > # Tried to use 'DBD::mysql'. > > # Error: Can't load > > suggests that, though DBD::mysql was made, the module can't be > found by perl (is not in @INC). You could try installing from scratch > again > > cpan> fforce install DBD::mysql > > The other issue may be that your mysql installation can't be found > or encounters > an error when > DBD::mysql is loaded. Try at the command line > > $ perl -MDBD::mysql -e 1 > > and see if any more helpful errors ensue. > > MAJ > > ----- Original Message ----- > From: "Hilmar Lapp" > To: "Powell Phd, Amy Jo" > Cc: "biosql-l" ; "Bolin,Samuel" > > Sent: Thursday, January 07, 2010 10:49 AM > Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) > dependencies > > > > Hi Amy, > > > > this looks like a problem with installing DBD::mysql, not BioSQL. > I don't > > know how you built DBD::mysql and DBI, and I haven't encountered > this error > > (but maybe someone else on the BioSQL list has come across > this?), so your > > best avenue for getting help is probably the DBD::mysql mailing > list. > > > > Cheers, > > > > -hilmar > > > > On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: > > > >> Dear Hilmar, > >> > >> Happy New Year! I hope you had enjoyable holidays. So, my sys > admin > >> colleague and I are trying to get BioSQL (with a BioPerl > language binding) > >> up and running ASAP. > >> > >> We have successfully installed MySQL and BioPerl. We are having > trouble, > >> however, getting the DBD::mysql module installed (on a Macbook > Pro running > >> OS X 10.6.1) to finish the last steps of BioSQL installation. > The error > >> message for our attempt is pasted below. We have also attempted > a manual > >> install, and get the same result (i.e., croaking at the make test > >> step)-failed installation. > >> > >> Would you please guide us through the necessary final steps in > getting > >> BioSQL up and running? Any help you can provide would be greatly > >> appreciated. Thanks very much and I look forward to hearing from > you. > >> Sincerely, AJP > >> > >> > >> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] > >> > >> cpan[1]> install Bundle::DBD::mysql > >> CPAN: Storable loaded ok (v2.21) > >> Going to read '/var/root/.cpan/Metadata' > >> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT > >> CPAN: YAML loaded ok (v0.70) > >> Going to read 52 yaml files from /var/root/.cpan/build/ > >> CPAN: Time::HiRes loaded ok (v1.9711) > >> DONE > >> Restored the state of none (in 1.1851 secs) > >> Has already been unwrapped into directory > >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > >> DBI is up to date (1.609). > >> Running install for module 'DBD::mysql' > >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > >> Has already been unwrapped into directory > >> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL > >> Has already been made > >> Running make test > >> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" > >> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t > >> t/00base.t .................. 1/6 > >> # Failed test 'use DBD::mysql;' > >> # at t/00base.t line 21. > >> # Tried to use 'DBD::mysql'. > >> # Error: Can't load > >> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mys > >> ql/mysql.bundle' for module DBD::mysql: > >> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ > arch/auto/D > >> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix > >> # Referenced from: > >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mysq > >> l/mysql.bundle > >> # Expected in: flat namespace > >> # in > >> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ > auto/ DBD/mysq > >> l/mysql.bundle at > >> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/ > DynaLoader.pm line > >> 207. > >> # at (eval 7) line 2 > >> # Compilation failed in require at (eval 7) line 2. > >> # BEGIN failed--compilation aborted at (eval 7) line 2. > >> Bailout called. Further testing stopped: Unable to load > DBD::mysql > >> FAILED--Further testing stopped: Unable to load DBD::mysql > >> make: *** [test_dynamic] Error 255 > >> CAPTTOFU/DBD-mysql-4.013.tar.gz > >> make test -- NOT OK > >> //hint// to see the cpan-testers results for installing this > module, try: > >> reports CAPTTOFU/DBD-mysql-4.013.tar.gz > >> Running make install > >> make test had returned bad status, won't install without force > >> Failed during this command: > >> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO > >> > >> > > > > -- > > =========================================================== > > : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : > > =========================================================== > > > > > > > > > > _______________________________________________ > > 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 drycafe dot net : =========================================================== From hlapp at drycafe.net Wed Jan 13 17:21:13 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Wed, 13 Jan 2010 12:21:13 -0500 Subject: [BioSQL-l] Help installing BioSQL and its (Perl) dependencies In-Reply-To: <51677525E6912B4FA646302AD6D1D78C80F9810C17@ES03SNLNT.srn.sandia.gov> References: <9F6B6EB3FA7E4C0C8F9471F17F249A09@NewLife> <51677525E6912B4FA646302AD6D1D78C80F9810C13@ES03SNLNT.srn.sandia.gov> <686C367C-A9E3-44E9-BC71-EA18A1C84CBD@drycafe.net> <51677525E6912B4FA646302AD6D1D78C80F9810C17@ES03SNLNT.srn.sandia.gov> Message-ID: Sammy - please always keep the list copied. Links to and documentation for downloads are at http://biosql.org. Specifically look for the section titled 'Downloads'. -hilmar On Jan 13, 2010, at 12:09 PM, Bolin, Samuel wrote: > I have not looked at the install file as I am unable to find a > biosql package/rpm/tar etc > Could you point me in the direction of that, I am working off of > instructions given to me by amy > > -----Original Message----- > From: Hilmar Lapp [mailto:hlapp at drycafe.net] > Sent: Wednesday, January 13, 2010 10:05 AM > To: Bolin, Samuel > Cc: Mark A. Jensen; biosql-l > Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) > dependencies > > (hit send erroneously ...) > > Hi Sammy, > > please always direct your questions to the mailing list. There are > many more people there who can help you out. > > Have you looked at the INSTALL file that comes with BioSQL and tried > to follow the instructions therein? If yes, what did you find not to > work? > > -hilmar > > On Jan 13, 2010, at 11:22 AM, Bolin, Samuel wrote: > >> Mark and Hilmar >> >> I am working with Amy Powell on getting BioSQL up and running >> Decided to take a different tact and am now using Fedora >> Was able to get MySQL BioPerl installed along with getting past the >> DBD and DBI issues >> However I have read thru the documentation and have been unable to >> figure out how BioSQL ties in must less get it installed >> Any guidance? >> >> Sammy >> >> From: Powell Phd, Amy Jo >> Sent: Thursday, January 07, 2010 10:29 AM >> To: Mark A. Jensen; Hilmar Lapp >> Cc: biosql-l; Bolin, Samuel >> Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) >> dependencies >> >> Hi there- >> >> Thanks very much for your suggestion. We'll give it a try and see >> what happens. Sincerely, AJP >> >> >> On 1/7/10 9:08 AM, "Mark A. Jensen" wrote: >> >> This portion >> >>> Running install for module 'DBD::mysql' >>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> Has already been unwrapped into directory >>> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >>> Has already been made >>> Running make test >>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >>> t/00base.t .................. 1/6 >>> # Failed test 'use DBD::mysql;' >>> # at t/00base.t line 21. >>> # Tried to use 'DBD::mysql'. >>> # Error: Can't load >> >> suggests that, though DBD::mysql was made, the module can't be >> found by perl (is not in @INC). You could try installing from scratch >> again >> >> cpan> fforce install DBD::mysql >> >> The other issue may be that your mysql installation can't be found >> or encounters >> an error when >> DBD::mysql is loaded. Try at the command line >> >> $ perl -MDBD::mysql -e 1 >> >> and see if any more helpful errors ensue. >> >> MAJ >> >> ----- Original Message ----- >> From: "Hilmar Lapp" >> To: "Powell Phd, Amy Jo" >> Cc: "biosql-l" ; "Bolin,Samuel" >> >> Sent: Thursday, January 07, 2010 10:49 AM >> Subject: Re: [BioSQL-l] Help installing BioSQL and its (Perl) >> dependencies >> >> >>> Hi Amy, >>> >>> this looks like a problem with installing DBD::mysql, not BioSQL. >> I don't >>> know how you built DBD::mysql and DBI, and I haven't encountered >> this error >>> (but maybe someone else on the BioSQL list has come across >> this?), so your >>> best avenue for getting help is probably the DBD::mysql mailing >> list. >>> >>> Cheers, >>> >>> -hilmar >>> >>> On Jan 6, 2010, at 6:19 PM, Powell Phd, Amy Jo wrote: >>> >>>> Dear Hilmar, >>>> >>>> Happy New Year! I hope you had enjoyable holidays. So, my sys >> admin >>>> colleague and I are trying to get BioSQL (with a BioPerl >> language binding) >>>> up and running ASAP. >>>> >>>> We have successfully installed MySQL and BioPerl. We are having >> trouble, >>>> however, getting the DBD::mysql module installed (on a Macbook >> Pro running >>>> OS X 10.6.1) to finish the last steps of BioSQL installation. >> The error >>>> message for our attempt is pasted below. We have also attempted >> a manual >>>> install, and get the same result (i.e., croaking at the make test >>>> step)-failed installation. >>>> >>>> Would you please guide us through the necessary final steps in >> getting >>>> BioSQL up and running? Any help you can provide would be greatly >>>> appreciated. Thanks very much and I look forward to hearing from >> you. >>>> Sincerely, AJP >>>> >>>> >>>> [ERROR MESSAGE RESULTING FROM ATTEMPTED CPAN INSTALLATION] >>>> >>>> cpan[1]> install Bundle::DBD::mysql >>>> CPAN: Storable loaded ok (v2.21) >>>> Going to read '/var/root/.cpan/Metadata' >>>> Database was generated on Wed, 06 Jan 2010 09:01:01 GMT >>>> CPAN: YAML loaded ok (v0.70) >>>> Going to read 52 yaml files from /var/root/.cpan/build/ >>>> CPAN: Time::HiRes loaded ok (v1.9711) >>>> DONE >>>> Restored the state of none (in 1.1851 secs) >>>> Has already been unwrapped into directory >>>> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >>>> DBI is up to date (1.609). >>>> Running install for module 'DBD::mysql' >>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> Has already been unwrapped into directory >>>> /var/root/.cpan/build/DBD-mysql-4.013-PBkPmL >>>> Has already been made >>>> Running make test >>>> PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" >>>> "test_harness(0, 'blib/lib', 'blib/arch')" t/*.t >>>> t/00base.t .................. 1/6 >>>> # Failed test 'use DBD::mysql;' >>>> # at t/00base.t line 21. >>>> # Tried to use 'DBD::mysql'. >>>> # Error: Can't load >>>> '/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ >> auto/ DBD/mys >>>> ql/mysql.bundle' for module DBD::mysql: >>>> dlopen(/private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/ >> arch/auto/D >>>> BD/mysql/mysql.bundle, 2): Symbol not found: _is_prefix >>>> # Referenced from: >>>> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ >> auto/ DBD/mysq >>>> l/mysql.bundle >>>> # Expected in: flat namespace >>>> # in >>>> /private/var/root/.cpan/build/DBD-mysql-4.013-PBkPmL/blib/arch/ >> auto/ DBD/mysq >>>> l/mysql.bundle at >>>> /System/Library/Perl/5.10.0/darwin-thread-multi-2level/ >> DynaLoader.pm line >>>> 207. >>>> # at (eval 7) line 2 >>>> # Compilation failed in require at (eval 7) line 2. >>>> # BEGIN failed--compilation aborted at (eval 7) line 2. >>>> Bailout called. Further testing stopped: Unable to load >> DBD::mysql >>>> FAILED--Further testing stopped: Unable to load DBD::mysql >>>> make: *** [test_dynamic] Error 255 >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> make test -- NOT OK >>>> //hint// to see the cpan-testers results for installing this >> module, try: >>>> reports CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> Running make install >>>> make test had returned bad status, won't install without force >>>> Failed during this command: >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz : make_test NO >>>> >>>> >>> >>> -- >>> =========================================================== >>> : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : >>> =========================================================== >>> >>> >>> >>> >>> _______________________________________________ >>> 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 drycafe dot net : > =========================================================== > > > > > > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net : =========================================================== From hlapp at gmx.net Wed Jan 13 17:06:39 2010 From: hlapp at gmx.net (Hilmar Lapp) Date: Wed, 13 Jan 2010 12:06:39 -0500 Subject: [BioSQL-l] SQLite support In-Reply-To: <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com> References: <1f864af10812150224y540f1ba6y6b30168102885fcd@mail.gmail.com> <320fb6e00812150243w4b0dc223g40abcf684af1ccf5@mail.gmail.com> <320fb6e00907050324i6d64d3abreb4d0c256bf1bdc4@mail.gmail.com> <320fb6e00907090529t61239952y1c86963f13c1db78@mail.gmail.com> <320fb6e00907280458q56f74ec6iefa420ac1caab8da@mail.gmail.com> <320fb6e00911240627o49bc1ec9nc0d26065ebc23423@mail.gmail.com> <070E8BA8-B2C1-4E44-AA2D-9934B3742406@illinois.edu> <320fb6e00911240907u32dca751ldb488cbc38f0e035@mail.gmail.com> <320fb6e00912100703g4e2b7068jb4fea67df3ebd8a8@mail.gmail.com> <320fb6e01001130337p1e0a361ci7ea1a5b5a9639731@mail.gmail.com> Message-ID: Hi Peter, yes, I know I'm remiss on doing that. Will do shortly. Please don't stop pestering if I seem to have forgotten :-) -hilmar On Jan 13, 2010, at 6:37 AM, Peter wrote: > On Thu, Dec 10, 2009 at 3:03 PM, Peter > wrote: >> >> Brad and I are hoping to include BioSQL on SQLite support in the >> imminent release of Biopython 1.53, although we will stress in the >> release notes that this (and the schema) is still experimental. >> >> For this initial release, the user probably still have to manually >> create the SQLite database - this is something I hope we can make >> much more user friendly in the subsequent releases of Biopython >> (taking advantage of the fact the SQLite is included with Python 2.5 >> onwards, so we can do this without any external dependencies). >> >> Peter >> >> See also: >> http://bugzilla.open-bio.org/show_bug.cgi?id=2870 >> http://bugzilla.open-bio.org/show_bug.cgi?id=2866 >> > > To keep you guys informed, we released Biopython 1.53 at the > end of 2009, and this did include BioSQL on SQLite support > based on the draft schema: > http://news.open-bio.org/news/2009/12/biopython-release-153/ > > Even if a BioSQL v1.0.2 release isn't imminent, could the draft > SQLite schema be checked into BioSQL's SVN repository please? > > Repository link to see the file (currently no revisions): > http://github.com/biopython/biopython/blob/master/Tests/BioSQL/biosqldb-sqlite.sql > > Alternatively you can grab the file here: > http://biopython.open-bio.org/SRC/biopython/Tests/BioSQL/biosqldb-sqlite.sql > (updated hourly, not that we have any revisions planned) > > As I said before, we'd like to make using BioSQL on SQLite > from within Biopython much easier (because unlike the other > database back ends, it is *very* simple to create or delete a > new SQLite database). This would require us to install a > copy of the schema as part of Biopython (currently we just > include a copy used for unit tests), so the sooner the schema > becomes "official", the better. > > Regards, > > Peter > -- =========================================================== : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net : =========================================================== From piotrborowiec at g.pl Mon Jan 18 17:54:45 2010 From: piotrborowiec at g.pl (Piotr Borowiec) Date: Mon, 18 Jan 2010 18:54:45 +0100 Subject: [BioSQL-l] Problems with installation Biosql Message-ID: <1c828cb91001180954r43b01287pc5f4258065d024e4@mail.gmail.com> Hi, I have problems with installation Biosql. Everything is progressing well to running a script load_ncbi_taxonomy.pl stage. Displays the message: Access denied for user 'Peter' @ 'localhost' (using password: NO) at load_ncbi_taxonomy.pl line 311 Please advice. Peter From biopython at maubp.freeserve.co.uk Mon Jan 18 21:10:55 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Mon, 18 Jan 2010 21:10:55 +0000 Subject: [BioSQL-l] Problems with installation Biosql In-Reply-To: <1c828cb91001180954r43b01287pc5f4258065d024e4@mail.gmail.com> References: <1c828cb91001180954r43b01287pc5f4258065d024e4@mail.gmail.com> Message-ID: <320fb6e01001181310n2be4889cked47da5d609c4223@mail.gmail.com> On Mon, Jan 18, 2010 at 5:54 PM, Piotr Borowiec wrote: > > Hi, > I have problems with installation Biosql. Everything is progressing > well to running a script load_ncbi_taxonomy.pl stage. Displays the > message: Access denied for user 'Peter' @ 'localhost' (using password: > NO) at load_ncbi_taxonomy.pl line 311 > Please advice. > > Peter You have to give the script a database username and password (which you should know or be able to create if it was you that setup the BioSQL database) via its optional command line options. Peter C From biopython at maubp.freeserve.co.uk Tue Jan 19 10:11:51 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Tue, 19 Jan 2010 10:11:51 +0000 Subject: [BioSQL-l] Problems with installation Biosql In-Reply-To: <1c828cb91001190142h11aca5a4o153e3c614a6a2fe2@mail.gmail.com> References: <1c828cb91001180954r43b01287pc5f4258065d024e4@mail.gmail.com> <320fb6e01001181310n2be4889cked47da5d609c4223@mail.gmail.com> <1c828cb91001190142h11aca5a4o153e3c614a6a2fe2@mail.gmail.com> Message-ID: <320fb6e01001190211u2905e1fbu36c0ceacba11bb86@mail.gmail.com> Hi, Don't forget to CC the mailing list on replies ;) On Tue, Jan 19, 2010 at 9:42 AM, Piotr Borowiec wrote: > > Thanks for advice. I gave the script all parameters and next there was > a message: > > Loading NCBI taxon database in taxdata: > ? ? ? ?... retrieving all taxon nodes in the database > ? ? ? ?... reading in taxon nodes from nodes.dmp > Couldn't open data file taxdata/nodes.dmp: No such file or directory > rollback ineffective with AutoCommit enabled at load_ncbi_taxonomy.pl line 841. > Use of uninitialized value in concatenation (.) or string at > load_ncbi_taxonomy.pl line 843. The script has an option to download the taxonomy file from the NCBI (--download true), or to use an existing copy (e.g. from a previous run). I suspect that you have a partial copy from an aborted run which is confusing the script. I would try again explicitly asking for a fresh download. I would also try removing the taxdata directory (if present) and any (partial) taxdata archive file - then try again. Peter From biopython at maubp.freeserve.co.uk Thu Jan 21 12:33:53 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Thu, 21 Jan 2010 12:33:53 +0000 Subject: [BioSQL-l] SwissProt DE lines and UniProt XML / TagTree as XML in BioSQL Message-ID: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> Hi all, This is cross posted to try and ensure relevant people see it. I suggest we continue the discussion on the BioSQL list (for how to serialise structured annotation to BioSQL), and/or the OpenBio list (for things like file format naming conventions). I am hoping we (Bio*) can be consistent in how we parse and load into BioSQL the SwissProt DE lines (known as "swiss" format in both BioPerl and Biopython's SeqIO, and by EMBOSS) or the equivalent UniProt XML tags (which we are tentatively going to call the "uniprot" format in Biopython's SeqIO - comments?). Like BioPerl (etc), Biopython can parse plain text SwissProt ("swiss") files and load them into BioSQL. Biopython currently treats the DE comment lines as a long string, as BioPerl used to: http://lists.open-bio.org/pipermail/bioperl-l/2009-May/030041.html http://lists.open-bio.org/pipermail/biosql-l/2009-May/001514.html I understand that BioPerl now turns the SwissProt DE lines into a TagTree, and for storing this in BioSQL this gets serialised as XML. I would like Biopython to handle this the same way (although rather than a Perl TagTree, we'd use a Python structure of course), and would appreciate clarification of what exactly was implemented (e.g. which bit of the BioPerl source code should be look at, and could you show a worked example?). Andrea Pierlenoin (CC'd - not sure if he is on the BioSQL or Open-Bio lists yet) has started work on parsing UniProt XML files for Biopython. Here the DE comment lines are already provided broken up with XML markup. Hopefully their nested structure matches what BioPerl was doing with the SwissProt DE lines. Regards, Peter From cjfields at illinois.edu Thu Jan 21 13:34:12 2010 From: cjfields at illinois.edu (Chris Fields) Date: Thu, 21 Jan 2010 07:34:12 -0600 Subject: [BioSQL-l] [Open-bio-l] SwissProt DE lines and UniProt XML / TagTree as XML in BioSQL In-Reply-To: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> References: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> Message-ID: Peter, The relevant code is in Bio::Annotation::TagTree in bioperl-live, which is a decorator for Data::Stag: http://search.cpan.org/~cmungall/Data-Stag-0.11/Data/Stag.pm This is where the text output is derived from. It's a bit of a heavyweight solution to the problem, but it's capable of round-tripping the DE data and parses out the data in a way that's approachable. We could probably abstract out the serialization backend there and allow a pure bioperl solution (or the current solution) as a fallback. If the plain-text DE info is represented in a hierarchy already in UniProt XML, we should probably conform as closely as possible to that (using a standard format like XML, JSON, etc.). chris On Jan 21, 2010, at 6:33 AM, Peter wrote: > Hi all, > > This is cross posted to try and ensure relevant people see it. > I suggest we continue the discussion on the BioSQL list > (for how to serialise structured annotation to BioSQL), and/or > the OpenBio list (for things like file format naming conventions). > > I am hoping we (Bio*) can be consistent in how we parse and load > into BioSQL the SwissProt DE lines (known as "swiss" format in > both BioPerl and Biopython's SeqIO, and by EMBOSS) or the > equivalent UniProt XML tags (which we are tentatively going to > call the "uniprot" format in Biopython's SeqIO - comments?). > > Like BioPerl (etc), Biopython can parse plain text SwissProt ("swiss") > files and load them into BioSQL. Biopython currently treats the DE > comment lines as a long string, as BioPerl used to: > > http://lists.open-bio.org/pipermail/bioperl-l/2009-May/030041.html > http://lists.open-bio.org/pipermail/biosql-l/2009-May/001514.html > > I understand that BioPerl now turns the SwissProt DE lines into a > TagTree, and for storing this in BioSQL this gets serialised as XML. > I would like Biopython to handle this the same way (although rather > than a Perl TagTree, we'd use a Python structure of course), and > would appreciate clarification of what exactly was implemented > (e.g. which bit of the BioPerl source code should be look at, > and could you show a worked example?). > > Andrea Pierlenoin (CC'd - not sure if he is on the BioSQL or > Open-Bio lists yet) has started work on parsing UniProt XML > files for Biopython. Here the DE comment lines are already > provided broken up with XML markup. Hopefully their nested > structure matches what BioPerl was doing with the SwissProt > DE lines. > > Regards, > > Peter From holland at eaglegenomics.com Fri Jan 22 10:51:52 2010 From: holland at eaglegenomics.com (Richard Holland) Date: Fri, 22 Jan 2010 10:51:52 +0000 Subject: [BioSQL-l] SwissProt DE lines and UniProt XML / TagTree as XML in BioSQL In-Reply-To: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> References: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> Message-ID: <8FECCBDE-2DE1-40EE-B5A4-73BDAC893E2D@eaglegenomics.com> Nice idea. Currently, BioJava just stores the complete section as a string without parsing it, but it provides a parser module for converting it into useful tag/value format within a user's program (but not to be stored in BioSQL). On 21 Jan 2010, at 12:33, Peter wrote: > Hi all, > > This is cross posted to try and ensure relevant people see it. > I suggest we continue the discussion on the BioSQL list > (for how to serialise structured annotation to BioSQL), and/or > the OpenBio list (for things like file format naming conventions). > > I am hoping we (Bio*) can be consistent in how we parse and load > into BioSQL the SwissProt DE lines (known as "swiss" format in > both BioPerl and Biopython's SeqIO, and by EMBOSS) or the > equivalent UniProt XML tags (which we are tentatively going to > call the "uniprot" format in Biopython's SeqIO - comments?). > > Like BioPerl (etc), Biopython can parse plain text SwissProt ("swiss") > files and load them into BioSQL. Biopython currently treats the DE > comment lines as a long string, as BioPerl used to: > > http://lists.open-bio.org/pipermail/bioperl-l/2009-May/030041.html > http://lists.open-bio.org/pipermail/biosql-l/2009-May/001514.html > > I understand that BioPerl now turns the SwissProt DE lines into a > TagTree, and for storing this in BioSQL this gets serialised as XML. > I would like Biopython to handle this the same way (although rather > than a Perl TagTree, we'd use a Python structure of course), and > would appreciate clarification of what exactly was implemented > (e.g. which bit of the BioPerl source code should be look at, > and could you show a worked example?). > > Andrea Pierlenoin (CC'd - not sure if he is on the BioSQL or > Open-Bio lists yet) has started work on parsing UniProt XML > files for Biopython. Here the DE comment lines are already > provided broken up with XML markup. Hopefully their nested > structure matches what BioPerl was doing with the SwissProt > DE lines. > > Regards, > > Peter > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com http://www.eaglegenomics.com/ From andrea at biocomp.unibo.it Fri Jan 22 12:18:32 2010 From: andrea at biocomp.unibo.it (Andrea Pierleoni) Date: Fri, 22 Jan 2010 13:18:32 +0100 (CET) Subject: [BioSQL-l] SwissProt DE lines and UniProt XML / TagTree as XML in BioSQL In-Reply-To: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> References: <320fb6e01001210433n6f42e617g6519ee2790d6add5@mail.gmail.com> Message-ID: <2b6e30c4628585042366646a7b46386e.squirrel@lipid.biocomp.unibo.it> I think that the point here can be a little broader, since not only the swissprot DE lines carry complex and structured data. To define a common, language-independent way to store structured data into the comment and *_qualifier_value tables of the actual BioSQL schema could be very useful. XML looks like a good candidate to me, and the UniprotXML format can be used as reference or as a template to start from. Each Bio* project will then parse and report this structured data in its own programming language data structure. Andrea > Hi all, > > This is cross posted to try and ensure relevant people see it. > I suggest we continue the discussion on the BioSQL list > (for how to serialise structured annotation to BioSQL), and/or > the OpenBio list (for things like file format naming conventions). > > I am hoping we (Bio*) can be consistent in how we parse and load > into BioSQL the SwissProt DE lines (known as "swiss" format in > both BioPerl and Biopython's SeqIO, and by EMBOSS) or the > equivalent UniProt XML tags (which we are tentatively going to > call the "uniprot" format in Biopython's SeqIO - comments?). > > Like BioPerl (etc), Biopython can parse plain text SwissProt ("swiss") > files and load them into BioSQL. Biopython currently treats the DE > comment lines as a long string, as BioPerl used to: > > http://lists.open-bio.org/pipermail/bioperl-l/2009-May/030041.html > http://lists.open-bio.org/pipermail/biosql-l/2009-May/001514.html > > I understand that BioPerl now turns the SwissProt DE lines into a > TagTree, and for storing this in BioSQL this gets serialised as XML. > I would like Biopython to handle this the same way (although rather > than a Perl TagTree, we'd use a Python structure of course), and > would appreciate clarification of what exactly was implemented > (e.g. which bit of the BioPerl source code should be look at, > and could you show a worked example?). > > Andrea Pierlenoin (CC'd - not sure if he is on the BioSQL or > Open-Bio lists yet) has started work on parsing UniProt XML > files for Biopython. Here the DE comment lines are already > provided broken up with XML markup. Hopefully their nested > structure matches what BioPerl was doing with the SwissProt > DE lines. > > Regards, > > Peter > From chapmanb at 50mail.com Thu Jan 28 20:35:05 2010 From: chapmanb at 50mail.com (Brad Chapman) Date: Thu, 28 Jan 2010 15:35:05 -0500 Subject: [BioSQL-l] OpenBio solution challenge: Project updates at BOSC 2010 Message-ID: <20100128203505.GG40046@sobchak.mgh.harvard.edu> Hello all; The BOSC 2010 organizing committee is hard at work getting prepared for this July's meeting in Boston: http://www.open-bio.org/wiki/BOSC_2010 One of the items we've traditionally had at the conference is a project update from each of the OpenBio affiliated groups. This year, we're thinking about organizing these talks around a central theme: the OpenBio solution challenge. We start with a biological question of general interest, and each of the project talks would focus around how you would solve that problem using your toolkit and programming language. This is meant to provide a challenge for OpenBio contributors, a nice tutorial style overview of various projects and approaches for other programmers, and a fun opportunity to compete and learn from other projects. Conference attendees will vote on their favorite solution, with the winner receiving fame and fortune (warning: fortune not guaranteed). For this to be successful, it of course requires interest and enthusiasm from y'all fine folks involved with the projects. Specifically: - Is there interest from your group in participating in the challenge? You'll want at least a few people to work on it, and someone to give a presentation at BOSC. - Do you have suggestions on a good theme or specific biological problem to tackle? We'll hope to pick something in a sweet spot that is challenging enough to be of interest, yet reasonable for presentation and preparation. Let's discuss ideas and get this together. Since the schedule for BOSC is developing rapidly, please give us an idea if you're interested by February 12th, and copy responses to the BOSC mailing list as a central place for discussion. bosc at open-bio.org Thanks, Brad, Michael, and the BOSC organizing committee From markw at illuminae.com Thu Jan 28 21:17:44 2010 From: markw at illuminae.com (Mark Wilkinson) Date: Thu, 28 Jan 2010 13:17:44 -0800 Subject: [BioSQL-l] [MOBY-dev] OpenBio solution challenge: Project updates at BOSC 2010 In-Reply-To: <20100128203505.GG40046@sobchak.mgh.harvard.edu> References: <20100128203505.GG40046@sobchak.mgh.harvard.edu> Message-ID: Brad, this sounds exciting! One thing strikes me, though - by asking for the sub-projects to propose the "grand challenge" themselves the one thing you can guarantee is that the "grand challenge" is solvable (or more likely, already solved!) Other "grand challenge" kinds of meetings have an independent third party pose the problem that has to be solved, and then all groups work toward a solution and compare their results. This would, IMO, be more revealing of the "state of the art" in each Open-Bio project, and point out where the weaknesses are that we should be focusing on... Someone (for example, you!) could act as the moderator to ensure that the "grand challenge" was at least a reasonable one, within the scope of what an Open-Bio project *should* be able to solve... Just my CAD $0.02 Mark On Thu, 28 Jan 2010 12:35:05 -0800, Brad Chapman wrote: > Hello all; > The BOSC 2010 organizing committee is hard at work getting prepared for > this > July's meeting in Boston: > > http://www.open-bio.org/wiki/BOSC_2010 > > One of the items we've traditionally had at the conference is a project > update from each of the OpenBio affiliated groups. This year, we're > thinking > about organizing these talks around a central theme: the OpenBio solution > challenge. We start with a biological question of general interest, and > each > of the project talks would focus around how you would solve that problem > using your toolkit and programming language. > > This is meant to provide a challenge for OpenBio contributors, a nice > tutorial > style overview of various projects and approaches for other programmers, > and a > fun opportunity to compete and learn from other projects. Conference > attendees > will vote on their favorite solution, with the winner receiving fame and > fortune (warning: fortune not guaranteed). > > For this to be successful, it of course requires interest and enthusiasm > from > y'all fine folks involved with the projects. Specifically: > > - Is there interest from your group in participating in the challenge? > You'll > want at least a few people to work on it, and someone to give a > presentation > at BOSC. > > - Do you have suggestions on a good theme or specific biological problem > to > tackle? We'll hope to pick something in a sweet spot that is > challenging > enough to be of interest, yet reasonable for presentation and > preparation. > > Let's discuss ideas and get this together. Since the schedule for BOSC is > developing rapidly, please give us an idea if you're interested by > February 12th, and copy responses to the BOSC mailing list as a central > place for discussion. > > bosc at open-bio.org > > Thanks, > Brad, Michael, and the BOSC organizing committee > _______________________________________________ > MOBY-dev mailing list > MOBY-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/moby-dev -- Mark D Wilkinson, PI Bioinformatics Assistant Professor, Medical Genetics The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research Providence Heart + Lung Institute University of British Columbia - St. Paul's Hospital Vancouver, BC, Canada From HWillis at scripps.edu Fri Jan 29 01:03:10 2010 From: HWillis at scripps.edu (Scooter Willis) Date: Thu, 28 Jan 2010 20:03:10 -0500 Subject: [BioSQL-l] [Biojava-dev] [MOBY-dev] OpenBio solution challenge: Project updates at BOSC 2010 In-Reply-To: References: <20100128203505.GG40046@sobchak.mgh.harvard.edu> Message-ID: <716E205A-5196-409F-A7BC-EF0F52AA997A@scripps.edu> Brad I agree with Mark that a particular problem may be biased towards a toolkit/language. Another approach would be to list a collection of problems and each group would then pick a problem to present. Could be a little more interesting to the audience as you are exposed to different problems and the various strengths of each toolkit. This could also help guide future development in the other toolkits as you would benefit from learning about the api and/or programming language. Each group would register a problem that they are going to present. From the group of problems not picked that becomes the surprise challenge where each group has 24 hours to either put together a presentation or an actual solution. Scooter On Jan 28, 2010, at 4:17 PM, Mark Wilkinson wrote: > > Brad, this sounds exciting! > > One thing strikes me, though - by asking for the sub-projects to propose > the "grand challenge" themselves the one thing you can guarantee is that > the "grand challenge" is solvable (or more likely, already solved!) > > Other "grand challenge" kinds of meetings have an independent third party > pose the problem that has to be solved, and then all groups work toward a > solution and compare their results. This would, IMO, be more revealing of > the "state of the art" in each Open-Bio project, and point out where the > weaknesses are that we should be focusing on... Someone (for example, > you!) could act as the moderator to ensure that the "grand challenge" was > at least a reasonable one, within the scope of what an Open-Bio project > *should* be able to solve... > > Just my CAD $0.02 > > Mark > > > > On Thu, 28 Jan 2010 12:35:05 -0800, Brad Chapman > wrote: > >> Hello all; >> The BOSC 2010 organizing committee is hard at work getting prepared for >> this >> July's meeting in Boston: >> >> http://www.open-bio.org/wiki/BOSC_2010 >> >> One of the items we've traditionally had at the conference is a project >> update from each of the OpenBio affiliated groups. This year, we're >> thinking >> about organizing these talks around a central theme: the OpenBio solution >> challenge. We start with a biological question of general interest, and >> each >> of the project talks would focus around how you would solve that problem >> using your toolkit and programming language. >> >> This is meant to provide a challenge for OpenBio contributors, a nice >> tutorial >> style overview of various projects and approaches for other programmers, >> and a >> fun opportunity to compete and learn from other projects. Conference >> attendees >> will vote on their favorite solution, with the winner receiving fame and >> fortune (warning: fortune not guaranteed). >> >> For this to be successful, it of course requires interest and enthusiasm >> from >> y'all fine folks involved with the projects. Specifically: >> >> - Is there interest from your group in participating in the challenge? >> You'll >> want at least a few people to work on it, and someone to give a >> presentation >> at BOSC. >> >> - Do you have suggestions on a good theme or specific biological problem >> to >> tackle? We'll hope to pick something in a sweet spot that is >> challenging >> enough to be of interest, yet reasonable for presentation and >> preparation. >> >> Let's discuss ideas and get this together. Since the schedule for BOSC is >> developing rapidly, please give us an idea if you're interested by >> February 12th, and copy responses to the BOSC mailing list as a central >> place for discussion. >> >> bosc at open-bio.org >> >> Thanks, >> Brad, Michael, and the BOSC organizing committee >> _______________________________________________ >> MOBY-dev mailing list >> MOBY-dev at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/moby-dev > > > -- > Mark D Wilkinson, PI Bioinformatics > Assistant Professor, Medical Genetics > The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research > Providence Heart + Lung Institute > University of British Columbia - St. Paul's Hospital > Vancouver, BC, Canada > _______________________________________________ > biojava-dev mailing list > biojava-dev at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biojava-dev From biopython at maubp.freeserve.co.uk Fri Jan 29 10:36:40 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Fri, 29 Jan 2010 10:36:40 +0000 Subject: [BioSQL-l] [Bioperl-l] [MOBY-dev] OpenBio solution challenge: Project updates at BOSC 2010 In-Reply-To: References: <20100128203505.GG40046@sobchak.mgh.harvard.edu> Message-ID: <320fb6e01001290236l1ad02515w403a19f94dbb6d15@mail.gmail.com> Hi all, This is a great topic but should be continue it on just the one mailing list? Is there a suitable BOSC list, or how about the general Open Bio list? On Thu, Jan 28, 2010 at 9:17 PM, Mark Wilkinson wrote: > > Brad, this sounds exciting! > > One thing strikes me, though - by asking for the sub-projects to propose > the "grand challenge" themselves the one thing you can guarantee is that > the "grand challenge" is solvable (or more likely, already solved!) > > Other "grand challenge" kinds of meetings have an independent third party > pose the problem that has to be solved, and then all groups work toward a > solution and compare their results. ?This would, IMO, be more revealing of > the "state of the art" in each Open-Bio project, and point out where the > weaknesses are that we should be focusing on... ?Someone (for example, > you!) could act as the moderator to ensure that the "grand challenge" was > at least a reasonable one, within the scope of what an Open-Bio project > *should* be able to solve... > > Just my CAD $0.02 > > Mark One possible problem with having Brad act as moderator is his ties to Biopython (plus it would be a shame if we'd be one man down for trying to solve the challenges - grin). Having a project representative "sign off" on the challenge might work - or simply the whole of the BOSC committee which is quite balanced. Alternatively some kind of panel of challenges does seem a good way to reduce individual project bias (as suggest by Scooter), but there will still need to be a judging committee. I'm curious what kind of challenges the BOSC committee had in mind - would something like taking a newly sequence bacteria and producing an automated annotation as a GenBank, EMBL, or GFF file be too ambitious for example? There are already several major projects to do this e.g. RAST http://rast.nmpdr.org/ Peter (@Biopython)