From piotrborowiec at g.pl Tue Feb 16 05:24:21 2010 From: piotrborowiec at g.pl (Piotr Borowiec) Date: Tue, 16 Feb 2010 11:24:21 +0100 Subject: [BioSQL-l] Some problem with installation DBD::mysql Message-ID: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> Hi! Last time I had a problem with loading_ncbi script so I decided to start with fresh biosql andy also Unix. When I want to install DBD::mysql module there is some mistakes. I`m not sure but maybe the version mysql is not correct. I already have 5.1 cpan[1]> install DBD::mysql CPAN: Storable loaded ok (v2.18) Going to read /home/scati/.cpan/Metadata Database was generated on Tue, 16 Feb 2010 07:53:49 GMT Running install for module 'DBD::mysql' CPAN: Data::Dumper loaded ok (v2.121_14) 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/home/scati/.cpan/prefs' Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz CPAN: Digest::SHA loaded ok (v5.45) CPAN: Compress::Zlib loaded ok (v2.008) Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz ok Scanning cache /home/scati/.cpan/build for sizes ............................................................................DONE DBD-mysql-4.013/ DBD-mysql-4.013/lib/ DBD-mysql-4.013/lib/DBD/ DBD-mysql-4.013/lib/DBD/mysql.pm DBD-mysql-4.013/lib/DBD/mysql/ DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod DBD-mysql-4.013/lib/Bundle/ DBD-mysql-4.013/lib/Bundle/DBD/ DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm DBD-mysql-4.013/mysql.xs DBD-mysql-4.013/dbdimp.c DBD-mysql-4.013/myld DBD-mysql-4.013/INSTALL.html DBD-mysql-4.013/Makefile.PL.embedded DBD-mysql-4.013/TODO DBD-mysql-4.013/README DBD-mysql-4.013/MANIFEST.SKIP DBD-mysql-4.013/ChangeLog DBD-mysql-4.013/Makefile.PL DBD-mysql-4.013/META.yml DBD-mysql-4.013/dbdimp.h DBD-mysql-4.013/eg/ DBD-mysql-4.013/eg/prepare_memory_usage.pl DBD-mysql-4.013/eg/proc_example2b.pl DBD-mysql-4.013/eg/proc_example2.pl DBD-mysql-4.013/eg/decimal_test.pl DBD-mysql-4.013/eg/bug30033pg.pl DBD-mysql-4.013/eg/proc_example2a.pl DBD-mysql-4.013/eg/proc_example4.pl DBD-mysql-4.013/eg/bug21028.pl DBD-mysql-4.013/eg/bug14979.pl DBD-mysql-4.013/eg/bug30033.pl DBD-mysql-4.013/eg/issue21946.pl DBD-mysql-4.013/eg/proc_example3.pl DBD-mysql-4.013/eg/proc_example1.pl DBD-mysql-4.013/constants.h DBD-mysql-4.013/t/ DBD-mysql-4.013/t/85init_command.t DBD-mysql-4.013/t/40listfields.t DBD-mysql-4.013/t/40bindparam.t DBD-mysql-4.013/t/mysql.mtest DBD-mysql-4.013/t/41bindparam.t DBD-mysql-4.013/t/76multi_statement.t DBD-mysql-4.013/t/40nulls.t DBD-mysql-4.013/t/32insert_error.t DBD-mysql-4.013/t/40catalog.t DBD-mysql-4.013/t/51bind_type_guessing.t DBD-mysql-4.013/t/40bindparam2.t DBD-mysql-4.013/t/41blobs_prepare.t DBD-mysql-4.013/t/20createdrop.t DBD-mysql-4.013/t/70takeimp.t DBD-mysql-4.013/t/42bindparam.t DBD-mysql-4.013/t/00base.t DBD-mysql-4.013/t/55utf8.t DBD-mysql-4.013/t/65types.t DBD-mysql-4.013/t/40server_prepare_error.t DBD-mysql-4.013/t/31insertid.t DBD-mysql-4.013/t/29warnings.t DBD-mysql-4.013/t/40types.t DBD-mysql-4.013/t/10connect.t DBD-mysql-4.013/t/lib.pl DBD-mysql-4.013/t/mysql.dbtest DBD-mysql-4.013/t/35limit.t DBD-mysql-4.013/t/71impdata.t DBD-mysql-4.013/t/40blobs.t DBD-mysql-4.013/t/40server_prepare.t DBD-mysql-4.013/t/40numrows.t DBD-mysql-4.013/t/35prepare.t DBD-mysql-4.013/t/40keyinfo.t DBD-mysql-4.013/t/75supported_sql.t DBD-mysql-4.013/t/60leaks.t DBD-mysql-4.013/t/50commit.t DBD-mysql-4.013/t/30insertfetch.t DBD-mysql-4.013/t/50chopblanks.t DBD-mysql-4.013/t/25lockunlock.t DBD-mysql-4.013/t/80procs.t DBD-mysql-4.013/MANIFEST CPAN: File::Temp loaded ok (v0.18) Warning (usually harmless): 'YAML' not installed, will not store persistent state CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. Cannot find the file 'mysql_config'! Your execution PATH doesn't seem not contain the path to mysql_config. Resorting to guessed values! Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located PLEASE NOTE: For 'make test' to run properly, you must ensure that the database user 'root' can connect to your MySQL server and has the proper privileges that these tests require such as 'drop table', 'create table', 'drop procedure', 'create procedure' as well as others. mysql> grant all privileges on test.* to 'root'@'localhost' identified by 's3kr1t'; You can also optionally set the user to run 'make test' with: perl Makefile.pl --testuser=username Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Failed to determine directory of mysql.h. Use perl Makefile.PL --cflags=-I to set this directory. For details see the INSTALL.html file, section "C Compiler flags" or type perl Makefile.PL --help Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] Warning (usually harmless): 'YAML' not installed, will not store persistent state CAPTTOFU/DBD-mysql-4.013.tar.gz /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK Running make test Make had some problems, won't test Running make install Make had some problems, won't install Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. Falling back to other methods to determine prerequisites Failed during this command: CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 cpan[1]> install DBD::mysql CPAN: Storable loaded ok (v2.18) Going to read /home/scati/.cpan/Metadata Database was generated on Tue, 16 Feb 2010 07:53:49 GMT Running install for module 'DBD::mysql' CPAN: Data::Dumper loaded ok (v2.121_14) 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/home/scati/.cpan/prefs' Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz CPAN: Digest::SHA loaded ok (v5.45) CPAN: Compress::Zlib loaded ok (v2.008) Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz ok Scanning cache /home/scati/.cpan/build for sizes ............................................................................DONE DBD-mysql-4.013/ DBD-mysql-4.013/lib/ DBD-mysql-4.013/lib/DBD/ DBD-mysql-4.013/lib/DBD/mysql.pm DBD-mysql-4.013/lib/DBD/mysql/ DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod DBD-mysql-4.013/lib/Bundle/ DBD-mysql-4.013/lib/Bundle/DBD/ DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm DBD-mysql-4.013/mysql.xs DBD-mysql-4.013/dbdimp.c DBD-mysql-4.013/myld DBD-mysql-4.013/INSTALL.html DBD-mysql-4.013/Makefile.PL.embedded DBD-mysql-4.013/TODO DBD-mysql-4.013/README DBD-mysql-4.013/MANIFEST.SKIP DBD-mysql-4.013/ChangeLog DBD-mysql-4.013/Makefile.PL DBD-mysql-4.013/META.yml DBD-mysql-4.013/dbdimp.h DBD-mysql-4.013/eg/ DBD-mysql-4.013/eg/prepare_memory_usage.pl DBD-mysql-4.013/eg/proc_example2b.pl DBD-mysql-4.013/eg/proc_example2.pl DBD-mysql-4.013/eg/decimal_test.pl DBD-mysql-4.013/eg/bug30033pg.pl DBD-mysql-4.013/eg/proc_example2a.pl DBD-mysql-4.013/eg/proc_example4.pl DBD-mysql-4.013/eg/bug21028.pl DBD-mysql-4.013/eg/bug14979.pl DBD-mysql-4.013/eg/bug30033.pl DBD-mysql-4.013/eg/issue21946.pl DBD-mysql-4.013/eg/proc_example3.pl DBD-mysql-4.013/eg/proc_example1.pl DBD-mysql-4.013/constants.h DBD-mysql-4.013/t/ DBD-mysql-4.013/t/85init_command.t DBD-mysql-4.013/t/40listfields.t DBD-mysql-4.013/t/40bindparam.t DBD-mysql-4.013/t/mysql.mtest DBD-mysql-4.013/t/41bindparam.t DBD-mysql-4.013/t/76multi_statement.t DBD-mysql-4.013/t/40nulls.t DBD-mysql-4.013/t/32insert_error.t DBD-mysql-4.013/t/40catalog.t DBD-mysql-4.013/t/51bind_type_guessing.t DBD-mysql-4.013/t/40bindparam2.t DBD-mysql-4.013/t/41blobs_prepare.t DBD-mysql-4.013/t/20createdrop.t DBD-mysql-4.013/t/70takeimp.t DBD-mysql-4.013/t/42bindparam.t DBD-mysql-4.013/t/00base.t DBD-mysql-4.013/t/55utf8.t DBD-mysql-4.013/t/65types.t DBD-mysql-4.013/t/40server_prepare_error.t DBD-mysql-4.013/t/31insertid.t DBD-mysql-4.013/t/29warnings.t DBD-mysql-4.013/t/40types.t DBD-mysql-4.013/t/10connect.t DBD-mysql-4.013/t/lib.pl DBD-mysql-4.013/t/mysql.dbtest DBD-mysql-4.013/t/35limit.t DBD-mysql-4.013/t/71impdata.t DBD-mysql-4.013/t/40blobs.t DBD-mysql-4.013/t/40server_prepare.t DBD-mysql-4.013/t/40numrows.t DBD-mysql-4.013/t/35prepare.t DBD-mysql-4.013/t/40keyinfo.t DBD-mysql-4.013/t/75supported_sql.t DBD-mysql-4.013/t/60leaks.t DBD-mysql-4.013/t/50commit.t DBD-mysql-4.013/t/30insertfetch.t DBD-mysql-4.013/t/50chopblanks.t DBD-mysql-4.013/t/25lockunlock.t DBD-mysql-4.013/t/80procs.t DBD-mysql-4.013/MANIFEST CPAN: File::Temp loaded ok (v0.18) Warning (usually harmless): 'YAML' not installed, will not store persistent state CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. Cannot find the file 'mysql_config'! Your execution PATH doesn't seem not contain the path to mysql_config. Resorting to guessed values! Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located PLEASE NOTE: For 'make test' to run properly, you must ensure that the database user 'root' can connect to your MySQL server and has the proper privileges that these tests require such as 'drop table', 'create table', 'drop procedure', 'create procedure' as well as others. mysql> grant all privileges on test.* to 'root'@'localhost' identified by 's3kr1t'; You can also optionally set the user to run 'make test' with: perl Makefile.pl --testuser=username Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Failed to determine directory of mysql.h. Use perl Makefile.PL --cflags=-I to set this directory. For details see the INSTALL.html file, section "C Compiler flags" or type perl Makefile.PL --help Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] Warning (usually harmless): 'YAML' not installed, will not store persistent state CAPTTOFU/DBD-mysql-4.013.tar.gz /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK Running make test Make had some problems, won't test Running make install Make had some problems, won't install Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. Falling back to other methods to determine prerequisites Failed during this command: CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 -- Piotr Borowiec From awitney at sgul.ac.uk Tue Feb 16 05:40:57 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Tue, 16 Feb 2010 10:40:57 +0000 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> Message-ID: Hi Piotr, this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try perl Makefile.PL --mysql_config= regards adam On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: > Hi! > > Last time I had a problem with loading_ncbi script so I decided to > start with fresh biosql andy also Unix. When I want to install > DBD::mysql module there is some mistakes. I`m not sure but maybe the > version mysql is not correct. I already have 5.1 > > cpan[1]> install DBD::mysql > CPAN: Storable loaded ok (v2.18) > Going to read /home/scati/.cpan/Metadata > Database was generated on Tue, 16 Feb 2010 07:53:49 GMT > Running install for module 'DBD::mysql' > CPAN: Data::Dumper loaded ok (v2.121_14) > 'YAML' not installed, falling back to Data::Dumper and Storable to > read prefs '/home/scati/.cpan/prefs' > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > ok > Scanning cache /home/scati/.cpan/build for sizes > ............................................................................DONE > DBD-mysql-4.013/ > DBD-mysql-4.013/lib/ > DBD-mysql-4.013/lib/DBD/ > DBD-mysql-4.013/lib/DBD/mysql.pm > DBD-mysql-4.013/lib/DBD/mysql/ > DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm > DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod > DBD-mysql-4.013/lib/Bundle/ > DBD-mysql-4.013/lib/Bundle/DBD/ > DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm > DBD-mysql-4.013/mysql.xs > DBD-mysql-4.013/dbdimp.c > DBD-mysql-4.013/myld > DBD-mysql-4.013/INSTALL.html > DBD-mysql-4.013/Makefile.PL.embedded > DBD-mysql-4.013/TODO > DBD-mysql-4.013/README > DBD-mysql-4.013/MANIFEST.SKIP > DBD-mysql-4.013/ChangeLog > DBD-mysql-4.013/Makefile.PL > DBD-mysql-4.013/META.yml > DBD-mysql-4.013/dbdimp.h > DBD-mysql-4.013/eg/ > DBD-mysql-4.013/eg/prepare_memory_usage.pl > DBD-mysql-4.013/eg/proc_example2b.pl > DBD-mysql-4.013/eg/proc_example2.pl > DBD-mysql-4.013/eg/decimal_test.pl > DBD-mysql-4.013/eg/bug30033pg.pl > DBD-mysql-4.013/eg/proc_example2a.pl > DBD-mysql-4.013/eg/proc_example4.pl > DBD-mysql-4.013/eg/bug21028.pl > DBD-mysql-4.013/eg/bug14979.pl > DBD-mysql-4.013/eg/bug30033.pl > DBD-mysql-4.013/eg/issue21946.pl > DBD-mysql-4.013/eg/proc_example3.pl > DBD-mysql-4.013/eg/proc_example1.pl > DBD-mysql-4.013/constants.h > DBD-mysql-4.013/t/ > DBD-mysql-4.013/t/85init_command.t > DBD-mysql-4.013/t/40listfields.t > DBD-mysql-4.013/t/40bindparam.t > DBD-mysql-4.013/t/mysql.mtest > DBD-mysql-4.013/t/41bindparam.t > DBD-mysql-4.013/t/76multi_statement.t > DBD-mysql-4.013/t/40nulls.t > DBD-mysql-4.013/t/32insert_error.t > DBD-mysql-4.013/t/40catalog.t > DBD-mysql-4.013/t/51bind_type_guessing.t > DBD-mysql-4.013/t/40bindparam2.t > DBD-mysql-4.013/t/41blobs_prepare.t > DBD-mysql-4.013/t/20createdrop.t > DBD-mysql-4.013/t/70takeimp.t > DBD-mysql-4.013/t/42bindparam.t > DBD-mysql-4.013/t/00base.t > DBD-mysql-4.013/t/55utf8.t > DBD-mysql-4.013/t/65types.t > DBD-mysql-4.013/t/40server_prepare_error.t > DBD-mysql-4.013/t/31insertid.t > DBD-mysql-4.013/t/29warnings.t > DBD-mysql-4.013/t/40types.t > DBD-mysql-4.013/t/10connect.t > DBD-mysql-4.013/t/lib.pl > DBD-mysql-4.013/t/mysql.dbtest > DBD-mysql-4.013/t/35limit.t > DBD-mysql-4.013/t/71impdata.t > DBD-mysql-4.013/t/40blobs.t > DBD-mysql-4.013/t/40server_prepare.t > DBD-mysql-4.013/t/40numrows.t > DBD-mysql-4.013/t/35prepare.t > DBD-mysql-4.013/t/40keyinfo.t > DBD-mysql-4.013/t/75supported_sql.t > DBD-mysql-4.013/t/60leaks.t > DBD-mysql-4.013/t/50commit.t > DBD-mysql-4.013/t/30insertfetch.t > DBD-mysql-4.013/t/50chopblanks.t > DBD-mysql-4.013/t/25lockunlock.t > DBD-mysql-4.013/t/80procs.t > DBD-mysql-4.013/MANIFEST > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > > CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > > Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. > > Cannot find the file 'mysql_config'! Your execution PATH doesn't seem > not contain the path to mysql_config. Resorting to guessed values! > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > > > PLEASE NOTE: > > For 'make test' to run properly, you must ensure that the > database user 'root' can connect to your MySQL server > and has the proper privileges that these tests require such > as 'drop table', 'create table', 'drop procedure', 'create procedure' > as well as others. > > mysql> grant all privileges on test.* to 'root'@'localhost' identified > by 's3kr1t'; > > You can also optionally set the user to run 'make test' with: > > perl Makefile.pl --testuser=username > > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Failed to determine directory of mysql.h. Use > > perl Makefile.PL --cflags=-I > > to set this directory. For details see the INSTALL.html file, > section "C Compiler flags" or type > > perl Makefile.PL --help > Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > CAPTTOFU/DBD-mysql-4.013.tar.gz > /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK > Running make test > Make had some problems, won't test > Running make install > Make had some problems, won't install > Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. > Falling back to other methods to determine prerequisites > Failed during this command: > CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO > '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 > cpan[1]> install DBD::mysql > CPAN: Storable loaded ok (v2.18) > Going to read /home/scati/.cpan/Metadata > Database was generated on Tue, 16 Feb 2010 07:53:49 GMT > Running install for module 'DBD::mysql' > CPAN: Data::Dumper loaded ok (v2.121_14) > 'YAML' not installed, falling back to Data::Dumper and Storable to > read prefs '/home/scati/.cpan/prefs' > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > ok > Scanning cache /home/scati/.cpan/build for sizes > ............................................................................DONE > DBD-mysql-4.013/ > DBD-mysql-4.013/lib/ > DBD-mysql-4.013/lib/DBD/ > DBD-mysql-4.013/lib/DBD/mysql.pm > DBD-mysql-4.013/lib/DBD/mysql/ > DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm > DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod > DBD-mysql-4.013/lib/Bundle/ > DBD-mysql-4.013/lib/Bundle/DBD/ > DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm > DBD-mysql-4.013/mysql.xs > DBD-mysql-4.013/dbdimp.c > DBD-mysql-4.013/myld > DBD-mysql-4.013/INSTALL.html > DBD-mysql-4.013/Makefile.PL.embedded > DBD-mysql-4.013/TODO > DBD-mysql-4.013/README > DBD-mysql-4.013/MANIFEST.SKIP > DBD-mysql-4.013/ChangeLog > DBD-mysql-4.013/Makefile.PL > DBD-mysql-4.013/META.yml > DBD-mysql-4.013/dbdimp.h > DBD-mysql-4.013/eg/ > DBD-mysql-4.013/eg/prepare_memory_usage.pl > DBD-mysql-4.013/eg/proc_example2b.pl > DBD-mysql-4.013/eg/proc_example2.pl > DBD-mysql-4.013/eg/decimal_test.pl > DBD-mysql-4.013/eg/bug30033pg.pl > DBD-mysql-4.013/eg/proc_example2a.pl > DBD-mysql-4.013/eg/proc_example4.pl > DBD-mysql-4.013/eg/bug21028.pl > DBD-mysql-4.013/eg/bug14979.pl > DBD-mysql-4.013/eg/bug30033.pl > DBD-mysql-4.013/eg/issue21946.pl > DBD-mysql-4.013/eg/proc_example3.pl > DBD-mysql-4.013/eg/proc_example1.pl > DBD-mysql-4.013/constants.h > DBD-mysql-4.013/t/ > DBD-mysql-4.013/t/85init_command.t > DBD-mysql-4.013/t/40listfields.t > DBD-mysql-4.013/t/40bindparam.t > DBD-mysql-4.013/t/mysql.mtest > DBD-mysql-4.013/t/41bindparam.t > DBD-mysql-4.013/t/76multi_statement.t > DBD-mysql-4.013/t/40nulls.t > DBD-mysql-4.013/t/32insert_error.t > DBD-mysql-4.013/t/40catalog.t > DBD-mysql-4.013/t/51bind_type_guessing.t > DBD-mysql-4.013/t/40bindparam2.t > DBD-mysql-4.013/t/41blobs_prepare.t > DBD-mysql-4.013/t/20createdrop.t > DBD-mysql-4.013/t/70takeimp.t > DBD-mysql-4.013/t/42bindparam.t > DBD-mysql-4.013/t/00base.t > DBD-mysql-4.013/t/55utf8.t > DBD-mysql-4.013/t/65types.t > DBD-mysql-4.013/t/40server_prepare_error.t > DBD-mysql-4.013/t/31insertid.t > DBD-mysql-4.013/t/29warnings.t > DBD-mysql-4.013/t/40types.t > DBD-mysql-4.013/t/10connect.t > DBD-mysql-4.013/t/lib.pl > DBD-mysql-4.013/t/mysql.dbtest > DBD-mysql-4.013/t/35limit.t > DBD-mysql-4.013/t/71impdata.t > DBD-mysql-4.013/t/40blobs.t > DBD-mysql-4.013/t/40server_prepare.t > DBD-mysql-4.013/t/40numrows.t > DBD-mysql-4.013/t/35prepare.t > DBD-mysql-4.013/t/40keyinfo.t > DBD-mysql-4.013/t/75supported_sql.t > DBD-mysql-4.013/t/60leaks.t > DBD-mysql-4.013/t/50commit.t > DBD-mysql-4.013/t/30insertfetch.t > DBD-mysql-4.013/t/50chopblanks.t > DBD-mysql-4.013/t/25lockunlock.t > DBD-mysql-4.013/t/80procs.t > DBD-mysql-4.013/MANIFEST > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > > CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > > Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. > > Cannot find the file 'mysql_config'! Your execution PATH doesn't seem > not contain the path to mysql_config. Resorting to guessed values! > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > > > PLEASE NOTE: > > For 'make test' to run properly, you must ensure that the > database user 'root' can connect to your MySQL server > and has the proper privileges that these tests require such > as 'drop table', 'create table', 'drop procedure', 'create procedure' > as well as others. > > mysql> grant all privileges on test.* to 'root'@'localhost' identified > by 's3kr1t'; > > You can also optionally set the user to run 'make test' with: > > perl Makefile.pl --testuser=username > > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Failed to determine directory of mysql.h. Use > > perl Makefile.PL --cflags=-I > > to set this directory. For details see the INSTALL.html file, > section "C Compiler flags" or type > > perl Makefile.PL --help > Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > CAPTTOFU/DBD-mysql-4.013.tar.gz > /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK > Running make test > Make had some problems, won't test > Running make install > Make had some problems, won't install > Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. > Falling back to other methods to determine prerequisites > Failed during this command: > CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO > '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 > > > -- > Piotr Borowiec > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From piotrborowiec at g.pl Tue Feb 16 06:14:29 2010 From: piotrborowiec at g.pl (Piotr Borowiec) Date: Tue, 16 Feb 2010 12:14:29 +0100 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> Message-ID: <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu 9.10. What should I check in first order? Thanks for advice @sgul.ac.uk>: > > Hi Piotr, > > this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. > > But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try > > perl Makefile.PL --mysql_config= > > regards > > adam > > > On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: > >> Hi! >> >> Last time I had a problem with loading_ncbi script so I decided to >> start with fresh biosql andy also Unix. When I want to install >> DBD::mysql module there is some mistakes. I`m not sure but maybe the >> version mysql is not correct. I already have 5.1 >> >> cpan[1]> install DBD::mysql >> CPAN: Storable loaded ok (v2.18) >> Going to read /home/scati/.cpan/Metadata >> ?Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >> Running install for module 'DBD::mysql' >> CPAN: Data::Dumper loaded ok (v2.121_14) >> 'YAML' not installed, falling back to Data::Dumper and Storable to >> read prefs '/home/scati/.cpan/prefs' >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> CPAN: Digest::SHA loaded ok (v5.45) >> CPAN: Compress::Zlib loaded ok (v2.008) >> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> ok >> Scanning cache /home/scati/.cpan/build for sizes >> ............................................................................DONE >> DBD-mysql-4.013/ >> DBD-mysql-4.013/lib/ >> DBD-mysql-4.013/lib/DBD/ >> DBD-mysql-4.013/lib/DBD/mysql.pm >> DBD-mysql-4.013/lib/DBD/mysql/ >> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >> DBD-mysql-4.013/lib/Bundle/ >> DBD-mysql-4.013/lib/Bundle/DBD/ >> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >> DBD-mysql-4.013/mysql.xs >> DBD-mysql-4.013/dbdimp.c >> DBD-mysql-4.013/myld >> DBD-mysql-4.013/INSTALL.html >> DBD-mysql-4.013/Makefile.PL.embedded >> DBD-mysql-4.013/TODO >> DBD-mysql-4.013/README >> DBD-mysql-4.013/MANIFEST.SKIP >> DBD-mysql-4.013/ChangeLog >> DBD-mysql-4.013/Makefile.PL >> DBD-mysql-4.013/META.yml >> DBD-mysql-4.013/dbdimp.h >> DBD-mysql-4.013/eg/ >> DBD-mysql-4.013/eg/prepare_memory_usage.pl >> DBD-mysql-4.013/eg/proc_example2b.pl >> DBD-mysql-4.013/eg/proc_example2.pl >> DBD-mysql-4.013/eg/decimal_test.pl >> DBD-mysql-4.013/eg/bug30033pg.pl >> DBD-mysql-4.013/eg/proc_example2a.pl >> DBD-mysql-4.013/eg/proc_example4.pl >> DBD-mysql-4.013/eg/bug21028.pl >> DBD-mysql-4.013/eg/bug14979.pl >> DBD-mysql-4.013/eg/bug30033.pl >> DBD-mysql-4.013/eg/issue21946.pl >> DBD-mysql-4.013/eg/proc_example3.pl >> DBD-mysql-4.013/eg/proc_example1.pl >> DBD-mysql-4.013/constants.h >> DBD-mysql-4.013/t/ >> DBD-mysql-4.013/t/85init_command.t >> DBD-mysql-4.013/t/40listfields.t >> DBD-mysql-4.013/t/40bindparam.t >> DBD-mysql-4.013/t/mysql.mtest >> DBD-mysql-4.013/t/41bindparam.t >> DBD-mysql-4.013/t/76multi_statement.t >> DBD-mysql-4.013/t/40nulls.t >> DBD-mysql-4.013/t/32insert_error.t >> DBD-mysql-4.013/t/40catalog.t >> DBD-mysql-4.013/t/51bind_type_guessing.t >> DBD-mysql-4.013/t/40bindparam2.t >> DBD-mysql-4.013/t/41blobs_prepare.t >> DBD-mysql-4.013/t/20createdrop.t >> DBD-mysql-4.013/t/70takeimp.t >> DBD-mysql-4.013/t/42bindparam.t >> DBD-mysql-4.013/t/00base.t >> DBD-mysql-4.013/t/55utf8.t >> DBD-mysql-4.013/t/65types.t >> DBD-mysql-4.013/t/40server_prepare_error.t >> DBD-mysql-4.013/t/31insertid.t >> DBD-mysql-4.013/t/29warnings.t >> DBD-mysql-4.013/t/40types.t >> DBD-mysql-4.013/t/10connect.t >> DBD-mysql-4.013/t/lib.pl >> DBD-mysql-4.013/t/mysql.dbtest >> DBD-mysql-4.013/t/35limit.t >> DBD-mysql-4.013/t/71impdata.t >> DBD-mysql-4.013/t/40blobs.t >> DBD-mysql-4.013/t/40server_prepare.t >> DBD-mysql-4.013/t/40numrows.t >> DBD-mysql-4.013/t/35prepare.t >> DBD-mysql-4.013/t/40keyinfo.t >> DBD-mysql-4.013/t/75supported_sql.t >> DBD-mysql-4.013/t/60leaks.t >> DBD-mysql-4.013/t/50commit.t >> DBD-mysql-4.013/t/30insertfetch.t >> DBD-mysql-4.013/t/50chopblanks.t >> DBD-mysql-4.013/t/25lockunlock.t >> DBD-mysql-4.013/t/80procs.t >> DBD-mysql-4.013/MANIFEST >> CPAN: File::Temp loaded ok (v0.18) >> Warning (usually harmless): 'YAML' not installed, will not store >> persistent state >> >> ?CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >> >> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >> not contain the path to mysql_config. Resorting to guessed values! >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> >> >> PLEASE NOTE: >> >> For 'make test' to run properly, you must ensure that the >> database user 'root' can connect to your MySQL server >> and has the proper privileges that these tests require such >> as 'drop table', 'create table', 'drop procedure', 'create procedure' >> as well as others. >> >> mysql> grant all privileges on test.* to 'root'@'localhost' identified >> by 's3kr1t'; >> >> You can also optionally set the user to run 'make test' with: >> >> perl Makefile.pl --testuser=username >> >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Failed to determine directory of mysql.h. Use >> >> ?perl Makefile.PL --cflags=-I >> >> to set this directory. For details see the INSTALL.html file, >> section "C Compiler flags" or type >> >> ?perl Makefile.PL --help >> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >> Warning (usually harmless): 'YAML' not installed, will not store >> persistent state >> ?CAPTTOFU/DBD-mysql-4.013.tar.gz >> ?/usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >> Running make test >> ?Make had some problems, won't test >> Running make install >> ?Make had some problems, won't install >> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >> Falling back to other methods to determine prerequisites >> Failed during this command: >> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >> cpan[1]> install DBD::mysql >> CPAN: Storable loaded ok (v2.18) >> Going to read /home/scati/.cpan/Metadata >> ?Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >> Running install for module 'DBD::mysql' >> CPAN: Data::Dumper loaded ok (v2.121_14) >> 'YAML' not installed, falling back to Data::Dumper and Storable to >> read prefs '/home/scati/.cpan/prefs' >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> CPAN: Digest::SHA loaded ok (v5.45) >> CPAN: Compress::Zlib loaded ok (v2.008) >> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> ok >> Scanning cache /home/scati/.cpan/build for sizes >> ............................................................................DONE >> DBD-mysql-4.013/ >> DBD-mysql-4.013/lib/ >> DBD-mysql-4.013/lib/DBD/ >> DBD-mysql-4.013/lib/DBD/mysql.pm >> DBD-mysql-4.013/lib/DBD/mysql/ >> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >> DBD-mysql-4.013/lib/Bundle/ >> DBD-mysql-4.013/lib/Bundle/DBD/ >> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >> DBD-mysql-4.013/mysql.xs >> DBD-mysql-4.013/dbdimp.c >> DBD-mysql-4.013/myld >> DBD-mysql-4.013/INSTALL.html >> DBD-mysql-4.013/Makefile.PL.embedded >> DBD-mysql-4.013/TODO >> DBD-mysql-4.013/README >> DBD-mysql-4.013/MANIFEST.SKIP >> DBD-mysql-4.013/ChangeLog >> DBD-mysql-4.013/Makefile.PL >> DBD-mysql-4.013/META.yml >> DBD-mysql-4.013/dbdimp.h >> DBD-mysql-4.013/eg/ >> DBD-mysql-4.013/eg/prepare_memory_usage.pl >> DBD-mysql-4.013/eg/proc_example2b.pl >> DBD-mysql-4.013/eg/proc_example2.pl >> DBD-mysql-4.013/eg/decimal_test.pl >> DBD-mysql-4.013/eg/bug30033pg.pl >> DBD-mysql-4.013/eg/proc_example2a.pl >> DBD-mysql-4.013/eg/proc_example4.pl >> DBD-mysql-4.013/eg/bug21028.pl >> DBD-mysql-4.013/eg/bug14979.pl >> DBD-mysql-4.013/eg/bug30033.pl >> DBD-mysql-4.013/eg/issue21946.pl >> DBD-mysql-4.013/eg/proc_example3.pl >> DBD-mysql-4.013/eg/proc_example1.pl >> DBD-mysql-4.013/constants.h >> DBD-mysql-4.013/t/ >> DBD-mysql-4.013/t/85init_command.t >> DBD-mysql-4.013/t/40listfields.t >> DBD-mysql-4.013/t/40bindparam.t >> DBD-mysql-4.013/t/mysql.mtest >> DBD-mysql-4.013/t/41bindparam.t >> DBD-mysql-4.013/t/76multi_statement.t >> DBD-mysql-4.013/t/40nulls.t >> DBD-mysql-4.013/t/32insert_error.t >> DBD-mysql-4.013/t/40catalog.t >> DBD-mysql-4.013/t/51bind_type_guessing.t >> DBD-mysql-4.013/t/40bindparam2.t >> DBD-mysql-4.013/t/41blobs_prepare.t >> DBD-mysql-4.013/t/20createdrop.t >> DBD-mysql-4.013/t/70takeimp.t >> DBD-mysql-4.013/t/42bindparam.t >> DBD-mysql-4.013/t/00base.t >> DBD-mysql-4.013/t/55utf8.t >> DBD-mysql-4.013/t/65types.t >> DBD-mysql-4.013/t/40server_prepare_error.t >> DBD-mysql-4.013/t/31insertid.t >> DBD-mysql-4.013/t/29warnings.t >> DBD-mysql-4.013/t/40types.t >> DBD-mysql-4.013/t/10connect.t >> DBD-mysql-4.013/t/lib.pl >> DBD-mysql-4.013/t/mysql.dbtest >> DBD-mysql-4.013/t/35limit.t >> DBD-mysql-4.013/t/71impdata.t >> DBD-mysql-4.013/t/40blobs.t >> DBD-mysql-4.013/t/40server_prepare.t >> DBD-mysql-4.013/t/40numrows.t >> DBD-mysql-4.013/t/35prepare.t >> DBD-mysql-4.013/t/40keyinfo.t >> DBD-mysql-4.013/t/75supported_sql.t >> DBD-mysql-4.013/t/60leaks.t >> DBD-mysql-4.013/t/50commit.t >> DBD-mysql-4.013/t/30insertfetch.t >> DBD-mysql-4.013/t/50chopblanks.t >> DBD-mysql-4.013/t/25lockunlock.t >> DBD-mysql-4.013/t/80procs.t >> DBD-mysql-4.013/MANIFEST >> CPAN: File::Temp loaded ok (v0.18) >> Warning (usually harmless): 'YAML' not installed, will not store >> persistent state >> >> ?CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >> >> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >> not contain the path to mysql_config. Resorting to guessed values! >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> >> >> PLEASE NOTE: >> >> For 'make test' to run properly, you must ensure that the >> database user 'root' can connect to your MySQL server >> and has the proper privileges that these tests require such >> as 'drop table', 'create table', 'drop procedure', 'create procedure' >> as well as others. >> >> mysql> grant all privileges on test.* to 'root'@'localhost' identified >> by 's3kr1t'; >> >> You can also optionally set the user to run 'make test' with: >> >> perl Makefile.pl --testuser=username >> >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Failed to determine directory of mysql.h. Use >> >> ?perl Makefile.PL --cflags=-I >> >> to set this directory. For details see the INSTALL.html file, >> section "C Compiler flags" or type >> >> ?perl Makefile.PL --help >> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >> Warning (usually harmless): 'YAML' not installed, will not store >> persistent state >> ?CAPTTOFU/DBD-mysql-4.013.tar.gz >> ?/usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >> Running make test >> ?Make had some problems, won't test >> Running make install >> ?Make had some problems, won't install >> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >> Falling back to other methods to determine prerequisites >> Failed during this command: >> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >> >> >> -- >> Piotr Borowiec >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- Piotr Borowiec From awitney at sgul.ac.uk Tue Feb 16 06:24:08 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Tue, 16 Feb 2010 11:24:08 +0000 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> Message-ID: As i said you need to check if you have mysql_config installed. If not then for Ubuntu take a look at this: http://ubuntuforums.org/showthread.php?t=573286 adam On 16 Feb 2010, at 11:14, Piotr Borowiec wrote: > I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu > 9.10. What should I check in first order? > > Thanks for advice > > @sgul.ac.uk>: >> >> Hi Piotr, >> >> this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. >> >> But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try >> >> perl Makefile.PL --mysql_config= >> >> regards >> >> adam >> >> >> On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: >> >>> Hi! >>> >>> Last time I had a problem with loading_ncbi script so I decided to >>> start with fresh biosql andy also Unix. When I want to install >>> DBD::mysql module there is some mistakes. I`m not sure but maybe the >>> version mysql is not correct. I already have 5.1 >>> >>> cpan[1]> install DBD::mysql >>> CPAN: Storable loaded ok (v2.18) >>> Going to read /home/scati/.cpan/Metadata >>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>> Running install for module 'DBD::mysql' >>> CPAN: Data::Dumper loaded ok (v2.121_14) >>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>> read prefs '/home/scati/.cpan/prefs' >>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> CPAN: Digest::SHA loaded ok (v5.45) >>> CPAN: Compress::Zlib loaded ok (v2.008) >>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> ok >>> Scanning cache /home/scati/.cpan/build for sizes >>> ............................................................................DONE >>> DBD-mysql-4.013/ >>> DBD-mysql-4.013/lib/ >>> DBD-mysql-4.013/lib/DBD/ >>> DBD-mysql-4.013/lib/DBD/mysql.pm >>> DBD-mysql-4.013/lib/DBD/mysql/ >>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>> DBD-mysql-4.013/lib/Bundle/ >>> DBD-mysql-4.013/lib/Bundle/DBD/ >>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>> DBD-mysql-4.013/mysql.xs >>> DBD-mysql-4.013/dbdimp.c >>> DBD-mysql-4.013/myld >>> DBD-mysql-4.013/INSTALL.html >>> DBD-mysql-4.013/Makefile.PL.embedded >>> DBD-mysql-4.013/TODO >>> DBD-mysql-4.013/README >>> DBD-mysql-4.013/MANIFEST.SKIP >>> DBD-mysql-4.013/ChangeLog >>> DBD-mysql-4.013/Makefile.PL >>> DBD-mysql-4.013/META.yml >>> DBD-mysql-4.013/dbdimp.h >>> DBD-mysql-4.013/eg/ >>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>> DBD-mysql-4.013/eg/proc_example2b.pl >>> DBD-mysql-4.013/eg/proc_example2.pl >>> DBD-mysql-4.013/eg/decimal_test.pl >>> DBD-mysql-4.013/eg/bug30033pg.pl >>> DBD-mysql-4.013/eg/proc_example2a.pl >>> DBD-mysql-4.013/eg/proc_example4.pl >>> DBD-mysql-4.013/eg/bug21028.pl >>> DBD-mysql-4.013/eg/bug14979.pl >>> DBD-mysql-4.013/eg/bug30033.pl >>> DBD-mysql-4.013/eg/issue21946.pl >>> DBD-mysql-4.013/eg/proc_example3.pl >>> DBD-mysql-4.013/eg/proc_example1.pl >>> DBD-mysql-4.013/constants.h >>> DBD-mysql-4.013/t/ >>> DBD-mysql-4.013/t/85init_command.t >>> DBD-mysql-4.013/t/40listfields.t >>> DBD-mysql-4.013/t/40bindparam.t >>> DBD-mysql-4.013/t/mysql.mtest >>> DBD-mysql-4.013/t/41bindparam.t >>> DBD-mysql-4.013/t/76multi_statement.t >>> DBD-mysql-4.013/t/40nulls.t >>> DBD-mysql-4.013/t/32insert_error.t >>> DBD-mysql-4.013/t/40catalog.t >>> DBD-mysql-4.013/t/51bind_type_guessing.t >>> DBD-mysql-4.013/t/40bindparam2.t >>> DBD-mysql-4.013/t/41blobs_prepare.t >>> DBD-mysql-4.013/t/20createdrop.t >>> DBD-mysql-4.013/t/70takeimp.t >>> DBD-mysql-4.013/t/42bindparam.t >>> DBD-mysql-4.013/t/00base.t >>> DBD-mysql-4.013/t/55utf8.t >>> DBD-mysql-4.013/t/65types.t >>> DBD-mysql-4.013/t/40server_prepare_error.t >>> DBD-mysql-4.013/t/31insertid.t >>> DBD-mysql-4.013/t/29warnings.t >>> DBD-mysql-4.013/t/40types.t >>> DBD-mysql-4.013/t/10connect.t >>> DBD-mysql-4.013/t/lib.pl >>> DBD-mysql-4.013/t/mysql.dbtest >>> DBD-mysql-4.013/t/35limit.t >>> DBD-mysql-4.013/t/71impdata.t >>> DBD-mysql-4.013/t/40blobs.t >>> DBD-mysql-4.013/t/40server_prepare.t >>> DBD-mysql-4.013/t/40numrows.t >>> DBD-mysql-4.013/t/35prepare.t >>> DBD-mysql-4.013/t/40keyinfo.t >>> DBD-mysql-4.013/t/75supported_sql.t >>> DBD-mysql-4.013/t/60leaks.t >>> DBD-mysql-4.013/t/50commit.t >>> DBD-mysql-4.013/t/30insertfetch.t >>> DBD-mysql-4.013/t/50chopblanks.t >>> DBD-mysql-4.013/t/25lockunlock.t >>> DBD-mysql-4.013/t/80procs.t >>> DBD-mysql-4.013/MANIFEST >>> CPAN: File::Temp loaded ok (v0.18) >>> Warning (usually harmless): 'YAML' not installed, will not store >>> persistent state >>> >>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>> >>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>> not contain the path to mysql_config. Resorting to guessed values! >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> >>> >>> PLEASE NOTE: >>> >>> For 'make test' to run properly, you must ensure that the >>> database user 'root' can connect to your MySQL server >>> and has the proper privileges that these tests require such >>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>> as well as others. >>> >>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>> by 's3kr1t'; >>> >>> You can also optionally set the user to run 'make test' with: >>> >>> perl Makefile.pl --testuser=username >>> >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Failed to determine directory of mysql.h. Use >>> >>> perl Makefile.PL --cflags=-I >>> >>> to set this directory. For details see the INSTALL.html file, >>> section "C Compiler flags" or type >>> >>> perl Makefile.PL --help >>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>> Warning (usually harmless): 'YAML' not installed, will not store >>> persistent state >>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>> Running make test >>> Make had some problems, won't test >>> Running make install >>> Make had some problems, won't install >>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>> Falling back to other methods to determine prerequisites >>> Failed during this command: >>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>> cpan[1]> install DBD::mysql >>> CPAN: Storable loaded ok (v2.18) >>> Going to read /home/scati/.cpan/Metadata >>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>> Running install for module 'DBD::mysql' >>> CPAN: Data::Dumper loaded ok (v2.121_14) >>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>> read prefs '/home/scati/.cpan/prefs' >>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> CPAN: Digest::SHA loaded ok (v5.45) >>> CPAN: Compress::Zlib loaded ok (v2.008) >>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> ok >>> Scanning cache /home/scati/.cpan/build for sizes >>> ............................................................................DONE >>> DBD-mysql-4.013/ >>> DBD-mysql-4.013/lib/ >>> DBD-mysql-4.013/lib/DBD/ >>> DBD-mysql-4.013/lib/DBD/mysql.pm >>> DBD-mysql-4.013/lib/DBD/mysql/ >>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>> DBD-mysql-4.013/lib/Bundle/ >>> DBD-mysql-4.013/lib/Bundle/DBD/ >>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>> DBD-mysql-4.013/mysql.xs >>> DBD-mysql-4.013/dbdimp.c >>> DBD-mysql-4.013/myld >>> DBD-mysql-4.013/INSTALL.html >>> DBD-mysql-4.013/Makefile.PL.embedded >>> DBD-mysql-4.013/TODO >>> DBD-mysql-4.013/README >>> DBD-mysql-4.013/MANIFEST.SKIP >>> DBD-mysql-4.013/ChangeLog >>> DBD-mysql-4.013/Makefile.PL >>> DBD-mysql-4.013/META.yml >>> DBD-mysql-4.013/dbdimp.h >>> DBD-mysql-4.013/eg/ >>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>> DBD-mysql-4.013/eg/proc_example2b.pl >>> DBD-mysql-4.013/eg/proc_example2.pl >>> DBD-mysql-4.013/eg/decimal_test.pl >>> DBD-mysql-4.013/eg/bug30033pg.pl >>> DBD-mysql-4.013/eg/proc_example2a.pl >>> DBD-mysql-4.013/eg/proc_example4.pl >>> DBD-mysql-4.013/eg/bug21028.pl >>> DBD-mysql-4.013/eg/bug14979.pl >>> DBD-mysql-4.013/eg/bug30033.pl >>> DBD-mysql-4.013/eg/issue21946.pl >>> DBD-mysql-4.013/eg/proc_example3.pl >>> DBD-mysql-4.013/eg/proc_example1.pl >>> DBD-mysql-4.013/constants.h >>> DBD-mysql-4.013/t/ >>> DBD-mysql-4.013/t/85init_command.t >>> DBD-mysql-4.013/t/40listfields.t >>> DBD-mysql-4.013/t/40bindparam.t >>> DBD-mysql-4.013/t/mysql.mtest >>> DBD-mysql-4.013/t/41bindparam.t >>> DBD-mysql-4.013/t/76multi_statement.t >>> DBD-mysql-4.013/t/40nulls.t >>> DBD-mysql-4.013/t/32insert_error.t >>> DBD-mysql-4.013/t/40catalog.t >>> DBD-mysql-4.013/t/51bind_type_guessing.t >>> DBD-mysql-4.013/t/40bindparam2.t >>> DBD-mysql-4.013/t/41blobs_prepare.t >>> DBD-mysql-4.013/t/20createdrop.t >>> DBD-mysql-4.013/t/70takeimp.t >>> DBD-mysql-4.013/t/42bindparam.t >>> DBD-mysql-4.013/t/00base.t >>> DBD-mysql-4.013/t/55utf8.t >>> DBD-mysql-4.013/t/65types.t >>> DBD-mysql-4.013/t/40server_prepare_error.t >>> DBD-mysql-4.013/t/31insertid.t >>> DBD-mysql-4.013/t/29warnings.t >>> DBD-mysql-4.013/t/40types.t >>> DBD-mysql-4.013/t/10connect.t >>> DBD-mysql-4.013/t/lib.pl >>> DBD-mysql-4.013/t/mysql.dbtest >>> DBD-mysql-4.013/t/35limit.t >>> DBD-mysql-4.013/t/71impdata.t >>> DBD-mysql-4.013/t/40blobs.t >>> DBD-mysql-4.013/t/40server_prepare.t >>> DBD-mysql-4.013/t/40numrows.t >>> DBD-mysql-4.013/t/35prepare.t >>> DBD-mysql-4.013/t/40keyinfo.t >>> DBD-mysql-4.013/t/75supported_sql.t >>> DBD-mysql-4.013/t/60leaks.t >>> DBD-mysql-4.013/t/50commit.t >>> DBD-mysql-4.013/t/30insertfetch.t >>> DBD-mysql-4.013/t/50chopblanks.t >>> DBD-mysql-4.013/t/25lockunlock.t >>> DBD-mysql-4.013/t/80procs.t >>> DBD-mysql-4.013/MANIFEST >>> CPAN: File::Temp loaded ok (v0.18) >>> Warning (usually harmless): 'YAML' not installed, will not store >>> persistent state >>> >>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>> >>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>> not contain the path to mysql_config. Resorting to guessed values! >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> >>> >>> PLEASE NOTE: >>> >>> For 'make test' to run properly, you must ensure that the >>> database user 'root' can connect to your MySQL server >>> and has the proper privileges that these tests require such >>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>> as well as others. >>> >>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>> by 's3kr1t'; >>> >>> You can also optionally set the user to run 'make test' with: >>> >>> perl Makefile.pl --testuser=username >>> >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Failed to determine directory of mysql.h. Use >>> >>> perl Makefile.PL --cflags=-I >>> >>> to set this directory. For details see the INSTALL.html file, >>> section "C Compiler flags" or type >>> >>> perl Makefile.PL --help >>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>> Warning (usually harmless): 'YAML' not installed, will not store >>> persistent state >>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>> Running make test >>> Make had some problems, won't test >>> Running make install >>> Make had some problems, won't install >>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>> Falling back to other methods to determine prerequisites >>> Failed during this command: >>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>> >>> >>> -- >>> Piotr Borowiec >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> > > > > -- > Piotr Borowiec From cjfields at illinois.edu Tue Feb 16 08:26:24 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 16 Feb 2010 07:26:24 -0600 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> Message-ID: <101DFF66-EE65-49AB-A993-0B904F92F6DC@illinois.edu> Piotr, Adam, I can conform that is the problem. I ran into the exact issue when running tests on my local Ubuntu 9.10 setup, and installing the libmysqld-dev package fixed it. You can also install the DBD::mysql package as well (libdbd-mysql-perl). chris On Feb 16, 2010, at 5:24 AM, Adam Witney wrote: > > As i said you need to check if you have mysql_config installed. If not then for Ubuntu take a look at this: > > http://ubuntuforums.org/showthread.php?t=573286 > > adam > > > On 16 Feb 2010, at 11:14, Piotr Borowiec wrote: > >> I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu >> 9.10. What should I check in first order? >> >> Thanks for advice >> >> @sgul.ac.uk>: >>> >>> Hi Piotr, >>> >>> this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. >>> >>> But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try >>> >>> perl Makefile.PL --mysql_config= >>> >>> regards >>> >>> adam >>> >>> >>> On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: >>> >>>> Hi! >>>> >>>> Last time I had a problem with loading_ncbi script so I decided to >>>> start with fresh biosql andy also Unix. When I want to install >>>> DBD::mysql module there is some mistakes. I`m not sure but maybe the >>>> version mysql is not correct. I already have 5.1 >>>> >>>> cpan[1]> install DBD::mysql >>>> CPAN: Storable loaded ok (v2.18) >>>> Going to read /home/scati/.cpan/Metadata >>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>> Running install for module 'DBD::mysql' >>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>> read prefs '/home/scati/.cpan/prefs' >>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> CPAN: Digest::SHA loaded ok (v5.45) >>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> ok >>>> Scanning cache /home/scati/.cpan/build for sizes >>>> ............................................................................DONE >>>> DBD-mysql-4.013/ >>>> DBD-mysql-4.013/lib/ >>>> DBD-mysql-4.013/lib/DBD/ >>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>> DBD-mysql-4.013/lib/Bundle/ >>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>> DBD-mysql-4.013/mysql.xs >>>> DBD-mysql-4.013/dbdimp.c >>>> DBD-mysql-4.013/myld >>>> DBD-mysql-4.013/INSTALL.html >>>> DBD-mysql-4.013/Makefile.PL.embedded >>>> DBD-mysql-4.013/TODO >>>> DBD-mysql-4.013/README >>>> DBD-mysql-4.013/MANIFEST.SKIP >>>> DBD-mysql-4.013/ChangeLog >>>> DBD-mysql-4.013/Makefile.PL >>>> DBD-mysql-4.013/META.yml >>>> DBD-mysql-4.013/dbdimp.h >>>> DBD-mysql-4.013/eg/ >>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>> DBD-mysql-4.013/eg/proc_example2.pl >>>> DBD-mysql-4.013/eg/decimal_test.pl >>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>> DBD-mysql-4.013/eg/proc_example4.pl >>>> DBD-mysql-4.013/eg/bug21028.pl >>>> DBD-mysql-4.013/eg/bug14979.pl >>>> DBD-mysql-4.013/eg/bug30033.pl >>>> DBD-mysql-4.013/eg/issue21946.pl >>>> DBD-mysql-4.013/eg/proc_example3.pl >>>> DBD-mysql-4.013/eg/proc_example1.pl >>>> DBD-mysql-4.013/constants.h >>>> DBD-mysql-4.013/t/ >>>> DBD-mysql-4.013/t/85init_command.t >>>> DBD-mysql-4.013/t/40listfields.t >>>> DBD-mysql-4.013/t/40bindparam.t >>>> DBD-mysql-4.013/t/mysql.mtest >>>> DBD-mysql-4.013/t/41bindparam.t >>>> DBD-mysql-4.013/t/76multi_statement.t >>>> DBD-mysql-4.013/t/40nulls.t >>>> DBD-mysql-4.013/t/32insert_error.t >>>> DBD-mysql-4.013/t/40catalog.t >>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>> DBD-mysql-4.013/t/40bindparam2.t >>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>> DBD-mysql-4.013/t/20createdrop.t >>>> DBD-mysql-4.013/t/70takeimp.t >>>> DBD-mysql-4.013/t/42bindparam.t >>>> DBD-mysql-4.013/t/00base.t >>>> DBD-mysql-4.013/t/55utf8.t >>>> DBD-mysql-4.013/t/65types.t >>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>> DBD-mysql-4.013/t/31insertid.t >>>> DBD-mysql-4.013/t/29warnings.t >>>> DBD-mysql-4.013/t/40types.t >>>> DBD-mysql-4.013/t/10connect.t >>>> DBD-mysql-4.013/t/lib.pl >>>> DBD-mysql-4.013/t/mysql.dbtest >>>> DBD-mysql-4.013/t/35limit.t >>>> DBD-mysql-4.013/t/71impdata.t >>>> DBD-mysql-4.013/t/40blobs.t >>>> DBD-mysql-4.013/t/40server_prepare.t >>>> DBD-mysql-4.013/t/40numrows.t >>>> DBD-mysql-4.013/t/35prepare.t >>>> DBD-mysql-4.013/t/40keyinfo.t >>>> DBD-mysql-4.013/t/75supported_sql.t >>>> DBD-mysql-4.013/t/60leaks.t >>>> DBD-mysql-4.013/t/50commit.t >>>> DBD-mysql-4.013/t/30insertfetch.t >>>> DBD-mysql-4.013/t/50chopblanks.t >>>> DBD-mysql-4.013/t/25lockunlock.t >>>> DBD-mysql-4.013/t/80procs.t >>>> DBD-mysql-4.013/MANIFEST >>>> CPAN: File::Temp loaded ok (v0.18) >>>> Warning (usually harmless): 'YAML' not installed, will not store >>>> persistent state >>>> >>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>> >>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>> not contain the path to mysql_config. Resorting to guessed values! >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> >>>> >>>> PLEASE NOTE: >>>> >>>> For 'make test' to run properly, you must ensure that the >>>> database user 'root' can connect to your MySQL server >>>> and has the proper privileges that these tests require such >>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>> as well as others. >>>> >>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>> by 's3kr1t'; >>>> >>>> You can also optionally set the user to run 'make test' with: >>>> >>>> perl Makefile.pl --testuser=username >>>> >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Failed to determine directory of mysql.h. Use >>>> >>>> perl Makefile.PL --cflags=-I >>>> >>>> to set this directory. For details see the INSTALL.html file, >>>> section "C Compiler flags" or type >>>> >>>> perl Makefile.PL --help >>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>> Warning (usually harmless): 'YAML' not installed, will not store >>>> persistent state >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>> Running make test >>>> Make had some problems, won't test >>>> Running make install >>>> Make had some problems, won't install >>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>> Falling back to other methods to determine prerequisites >>>> Failed during this command: >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>> cpan[1]> install DBD::mysql >>>> CPAN: Storable loaded ok (v2.18) >>>> Going to read /home/scati/.cpan/Metadata >>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>> Running install for module 'DBD::mysql' >>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>> read prefs '/home/scati/.cpan/prefs' >>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> CPAN: Digest::SHA loaded ok (v5.45) >>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> ok >>>> Scanning cache /home/scati/.cpan/build for sizes >>>> ............................................................................DONE >>>> DBD-mysql-4.013/ >>>> DBD-mysql-4.013/lib/ >>>> DBD-mysql-4.013/lib/DBD/ >>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>> DBD-mysql-4.013/lib/Bundle/ >>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>> DBD-mysql-4.013/mysql.xs >>>> DBD-mysql-4.013/dbdimp.c >>>> DBD-mysql-4.013/myld >>>> DBD-mysql-4.013/INSTALL.html >>>> DBD-mysql-4.013/Makefile.PL.embedded >>>> DBD-mysql-4.013/TODO >>>> DBD-mysql-4.013/README >>>> DBD-mysql-4.013/MANIFEST.SKIP >>>> DBD-mysql-4.013/ChangeLog >>>> DBD-mysql-4.013/Makefile.PL >>>> DBD-mysql-4.013/META.yml >>>> DBD-mysql-4.013/dbdimp.h >>>> DBD-mysql-4.013/eg/ >>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>> DBD-mysql-4.013/eg/proc_example2.pl >>>> DBD-mysql-4.013/eg/decimal_test.pl >>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>> DBD-mysql-4.013/eg/proc_example4.pl >>>> DBD-mysql-4.013/eg/bug21028.pl >>>> DBD-mysql-4.013/eg/bug14979.pl >>>> DBD-mysql-4.013/eg/bug30033.pl >>>> DBD-mysql-4.013/eg/issue21946.pl >>>> DBD-mysql-4.013/eg/proc_example3.pl >>>> DBD-mysql-4.013/eg/proc_example1.pl >>>> DBD-mysql-4.013/constants.h >>>> DBD-mysql-4.013/t/ >>>> DBD-mysql-4.013/t/85init_command.t >>>> DBD-mysql-4.013/t/40listfields.t >>>> DBD-mysql-4.013/t/40bindparam.t >>>> DBD-mysql-4.013/t/mysql.mtest >>>> DBD-mysql-4.013/t/41bindparam.t >>>> DBD-mysql-4.013/t/76multi_statement.t >>>> DBD-mysql-4.013/t/40nulls.t >>>> DBD-mysql-4.013/t/32insert_error.t >>>> DBD-mysql-4.013/t/40catalog.t >>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>> DBD-mysql-4.013/t/40bindparam2.t >>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>> DBD-mysql-4.013/t/20createdrop.t >>>> DBD-mysql-4.013/t/70takeimp.t >>>> DBD-mysql-4.013/t/42bindparam.t >>>> DBD-mysql-4.013/t/00base.t >>>> DBD-mysql-4.013/t/55utf8.t >>>> DBD-mysql-4.013/t/65types.t >>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>> DBD-mysql-4.013/t/31insertid.t >>>> DBD-mysql-4.013/t/29warnings.t >>>> DBD-mysql-4.013/t/40types.t >>>> DBD-mysql-4.013/t/10connect.t >>>> DBD-mysql-4.013/t/lib.pl >>>> DBD-mysql-4.013/t/mysql.dbtest >>>> DBD-mysql-4.013/t/35limit.t >>>> DBD-mysql-4.013/t/71impdata.t >>>> DBD-mysql-4.013/t/40blobs.t >>>> DBD-mysql-4.013/t/40server_prepare.t >>>> DBD-mysql-4.013/t/40numrows.t >>>> DBD-mysql-4.013/t/35prepare.t >>>> DBD-mysql-4.013/t/40keyinfo.t >>>> DBD-mysql-4.013/t/75supported_sql.t >>>> DBD-mysql-4.013/t/60leaks.t >>>> DBD-mysql-4.013/t/50commit.t >>>> DBD-mysql-4.013/t/30insertfetch.t >>>> DBD-mysql-4.013/t/50chopblanks.t >>>> DBD-mysql-4.013/t/25lockunlock.t >>>> DBD-mysql-4.013/t/80procs.t >>>> DBD-mysql-4.013/MANIFEST >>>> CPAN: File::Temp loaded ok (v0.18) >>>> Warning (usually harmless): 'YAML' not installed, will not store >>>> persistent state >>>> >>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>> >>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>> not contain the path to mysql_config. Resorting to guessed values! >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> >>>> >>>> PLEASE NOTE: >>>> >>>> For 'make test' to run properly, you must ensure that the >>>> database user 'root' can connect to your MySQL server >>>> and has the proper privileges that these tests require such >>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>> as well as others. >>>> >>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>> by 's3kr1t'; >>>> >>>> You can also optionally set the user to run 'make test' with: >>>> >>>> perl Makefile.pl --testuser=username >>>> >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Failed to determine directory of mysql.h. Use >>>> >>>> perl Makefile.PL --cflags=-I >>>> >>>> to set this directory. For details see the INSTALL.html file, >>>> section "C Compiler flags" or type >>>> >>>> perl Makefile.PL --help >>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>> Warning (usually harmless): 'YAML' not installed, will not store >>>> persistent state >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>> Running make test >>>> Make had some problems, won't test >>>> Running make install >>>> Make had some problems, won't install >>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>> Falling back to other methods to determine prerequisites >>>> Failed during this command: >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>> >>>> >>>> -- >>>> Piotr Borowiec >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >>> >> >> >> >> -- >> Piotr Borowiec > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From piotrborowiec at g.pl Tue Feb 16 09:19:37 2010 From: piotrborowiec at g.pl (Piotr Borowiec) Date: Tue, 16 Feb 2010 15:19:37 +0100 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: <101DFF66-EE65-49AB-A993-0B904F92F6DC@illinois.edu> References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> <101DFF66-EE65-49AB-A993-0B904F92F6DC@illinois.edu> Message-ID: <1c828cb91002160619xa82aedcj1578a74d6e2b329a@mail.gmail.com> HI, I`ve solved that problem, I installed libmysqlclient16-dev. So, that is a time to start script - load_ncbi_taxonomy.pl. I was puting in to terminal: sudo perl load_ncbi_taxonomy.pl etc. After that, there was another bug: 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 919. Use of uninitialized value in concatenation (.) or string at load_ncbi_taxonomy.pl line 921. So, I come back to same point. 2010/2/16 Chris Fields : > Piotr, Adam, > > I can conform that is the problem. ?I ran into the exact issue when running tests on my local Ubuntu 9.10 setup, and installing the libmysqld-dev package fixed it. ?You can also install the DBD::mysql package as well (libdbd-mysql-perl). > > chris > > On Feb 16, 2010, at 5:24 AM, Adam Witney wrote: > >> >> As i said you need to check if you have mysql_config installed. If not then for Ubuntu take a look at this: >> >> http://ubuntuforums.org/showthread.php?t=573286 >> >> adam >> >> >> On 16 Feb 2010, at 11:14, Piotr Borowiec wrote: >> >>> I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu >>> 9.10. What should I check in first order? >>> >>> Thanks for advice >>> >>> @sgul.ac.uk>: >>>> >>>> Hi Piotr, >>>> >>>> this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. >>>> >>>> But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try >>>> >>>> perl Makefile.PL --mysql_config= >>>> >>>> regards >>>> >>>> adam >>>> >>>> >>>> On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: >>>> >>>>> Hi! >>>>> >>>>> Last time I had a problem with loading_ncbi script so I decided to >>>>> start with fresh biosql andy also Unix. When I want to install >>>>> DBD::mysql module there is some mistakes. I`m not sure but maybe the >>>>> version mysql is not correct. I already have 5.1 >>>>> >>>>> cpan[1]> install DBD::mysql >>>>> CPAN: Storable loaded ok (v2.18) >>>>> Going to read /home/scati/.cpan/Metadata >>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>> Running install for module 'DBD::mysql' >>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>> read prefs '/home/scati/.cpan/prefs' >>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> ok >>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>> ............................................................................DONE >>>>> DBD-mysql-4.013/ >>>>> DBD-mysql-4.013/lib/ >>>>> DBD-mysql-4.013/lib/DBD/ >>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>> DBD-mysql-4.013/lib/Bundle/ >>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>> DBD-mysql-4.013/mysql.xs >>>>> DBD-mysql-4.013/dbdimp.c >>>>> DBD-mysql-4.013/myld >>>>> DBD-mysql-4.013/INSTALL.html >>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>> DBD-mysql-4.013/TODO >>>>> DBD-mysql-4.013/README >>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>> DBD-mysql-4.013/ChangeLog >>>>> DBD-mysql-4.013/Makefile.PL >>>>> DBD-mysql-4.013/META.yml >>>>> DBD-mysql-4.013/dbdimp.h >>>>> DBD-mysql-4.013/eg/ >>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>> DBD-mysql-4.013/constants.h >>>>> DBD-mysql-4.013/t/ >>>>> DBD-mysql-4.013/t/85init_command.t >>>>> DBD-mysql-4.013/t/40listfields.t >>>>> DBD-mysql-4.013/t/40bindparam.t >>>>> DBD-mysql-4.013/t/mysql.mtest >>>>> DBD-mysql-4.013/t/41bindparam.t >>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>> DBD-mysql-4.013/t/40nulls.t >>>>> DBD-mysql-4.013/t/32insert_error.t >>>>> DBD-mysql-4.013/t/40catalog.t >>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>> DBD-mysql-4.013/t/20createdrop.t >>>>> DBD-mysql-4.013/t/70takeimp.t >>>>> DBD-mysql-4.013/t/42bindparam.t >>>>> DBD-mysql-4.013/t/00base.t >>>>> DBD-mysql-4.013/t/55utf8.t >>>>> DBD-mysql-4.013/t/65types.t >>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>> DBD-mysql-4.013/t/31insertid.t >>>>> DBD-mysql-4.013/t/29warnings.t >>>>> DBD-mysql-4.013/t/40types.t >>>>> DBD-mysql-4.013/t/10connect.t >>>>> DBD-mysql-4.013/t/lib.pl >>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>> DBD-mysql-4.013/t/35limit.t >>>>> DBD-mysql-4.013/t/71impdata.t >>>>> DBD-mysql-4.013/t/40blobs.t >>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>> DBD-mysql-4.013/t/40numrows.t >>>>> DBD-mysql-4.013/t/35prepare.t >>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>> DBD-mysql-4.013/t/60leaks.t >>>>> DBD-mysql-4.013/t/50commit.t >>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>> DBD-mysql-4.013/t/80procs.t >>>>> DBD-mysql-4.013/MANIFEST >>>>> CPAN: File::Temp loaded ok (v0.18) >>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>> persistent state >>>>> >>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>> >>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> >>>>> >>>>> PLEASE NOTE: >>>>> >>>>> For 'make test' to run properly, you must ensure that the >>>>> database user 'root' can connect to your MySQL server >>>>> and has the proper privileges that these tests require such >>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>> as well as others. >>>>> >>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>> by 's3kr1t'; >>>>> >>>>> You can also optionally set the user to run 'make test' with: >>>>> >>>>> perl Makefile.pl --testuser=username >>>>> >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Failed to determine directory of mysql.h. Use >>>>> >>>>> perl Makefile.PL --cflags=-I >>>>> >>>>> to set this directory. For details see the INSTALL.html file, >>>>> section "C Compiler flags" or type >>>>> >>>>> perl Makefile.PL --help >>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>> persistent state >>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>> Running make test >>>>> Make had some problems, won't test >>>>> Running make install >>>>> Make had some problems, won't install >>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>> Falling back to other methods to determine prerequisites >>>>> Failed during this command: >>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>> cpan[1]> install DBD::mysql >>>>> CPAN: Storable loaded ok (v2.18) >>>>> Going to read /home/scati/.cpan/Metadata >>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>> Running install for module 'DBD::mysql' >>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>> read prefs '/home/scati/.cpan/prefs' >>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> ok >>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>> ............................................................................DONE >>>>> DBD-mysql-4.013/ >>>>> DBD-mysql-4.013/lib/ >>>>> DBD-mysql-4.013/lib/DBD/ >>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>> DBD-mysql-4.013/lib/Bundle/ >>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>> DBD-mysql-4.013/mysql.xs >>>>> DBD-mysql-4.013/dbdimp.c >>>>> DBD-mysql-4.013/myld >>>>> DBD-mysql-4.013/INSTALL.html >>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>> DBD-mysql-4.013/TODO >>>>> DBD-mysql-4.013/README >>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>> DBD-mysql-4.013/ChangeLog >>>>> DBD-mysql-4.013/Makefile.PL >>>>> DBD-mysql-4.013/META.yml >>>>> DBD-mysql-4.013/dbdimp.h >>>>> DBD-mysql-4.013/eg/ >>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>> DBD-mysql-4.013/constants.h >>>>> DBD-mysql-4.013/t/ >>>>> DBD-mysql-4.013/t/85init_command.t >>>>> DBD-mysql-4.013/t/40listfields.t >>>>> DBD-mysql-4.013/t/40bindparam.t >>>>> DBD-mysql-4.013/t/mysql.mtest >>>>> DBD-mysql-4.013/t/41bindparam.t >>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>> DBD-mysql-4.013/t/40nulls.t >>>>> DBD-mysql-4.013/t/32insert_error.t >>>>> DBD-mysql-4.013/t/40catalog.t >>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>> DBD-mysql-4.013/t/20createdrop.t >>>>> DBD-mysql-4.013/t/70takeimp.t >>>>> DBD-mysql-4.013/t/42bindparam.t >>>>> DBD-mysql-4.013/t/00base.t >>>>> DBD-mysql-4.013/t/55utf8.t >>>>> DBD-mysql-4.013/t/65types.t >>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>> DBD-mysql-4.013/t/31insertid.t >>>>> DBD-mysql-4.013/t/29warnings.t >>>>> DBD-mysql-4.013/t/40types.t >>>>> DBD-mysql-4.013/t/10connect.t >>>>> DBD-mysql-4.013/t/lib.pl >>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>> DBD-mysql-4.013/t/35limit.t >>>>> DBD-mysql-4.013/t/71impdata.t >>>>> DBD-mysql-4.013/t/40blobs.t >>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>> DBD-mysql-4.013/t/40numrows.t >>>>> DBD-mysql-4.013/t/35prepare.t >>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>> DBD-mysql-4.013/t/60leaks.t >>>>> DBD-mysql-4.013/t/50commit.t >>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>> DBD-mysql-4.013/t/80procs.t >>>>> DBD-mysql-4.013/MANIFEST >>>>> CPAN: File::Temp loaded ok (v0.18) >>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>> persistent state >>>>> >>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>> >>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> >>>>> >>>>> PLEASE NOTE: >>>>> >>>>> For 'make test' to run properly, you must ensure that the >>>>> database user 'root' can connect to your MySQL server >>>>> and has the proper privileges that these tests require such >>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>> as well as others. >>>>> >>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>> by 's3kr1t'; >>>>> >>>>> You can also optionally set the user to run 'make test' with: >>>>> >>>>> perl Makefile.pl --testuser=username >>>>> >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Failed to determine directory of mysql.h. Use >>>>> >>>>> perl Makefile.PL --cflags=-I >>>>> >>>>> to set this directory. For details see the INSTALL.html file, >>>>> section "C Compiler flags" or type >>>>> >>>>> perl Makefile.PL --help >>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>> persistent state >>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>> Running make test >>>>> Make had some problems, won't test >>>>> Running make install >>>>> Make had some problems, won't install >>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>> Falling back to other methods to determine prerequisites >>>>> Failed during this command: >>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>> >>>>> >>>>> -- >>>>> Piotr Borowiec >>>>> _______________________________________________ >>>>> BioSQL-l mailing list >>>>> BioSQL-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>> >>>> >>> >>> >>> >>> -- >>> Piotr Borowiec >> >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- Piotr Borowiec From piotrborowiec at g.pl Tue Feb 16 09:32:40 2010 From: piotrborowiec at g.pl (Piotr Borowiec) Date: Tue, 16 Feb 2010 15:32:40 +0100 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: <78EE6F34-9BC7-4505-8858-6D9F3DBA2152@illinois.edu> References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> <101DFF66-EE65-49AB-A993-0B904F92F6DC@illinois.edu> <1c828cb91002160619xa82aedcj1578a74d6e2b329a@mail.gmail.com> <78EE6F34-9BC7-4505-8858-6D9F3DBA2152@illinois.edu> Message-ID: <1c828cb91002160632q5298839fje490e43b9e7034f@mail.gmail.com> Right, sorry for that. I was found answer http://bioperl.open-bio.org/SRC/bioperl-live/INSTALL.WIN So need to download, unzip and re-start script. 2010/2/16 Chris Fields : > That's not a bug. ?You need to use the --download option to retrieve the taxonomy files, they aren't included with the distribution. > > chris > > On Feb 16, 2010, at 8:19 AM, Piotr Borowiec wrote: > >> HI, I`ve solved that problem, I installed libmysqlclient16-dev. So, >> that is a time to start script - load_ncbi_taxonomy.pl. I was puting >> in to terminal: sudo perl load_ncbi_taxonomy.pl etc. After that, there >> was another bug: >> >> 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 919. >> Use of uninitialized value in concatenation (.) or string at >> load_ncbi_taxonomy.pl line 921. >> >> So, I come back to same point. >> >> 2010/2/16 Chris Fields : >>> Piotr, Adam, >>> >>> I can conform that is the problem. ?I ran into the exact issue when running tests on my local Ubuntu 9.10 setup, and installing the libmysqld-dev package fixed it. ?You can also install the DBD::mysql package as well (libdbd-mysql-perl). >>> >>> chris >>> >>> On Feb 16, 2010, at 5:24 AM, Adam Witney wrote: >>> >>>> >>>> As i said you need to check if you have mysql_config installed. If not then for Ubuntu take a look at this: >>>> >>>> http://ubuntuforums.org/showthread.php?t=573286 >>>> >>>> adam >>>> >>>> >>>> On 16 Feb 2010, at 11:14, Piotr Borowiec wrote: >>>> >>>>> I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu >>>>> 9.10. What should I check in first order? >>>>> >>>>> Thanks for advice >>>>> >>>>> @sgul.ac.uk>: >>>>>> >>>>>> Hi Piotr, >>>>>> >>>>>> this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. >>>>>> >>>>>> But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try >>>>>> >>>>>> perl Makefile.PL --mysql_config= >>>>>> >>>>>> regards >>>>>> >>>>>> adam >>>>>> >>>>>> >>>>>> On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: >>>>>> >>>>>>> Hi! >>>>>>> >>>>>>> Last time I had a problem with loading_ncbi script so I decided to >>>>>>> start with fresh biosql andy also Unix. When I want to install >>>>>>> DBD::mysql module there is some mistakes. I`m not sure but maybe the >>>>>>> version mysql is not correct. I already have 5.1 >>>>>>> >>>>>>> cpan[1]> install DBD::mysql >>>>>>> CPAN: Storable loaded ok (v2.18) >>>>>>> Going to read /home/scati/.cpan/Metadata >>>>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>>>> Running install for module 'DBD::mysql' >>>>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>>>> read prefs '/home/scati/.cpan/prefs' >>>>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> ok >>>>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>>>> ............................................................................DONE >>>>>>> DBD-mysql-4.013/ >>>>>>> DBD-mysql-4.013/lib/ >>>>>>> DBD-mysql-4.013/lib/DBD/ >>>>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>>>> DBD-mysql-4.013/lib/Bundle/ >>>>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>>>> DBD-mysql-4.013/mysql.xs >>>>>>> DBD-mysql-4.013/dbdimp.c >>>>>>> DBD-mysql-4.013/myld >>>>>>> DBD-mysql-4.013/INSTALL.html >>>>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>>>> DBD-mysql-4.013/TODO >>>>>>> DBD-mysql-4.013/README >>>>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>>>> DBD-mysql-4.013/ChangeLog >>>>>>> DBD-mysql-4.013/Makefile.PL >>>>>>> DBD-mysql-4.013/META.yml >>>>>>> DBD-mysql-4.013/dbdimp.h >>>>>>> DBD-mysql-4.013/eg/ >>>>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>>>> DBD-mysql-4.013/constants.h >>>>>>> DBD-mysql-4.013/t/ >>>>>>> DBD-mysql-4.013/t/85init_command.t >>>>>>> DBD-mysql-4.013/t/40listfields.t >>>>>>> DBD-mysql-4.013/t/40bindparam.t >>>>>>> DBD-mysql-4.013/t/mysql.mtest >>>>>>> DBD-mysql-4.013/t/41bindparam.t >>>>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>>>> DBD-mysql-4.013/t/40nulls.t >>>>>>> DBD-mysql-4.013/t/32insert_error.t >>>>>>> DBD-mysql-4.013/t/40catalog.t >>>>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>>>> DBD-mysql-4.013/t/20createdrop.t >>>>>>> DBD-mysql-4.013/t/70takeimp.t >>>>>>> DBD-mysql-4.013/t/42bindparam.t >>>>>>> DBD-mysql-4.013/t/00base.t >>>>>>> DBD-mysql-4.013/t/55utf8.t >>>>>>> DBD-mysql-4.013/t/65types.t >>>>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>>>> DBD-mysql-4.013/t/31insertid.t >>>>>>> DBD-mysql-4.013/t/29warnings.t >>>>>>> DBD-mysql-4.013/t/40types.t >>>>>>> DBD-mysql-4.013/t/10connect.t >>>>>>> DBD-mysql-4.013/t/lib.pl >>>>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>>>> DBD-mysql-4.013/t/35limit.t >>>>>>> DBD-mysql-4.013/t/71impdata.t >>>>>>> DBD-mysql-4.013/t/40blobs.t >>>>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>>>> DBD-mysql-4.013/t/40numrows.t >>>>>>> DBD-mysql-4.013/t/35prepare.t >>>>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>>>> DBD-mysql-4.013/t/60leaks.t >>>>>>> DBD-mysql-4.013/t/50commit.t >>>>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>>>> DBD-mysql-4.013/t/80procs.t >>>>>>> DBD-mysql-4.013/MANIFEST >>>>>>> CPAN: File::Temp loaded ok (v0.18) >>>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>>> persistent state >>>>>>> >>>>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>>>> >>>>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> >>>>>>> >>>>>>> PLEASE NOTE: >>>>>>> >>>>>>> For 'make test' to run properly, you must ensure that the >>>>>>> database user 'root' can connect to your MySQL server >>>>>>> and has the proper privileges that these tests require such >>>>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>>>> as well as others. >>>>>>> >>>>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>>>> by 's3kr1t'; >>>>>>> >>>>>>> You can also optionally set the user to run 'make test' with: >>>>>>> >>>>>>> perl Makefile.pl --testuser=username >>>>>>> >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Failed to determine directory of mysql.h. Use >>>>>>> >>>>>>> perl Makefile.PL --cflags=-I >>>>>>> >>>>>>> to set this directory. For details see the INSTALL.html file, >>>>>>> section "C Compiler flags" or type >>>>>>> >>>>>>> perl Makefile.PL --help >>>>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>>> persistent state >>>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>>>> Running make test >>>>>>> Make had some problems, won't test >>>>>>> Running make install >>>>>>> Make had some problems, won't install >>>>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>>>> Falling back to other methods to determine prerequisites >>>>>>> Failed during this command: >>>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >>>>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>>>> cpan[1]> install DBD::mysql >>>>>>> CPAN: Storable loaded ok (v2.18) >>>>>>> Going to read /home/scati/.cpan/Metadata >>>>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>>>> Running install for module 'DBD::mysql' >>>>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>>>> read prefs '/home/scati/.cpan/prefs' >>>>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> ok >>>>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>>>> ............................................................................DONE >>>>>>> DBD-mysql-4.013/ >>>>>>> DBD-mysql-4.013/lib/ >>>>>>> DBD-mysql-4.013/lib/DBD/ >>>>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>>>> DBD-mysql-4.013/lib/Bundle/ >>>>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>>>> DBD-mysql-4.013/mysql.xs >>>>>>> DBD-mysql-4.013/dbdimp.c >>>>>>> DBD-mysql-4.013/myld >>>>>>> DBD-mysql-4.013/INSTALL.html >>>>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>>>> DBD-mysql-4.013/TODO >>>>>>> DBD-mysql-4.013/README >>>>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>>>> DBD-mysql-4.013/ChangeLog >>>>>>> DBD-mysql-4.013/Makefile.PL >>>>>>> DBD-mysql-4.013/META.yml >>>>>>> DBD-mysql-4.013/dbdimp.h >>>>>>> DBD-mysql-4.013/eg/ >>>>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>>>> DBD-mysql-4.013/constants.h >>>>>>> DBD-mysql-4.013/t/ >>>>>>> DBD-mysql-4.013/t/85init_command.t >>>>>>> DBD-mysql-4.013/t/40listfields.t >>>>>>> DBD-mysql-4.013/t/40bindparam.t >>>>>>> DBD-mysql-4.013/t/mysql.mtest >>>>>>> DBD-mysql-4.013/t/41bindparam.t >>>>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>>>> DBD-mysql-4.013/t/40nulls.t >>>>>>> DBD-mysql-4.013/t/32insert_error.t >>>>>>> DBD-mysql-4.013/t/40catalog.t >>>>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>>>> DBD-mysql-4.013/t/20createdrop.t >>>>>>> DBD-mysql-4.013/t/70takeimp.t >>>>>>> DBD-mysql-4.013/t/42bindparam.t >>>>>>> DBD-mysql-4.013/t/00base.t >>>>>>> DBD-mysql-4.013/t/55utf8.t >>>>>>> DBD-mysql-4.013/t/65types.t >>>>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>>>> DBD-mysql-4.013/t/31insertid.t >>>>>>> DBD-mysql-4.013/t/29warnings.t >>>>>>> DBD-mysql-4.013/t/40types.t >>>>>>> DBD-mysql-4.013/t/10connect.t >>>>>>> DBD-mysql-4.013/t/lib.pl >>>>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>>>> DBD-mysql-4.013/t/35limit.t >>>>>>> DBD-mysql-4.013/t/71impdata.t >>>>>>> DBD-mysql-4.013/t/40blobs.t >>>>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>>>> DBD-mysql-4.013/t/40numrows.t >>>>>>> DBD-mysql-4.013/t/35prepare.t >>>>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>>>> DBD-mysql-4.013/t/60leaks.t >>>>>>> DBD-mysql-4.013/t/50commit.t >>>>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>>>> DBD-mysql-4.013/t/80procs.t >>>>>>> DBD-mysql-4.013/MANIFEST >>>>>>> CPAN: File::Temp loaded ok (v0.18) >>>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>>> persistent state >>>>>>> >>>>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>>>> >>>>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> >>>>>>> >>>>>>> PLEASE NOTE: >>>>>>> >>>>>>> For 'make test' to run properly, you must ensure that the >>>>>>> database user 'root' can connect to your MySQL server >>>>>>> and has the proper privileges that these tests require such >>>>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>>>> as well as others. >>>>>>> >>>>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>>>> by 's3kr1t'; >>>>>>> >>>>>>> You can also optionally set the user to run 'make test' with: >>>>>>> >>>>>>> perl Makefile.pl --testuser=username >>>>>>> >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Failed to determine directory of mysql.h. Use >>>>>>> >>>>>>> perl Makefile.PL --cflags=-I >>>>>>> >>>>>>> to set this directory. For details see the INSTALL.html file, >>>>>>> section "C Compiler flags" or type >>>>>>> >>>>>>> perl Makefile.PL --help >>>>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>>> persistent state >>>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>>>> Running make test >>>>>>> Make had some problems, won't test >>>>>>> Running make install >>>>>>> Make had some problems, won't install >>>>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>>>> Falling back to other methods to determine prerequisites >>>>>>> Failed during this command: >>>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >>>>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Piotr Borowiec >>>>>>> _______________________________________________ >>>>>>> BioSQL-l mailing list >>>>>>> BioSQL-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Piotr Borowiec >>>> >>>> >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >>> >> >> >> >> -- >> Piotr Borowiec > > -- Piotr Borowiec From cjfields at illinois.edu Tue Feb 16 09:24:51 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 16 Feb 2010 08:24:51 -0600 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: <1c828cb91002160619xa82aedcj1578a74d6e2b329a@mail.gmail.com> References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> <101DFF66-EE65-49AB-A993-0B904F92F6DC@illinois.edu> <1c828cb91002160619xa82aedcj1578a74d6e2b329a@mail.gmail.com> Message-ID: <78EE6F34-9BC7-4505-8858-6D9F3DBA2152@illinois.edu> That's not a bug. You need to use the --download option to retrieve the taxonomy files, they aren't included with the distribution. chris On Feb 16, 2010, at 8:19 AM, Piotr Borowiec wrote: > HI, I`ve solved that problem, I installed libmysqlclient16-dev. So, > that is a time to start script - load_ncbi_taxonomy.pl. I was puting > in to terminal: sudo perl load_ncbi_taxonomy.pl etc. After that, there > was another bug: > > 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 919. > Use of uninitialized value in concatenation (.) or string at > load_ncbi_taxonomy.pl line 921. > > So, I come back to same point. > > 2010/2/16 Chris Fields : >> Piotr, Adam, >> >> I can conform that is the problem. I ran into the exact issue when running tests on my local Ubuntu 9.10 setup, and installing the libmysqld-dev package fixed it. You can also install the DBD::mysql package as well (libdbd-mysql-perl). >> >> chris >> >> On Feb 16, 2010, at 5:24 AM, Adam Witney wrote: >> >>> >>> As i said you need to check if you have mysql_config installed. If not then for Ubuntu take a look at this: >>> >>> http://ubuntuforums.org/showthread.php?t=573286 >>> >>> adam >>> >>> >>> On 16 Feb 2010, at 11:14, Piotr Borowiec wrote: >>> >>>> I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu >>>> 9.10. What should I check in first order? >>>> >>>> Thanks for advice >>>> >>>> @sgul.ac.uk>: >>>>> >>>>> Hi Piotr, >>>>> >>>>> this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. >>>>> >>>>> But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try >>>>> >>>>> perl Makefile.PL --mysql_config= >>>>> >>>>> regards >>>>> >>>>> adam >>>>> >>>>> >>>>> On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: >>>>> >>>>>> Hi! >>>>>> >>>>>> Last time I had a problem with loading_ncbi script so I decided to >>>>>> start with fresh biosql andy also Unix. When I want to install >>>>>> DBD::mysql module there is some mistakes. I`m not sure but maybe the >>>>>> version mysql is not correct. I already have 5.1 >>>>>> >>>>>> cpan[1]> install DBD::mysql >>>>>> CPAN: Storable loaded ok (v2.18) >>>>>> Going to read /home/scati/.cpan/Metadata >>>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>>> Running install for module 'DBD::mysql' >>>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>>> read prefs '/home/scati/.cpan/prefs' >>>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> ok >>>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>>> ............................................................................DONE >>>>>> DBD-mysql-4.013/ >>>>>> DBD-mysql-4.013/lib/ >>>>>> DBD-mysql-4.013/lib/DBD/ >>>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>>> DBD-mysql-4.013/lib/Bundle/ >>>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>>> DBD-mysql-4.013/mysql.xs >>>>>> DBD-mysql-4.013/dbdimp.c >>>>>> DBD-mysql-4.013/myld >>>>>> DBD-mysql-4.013/INSTALL.html >>>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>>> DBD-mysql-4.013/TODO >>>>>> DBD-mysql-4.013/README >>>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>>> DBD-mysql-4.013/ChangeLog >>>>>> DBD-mysql-4.013/Makefile.PL >>>>>> DBD-mysql-4.013/META.yml >>>>>> DBD-mysql-4.013/dbdimp.h >>>>>> DBD-mysql-4.013/eg/ >>>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>>> DBD-mysql-4.013/constants.h >>>>>> DBD-mysql-4.013/t/ >>>>>> DBD-mysql-4.013/t/85init_command.t >>>>>> DBD-mysql-4.013/t/40listfields.t >>>>>> DBD-mysql-4.013/t/40bindparam.t >>>>>> DBD-mysql-4.013/t/mysql.mtest >>>>>> DBD-mysql-4.013/t/41bindparam.t >>>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>>> DBD-mysql-4.013/t/40nulls.t >>>>>> DBD-mysql-4.013/t/32insert_error.t >>>>>> DBD-mysql-4.013/t/40catalog.t >>>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>>> DBD-mysql-4.013/t/20createdrop.t >>>>>> DBD-mysql-4.013/t/70takeimp.t >>>>>> DBD-mysql-4.013/t/42bindparam.t >>>>>> DBD-mysql-4.013/t/00base.t >>>>>> DBD-mysql-4.013/t/55utf8.t >>>>>> DBD-mysql-4.013/t/65types.t >>>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>>> DBD-mysql-4.013/t/31insertid.t >>>>>> DBD-mysql-4.013/t/29warnings.t >>>>>> DBD-mysql-4.013/t/40types.t >>>>>> DBD-mysql-4.013/t/10connect.t >>>>>> DBD-mysql-4.013/t/lib.pl >>>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>>> DBD-mysql-4.013/t/35limit.t >>>>>> DBD-mysql-4.013/t/71impdata.t >>>>>> DBD-mysql-4.013/t/40blobs.t >>>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>>> DBD-mysql-4.013/t/40numrows.t >>>>>> DBD-mysql-4.013/t/35prepare.t >>>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>>> DBD-mysql-4.013/t/60leaks.t >>>>>> DBD-mysql-4.013/t/50commit.t >>>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>>> DBD-mysql-4.013/t/80procs.t >>>>>> DBD-mysql-4.013/MANIFEST >>>>>> CPAN: File::Temp loaded ok (v0.18) >>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>> persistent state >>>>>> >>>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>>> >>>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> >>>>>> >>>>>> PLEASE NOTE: >>>>>> >>>>>> For 'make test' to run properly, you must ensure that the >>>>>> database user 'root' can connect to your MySQL server >>>>>> and has the proper privileges that these tests require such >>>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>>> as well as others. >>>>>> >>>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>>> by 's3kr1t'; >>>>>> >>>>>> You can also optionally set the user to run 'make test' with: >>>>>> >>>>>> perl Makefile.pl --testuser=username >>>>>> >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Failed to determine directory of mysql.h. Use >>>>>> >>>>>> perl Makefile.PL --cflags=-I >>>>>> >>>>>> to set this directory. For details see the INSTALL.html file, >>>>>> section "C Compiler flags" or type >>>>>> >>>>>> perl Makefile.PL --help >>>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>> persistent state >>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>>> Running make test >>>>>> Make had some problems, won't test >>>>>> Running make install >>>>>> Make had some problems, won't install >>>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>>> Falling back to other methods to determine prerequisites >>>>>> Failed during this command: >>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>>> cpan[1]> install DBD::mysql >>>>>> CPAN: Storable loaded ok (v2.18) >>>>>> Going to read /home/scati/.cpan/Metadata >>>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>>> Running install for module 'DBD::mysql' >>>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>>> read prefs '/home/scati/.cpan/prefs' >>>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> ok >>>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>>> ............................................................................DONE >>>>>> DBD-mysql-4.013/ >>>>>> DBD-mysql-4.013/lib/ >>>>>> DBD-mysql-4.013/lib/DBD/ >>>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>>> DBD-mysql-4.013/lib/Bundle/ >>>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>>> DBD-mysql-4.013/mysql.xs >>>>>> DBD-mysql-4.013/dbdimp.c >>>>>> DBD-mysql-4.013/myld >>>>>> DBD-mysql-4.013/INSTALL.html >>>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>>> DBD-mysql-4.013/TODO >>>>>> DBD-mysql-4.013/README >>>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>>> DBD-mysql-4.013/ChangeLog >>>>>> DBD-mysql-4.013/Makefile.PL >>>>>> DBD-mysql-4.013/META.yml >>>>>> DBD-mysql-4.013/dbdimp.h >>>>>> DBD-mysql-4.013/eg/ >>>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>>> DBD-mysql-4.013/constants.h >>>>>> DBD-mysql-4.013/t/ >>>>>> DBD-mysql-4.013/t/85init_command.t >>>>>> DBD-mysql-4.013/t/40listfields.t >>>>>> DBD-mysql-4.013/t/40bindparam.t >>>>>> DBD-mysql-4.013/t/mysql.mtest >>>>>> DBD-mysql-4.013/t/41bindparam.t >>>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>>> DBD-mysql-4.013/t/40nulls.t >>>>>> DBD-mysql-4.013/t/32insert_error.t >>>>>> DBD-mysql-4.013/t/40catalog.t >>>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>>> DBD-mysql-4.013/t/20createdrop.t >>>>>> DBD-mysql-4.013/t/70takeimp.t >>>>>> DBD-mysql-4.013/t/42bindparam.t >>>>>> DBD-mysql-4.013/t/00base.t >>>>>> DBD-mysql-4.013/t/55utf8.t >>>>>> DBD-mysql-4.013/t/65types.t >>>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>>> DBD-mysql-4.013/t/31insertid.t >>>>>> DBD-mysql-4.013/t/29warnings.t >>>>>> DBD-mysql-4.013/t/40types.t >>>>>> DBD-mysql-4.013/t/10connect.t >>>>>> DBD-mysql-4.013/t/lib.pl >>>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>>> DBD-mysql-4.013/t/35limit.t >>>>>> DBD-mysql-4.013/t/71impdata.t >>>>>> DBD-mysql-4.013/t/40blobs.t >>>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>>> DBD-mysql-4.013/t/40numrows.t >>>>>> DBD-mysql-4.013/t/35prepare.t >>>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>>> DBD-mysql-4.013/t/60leaks.t >>>>>> DBD-mysql-4.013/t/50commit.t >>>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>>> DBD-mysql-4.013/t/80procs.t >>>>>> DBD-mysql-4.013/MANIFEST >>>>>> CPAN: File::Temp loaded ok (v0.18) >>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>> persistent state >>>>>> >>>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>>> >>>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> >>>>>> >>>>>> PLEASE NOTE: >>>>>> >>>>>> For 'make test' to run properly, you must ensure that the >>>>>> database user 'root' can connect to your MySQL server >>>>>> and has the proper privileges that these tests require such >>>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>>> as well as others. >>>>>> >>>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>>> by 's3kr1t'; >>>>>> >>>>>> You can also optionally set the user to run 'make test' with: >>>>>> >>>>>> perl Makefile.pl --testuser=username >>>>>> >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Failed to determine directory of mysql.h. Use >>>>>> >>>>>> perl Makefile.PL --cflags=-I >>>>>> >>>>>> to set this directory. For details see the INSTALL.html file, >>>>>> section "C Compiler flags" or type >>>>>> >>>>>> perl Makefile.PL --help >>>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>> persistent state >>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>>> Running make test >>>>>> Make had some problems, won't test >>>>>> Running make install >>>>>> Make had some problems, won't install >>>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>>> Falling back to other methods to determine prerequisites >>>>>> Failed during this command: >>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>>> >>>>>> >>>>>> -- >>>>>> Piotr Borowiec >>>>>> _______________________________________________ >>>>>> BioSQL-l mailing list >>>>>> BioSQL-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> Piotr Borowiec >>> >>> >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> > > > > -- > Piotr Borowiec From mysarapa at cyf-kr.edu.pl Tue Feb 16 11:59:10 2010 From: mysarapa at cyf-kr.edu.pl (Krzysztof Sarapata) Date: Tue, 16 Feb 2010 17:59:10 +0100 Subject: [BioSQL-l] some problems with loading GenBank Message-ID: <006401caaf29$5c0c9990$2f0c9c95@rubin> Hi I've loaded GenBank file into bioSQL structure with "load_seqdatabase.pl" script. Is it correct that each entity (qualifier) from FEATURES even "db_xref" e.g. FEATURES Location/Qualifiers source 1..257719 /organism="Homo sapiens" /mol_type="genomic DNA" /db_xref="taxon:9606" /chromosome="1" ..... /db_xref="GeneID:100287102" is put into "Seqfeature Qualifier Value" table, if we have exactly table "Dbxref"? Why value of this qualifier (db_xref) isn't put into "Dbxref" table? With regards Krzysztof Sarapata From hlapp at drycafe.net Thu Feb 18 13:18:52 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Thu, 18 Feb 2010 13:18:52 -0500 Subject: [BioSQL-l] some problems with loading GenBank In-Reply-To: <006401caaf29$5c0c9990$2f0c9c95@rubin> References: <006401caaf29$5c0c9990$2f0c9c95@rubin> Message-ID: <9334383A-BB0D-4AE3-9536-762C4123964F@drycafe.net> Hi Krzysztof - your question really is about the BioPerl object- relational mapping to BioSQL, and I see you have posted your question to the BioPerl list already. Roy's answer there is correct - where stuff ends up depends solely on the object-relational mapping (which put feature tag/value pairs into feature_qualifier_value) and the structure of the sequence object in BioPerl. You can easily manipulate the destination of stuff by manipulating the BioPerl object itself to have the representation you want. If there are certain feature tags that have a special meaning to you (such as being dbxrefs), pull them out of feature tag/values and add them back in as Bio::Annotation::DBLink annotation on the sequence (or the feature). Writing a SeqProcessor will allow you to do that seamlessly; i.e., you do not need to change BioPerl itself, since load_seqdatabase.pl allows you to specify the SeqProcessors you want to employ. -hilmar On Feb 16, 2010, at 11:59 AM, Krzysztof Sarapata wrote: > Hi > > > > I've loaded GenBank file into bioSQL structure with > "load_seqdatabase.pl" script. > > Is it correct that each entity (qualifier) from FEATURES even > "db_xref" e.g. > > > > FEATURES Location/Qualifiers > > source 1..257719 > > /organism="Homo sapiens" > > /mol_type="genomic DNA" > > /db_xref="taxon:9606" > > /chromosome="1" > > ..... > > /db_xref="GeneID:100287102" > > > > is put into "Seqfeature Qualifier Value" table, if we have exactly > table "Dbxref"? > > Why value of this qualifier (db_xref) isn't put into "Dbxref" table? > > > > With regards > > Krzysztof Sarapata > > _______________________________________________ > 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 piotrborowiec at g.pl Tue Feb 16 10:24:21 2010 From: piotrborowiec at g.pl (Piotr Borowiec) Date: Tue, 16 Feb 2010 11:24:21 +0100 Subject: [BioSQL-l] Some problem with installation DBD::mysql Message-ID: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> Hi! Last time I had a problem with loading_ncbi script so I decided to start with fresh biosql andy also Unix. When I want to install DBD::mysql module there is some mistakes. I`m not sure but maybe the version mysql is not correct. I already have 5.1 cpan[1]> install DBD::mysql CPAN: Storable loaded ok (v2.18) Going to read /home/scati/.cpan/Metadata Database was generated on Tue, 16 Feb 2010 07:53:49 GMT Running install for module 'DBD::mysql' CPAN: Data::Dumper loaded ok (v2.121_14) 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/home/scati/.cpan/prefs' Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz CPAN: Digest::SHA loaded ok (v5.45) CPAN: Compress::Zlib loaded ok (v2.008) Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz ok Scanning cache /home/scati/.cpan/build for sizes ............................................................................DONE DBD-mysql-4.013/ DBD-mysql-4.013/lib/ DBD-mysql-4.013/lib/DBD/ DBD-mysql-4.013/lib/DBD/mysql.pm DBD-mysql-4.013/lib/DBD/mysql/ DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod DBD-mysql-4.013/lib/Bundle/ DBD-mysql-4.013/lib/Bundle/DBD/ DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm DBD-mysql-4.013/mysql.xs DBD-mysql-4.013/dbdimp.c DBD-mysql-4.013/myld DBD-mysql-4.013/INSTALL.html DBD-mysql-4.013/Makefile.PL.embedded DBD-mysql-4.013/TODO DBD-mysql-4.013/README DBD-mysql-4.013/MANIFEST.SKIP DBD-mysql-4.013/ChangeLog DBD-mysql-4.013/Makefile.PL DBD-mysql-4.013/META.yml DBD-mysql-4.013/dbdimp.h DBD-mysql-4.013/eg/ DBD-mysql-4.013/eg/prepare_memory_usage.pl DBD-mysql-4.013/eg/proc_example2b.pl DBD-mysql-4.013/eg/proc_example2.pl DBD-mysql-4.013/eg/decimal_test.pl DBD-mysql-4.013/eg/bug30033pg.pl DBD-mysql-4.013/eg/proc_example2a.pl DBD-mysql-4.013/eg/proc_example4.pl DBD-mysql-4.013/eg/bug21028.pl DBD-mysql-4.013/eg/bug14979.pl DBD-mysql-4.013/eg/bug30033.pl DBD-mysql-4.013/eg/issue21946.pl DBD-mysql-4.013/eg/proc_example3.pl DBD-mysql-4.013/eg/proc_example1.pl DBD-mysql-4.013/constants.h DBD-mysql-4.013/t/ DBD-mysql-4.013/t/85init_command.t DBD-mysql-4.013/t/40listfields.t DBD-mysql-4.013/t/40bindparam.t DBD-mysql-4.013/t/mysql.mtest DBD-mysql-4.013/t/41bindparam.t DBD-mysql-4.013/t/76multi_statement.t DBD-mysql-4.013/t/40nulls.t DBD-mysql-4.013/t/32insert_error.t DBD-mysql-4.013/t/40catalog.t DBD-mysql-4.013/t/51bind_type_guessing.t DBD-mysql-4.013/t/40bindparam2.t DBD-mysql-4.013/t/41blobs_prepare.t DBD-mysql-4.013/t/20createdrop.t DBD-mysql-4.013/t/70takeimp.t DBD-mysql-4.013/t/42bindparam.t DBD-mysql-4.013/t/00base.t DBD-mysql-4.013/t/55utf8.t DBD-mysql-4.013/t/65types.t DBD-mysql-4.013/t/40server_prepare_error.t DBD-mysql-4.013/t/31insertid.t DBD-mysql-4.013/t/29warnings.t DBD-mysql-4.013/t/40types.t DBD-mysql-4.013/t/10connect.t DBD-mysql-4.013/t/lib.pl DBD-mysql-4.013/t/mysql.dbtest DBD-mysql-4.013/t/35limit.t DBD-mysql-4.013/t/71impdata.t DBD-mysql-4.013/t/40blobs.t DBD-mysql-4.013/t/40server_prepare.t DBD-mysql-4.013/t/40numrows.t DBD-mysql-4.013/t/35prepare.t DBD-mysql-4.013/t/40keyinfo.t DBD-mysql-4.013/t/75supported_sql.t DBD-mysql-4.013/t/60leaks.t DBD-mysql-4.013/t/50commit.t DBD-mysql-4.013/t/30insertfetch.t DBD-mysql-4.013/t/50chopblanks.t DBD-mysql-4.013/t/25lockunlock.t DBD-mysql-4.013/t/80procs.t DBD-mysql-4.013/MANIFEST CPAN: File::Temp loaded ok (v0.18) Warning (usually harmless): 'YAML' not installed, will not store persistent state CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. Cannot find the file 'mysql_config'! Your execution PATH doesn't seem not contain the path to mysql_config. Resorting to guessed values! Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located PLEASE NOTE: For 'make test' to run properly, you must ensure that the database user 'root' can connect to your MySQL server and has the proper privileges that these tests require such as 'drop table', 'create table', 'drop procedure', 'create procedure' as well as others. mysql> grant all privileges on test.* to 'root'@'localhost' identified by 's3kr1t'; You can also optionally set the user to run 'make test' with: perl Makefile.pl --testuser=username Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Failed to determine directory of mysql.h. Use perl Makefile.PL --cflags=-I to set this directory. For details see the INSTALL.html file, section "C Compiler flags" or type perl Makefile.PL --help Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] Warning (usually harmless): 'YAML' not installed, will not store persistent state CAPTTOFU/DBD-mysql-4.013.tar.gz /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK Running make test Make had some problems, won't test Running make install Make had some problems, won't install Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. Falling back to other methods to determine prerequisites Failed during this command: CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 cpan[1]> install DBD::mysql CPAN: Storable loaded ok (v2.18) Going to read /home/scati/.cpan/Metadata Database was generated on Tue, 16 Feb 2010 07:53:49 GMT Running install for module 'DBD::mysql' CPAN: Data::Dumper loaded ok (v2.121_14) 'YAML' not installed, falling back to Data::Dumper and Storable to read prefs '/home/scati/.cpan/prefs' Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz CPAN: Digest::SHA loaded ok (v5.45) CPAN: Compress::Zlib loaded ok (v2.008) Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz ok Scanning cache /home/scati/.cpan/build for sizes ............................................................................DONE DBD-mysql-4.013/ DBD-mysql-4.013/lib/ DBD-mysql-4.013/lib/DBD/ DBD-mysql-4.013/lib/DBD/mysql.pm DBD-mysql-4.013/lib/DBD/mysql/ DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod DBD-mysql-4.013/lib/Bundle/ DBD-mysql-4.013/lib/Bundle/DBD/ DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm DBD-mysql-4.013/mysql.xs DBD-mysql-4.013/dbdimp.c DBD-mysql-4.013/myld DBD-mysql-4.013/INSTALL.html DBD-mysql-4.013/Makefile.PL.embedded DBD-mysql-4.013/TODO DBD-mysql-4.013/README DBD-mysql-4.013/MANIFEST.SKIP DBD-mysql-4.013/ChangeLog DBD-mysql-4.013/Makefile.PL DBD-mysql-4.013/META.yml DBD-mysql-4.013/dbdimp.h DBD-mysql-4.013/eg/ DBD-mysql-4.013/eg/prepare_memory_usage.pl DBD-mysql-4.013/eg/proc_example2b.pl DBD-mysql-4.013/eg/proc_example2.pl DBD-mysql-4.013/eg/decimal_test.pl DBD-mysql-4.013/eg/bug30033pg.pl DBD-mysql-4.013/eg/proc_example2a.pl DBD-mysql-4.013/eg/proc_example4.pl DBD-mysql-4.013/eg/bug21028.pl DBD-mysql-4.013/eg/bug14979.pl DBD-mysql-4.013/eg/bug30033.pl DBD-mysql-4.013/eg/issue21946.pl DBD-mysql-4.013/eg/proc_example3.pl DBD-mysql-4.013/eg/proc_example1.pl DBD-mysql-4.013/constants.h DBD-mysql-4.013/t/ DBD-mysql-4.013/t/85init_command.t DBD-mysql-4.013/t/40listfields.t DBD-mysql-4.013/t/40bindparam.t DBD-mysql-4.013/t/mysql.mtest DBD-mysql-4.013/t/41bindparam.t DBD-mysql-4.013/t/76multi_statement.t DBD-mysql-4.013/t/40nulls.t DBD-mysql-4.013/t/32insert_error.t DBD-mysql-4.013/t/40catalog.t DBD-mysql-4.013/t/51bind_type_guessing.t DBD-mysql-4.013/t/40bindparam2.t DBD-mysql-4.013/t/41blobs_prepare.t DBD-mysql-4.013/t/20createdrop.t DBD-mysql-4.013/t/70takeimp.t DBD-mysql-4.013/t/42bindparam.t DBD-mysql-4.013/t/00base.t DBD-mysql-4.013/t/55utf8.t DBD-mysql-4.013/t/65types.t DBD-mysql-4.013/t/40server_prepare_error.t DBD-mysql-4.013/t/31insertid.t DBD-mysql-4.013/t/29warnings.t DBD-mysql-4.013/t/40types.t DBD-mysql-4.013/t/10connect.t DBD-mysql-4.013/t/lib.pl DBD-mysql-4.013/t/mysql.dbtest DBD-mysql-4.013/t/35limit.t DBD-mysql-4.013/t/71impdata.t DBD-mysql-4.013/t/40blobs.t DBD-mysql-4.013/t/40server_prepare.t DBD-mysql-4.013/t/40numrows.t DBD-mysql-4.013/t/35prepare.t DBD-mysql-4.013/t/40keyinfo.t DBD-mysql-4.013/t/75supported_sql.t DBD-mysql-4.013/t/60leaks.t DBD-mysql-4.013/t/50commit.t DBD-mysql-4.013/t/30insertfetch.t DBD-mysql-4.013/t/50chopblanks.t DBD-mysql-4.013/t/25lockunlock.t DBD-mysql-4.013/t/80procs.t DBD-mysql-4.013/MANIFEST CPAN: File::Temp loaded ok (v0.18) Warning (usually harmless): 'YAML' not installed, will not store persistent state CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. Cannot find the file 'mysql_config'! Your execution PATH doesn't seem not contain the path to mysql_config. Resorting to guessed values! Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located PLEASE NOTE: For 'make test' to run properly, you must ensure that the database user 'root' can connect to your MySQL server and has the proper privileges that these tests require such as 'drop table', 'create table', 'drop procedure', 'create procedure' as well as others. mysql> grant all privileges on test.* to 'root'@'localhost' identified by 's3kr1t'; You can also optionally set the user to run 'make test' with: perl Makefile.pl --testuser=username Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. Can't find mysql_config. Use --mysql_config option to specify where mysql_config is located Failed to determine directory of mysql.h. Use perl Makefile.PL --cflags=-I to set this directory. For details see the INSTALL.html file, section "C Compiler flags" or type perl Makefile.PL --help Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] Warning (usually harmless): 'YAML' not installed, will not store persistent state CAPTTOFU/DBD-mysql-4.013.tar.gz /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK Running make test Make had some problems, won't test Running make install Make had some problems, won't install Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. Falling back to other methods to determine prerequisites Failed during this command: CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 -- Piotr Borowiec From awitney at sgul.ac.uk Tue Feb 16 10:40:57 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Tue, 16 Feb 2010 10:40:57 +0000 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> Message-ID: Hi Piotr, this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try perl Makefile.PL --mysql_config= regards adam On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: > Hi! > > Last time I had a problem with loading_ncbi script so I decided to > start with fresh biosql andy also Unix. When I want to install > DBD::mysql module there is some mistakes. I`m not sure but maybe the > version mysql is not correct. I already have 5.1 > > cpan[1]> install DBD::mysql > CPAN: Storable loaded ok (v2.18) > Going to read /home/scati/.cpan/Metadata > Database was generated on Tue, 16 Feb 2010 07:53:49 GMT > Running install for module 'DBD::mysql' > CPAN: Data::Dumper loaded ok (v2.121_14) > 'YAML' not installed, falling back to Data::Dumper and Storable to > read prefs '/home/scati/.cpan/prefs' > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > ok > Scanning cache /home/scati/.cpan/build for sizes > ............................................................................DONE > DBD-mysql-4.013/ > DBD-mysql-4.013/lib/ > DBD-mysql-4.013/lib/DBD/ > DBD-mysql-4.013/lib/DBD/mysql.pm > DBD-mysql-4.013/lib/DBD/mysql/ > DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm > DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod > DBD-mysql-4.013/lib/Bundle/ > DBD-mysql-4.013/lib/Bundle/DBD/ > DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm > DBD-mysql-4.013/mysql.xs > DBD-mysql-4.013/dbdimp.c > DBD-mysql-4.013/myld > DBD-mysql-4.013/INSTALL.html > DBD-mysql-4.013/Makefile.PL.embedded > DBD-mysql-4.013/TODO > DBD-mysql-4.013/README > DBD-mysql-4.013/MANIFEST.SKIP > DBD-mysql-4.013/ChangeLog > DBD-mysql-4.013/Makefile.PL > DBD-mysql-4.013/META.yml > DBD-mysql-4.013/dbdimp.h > DBD-mysql-4.013/eg/ > DBD-mysql-4.013/eg/prepare_memory_usage.pl > DBD-mysql-4.013/eg/proc_example2b.pl > DBD-mysql-4.013/eg/proc_example2.pl > DBD-mysql-4.013/eg/decimal_test.pl > DBD-mysql-4.013/eg/bug30033pg.pl > DBD-mysql-4.013/eg/proc_example2a.pl > DBD-mysql-4.013/eg/proc_example4.pl > DBD-mysql-4.013/eg/bug21028.pl > DBD-mysql-4.013/eg/bug14979.pl > DBD-mysql-4.013/eg/bug30033.pl > DBD-mysql-4.013/eg/issue21946.pl > DBD-mysql-4.013/eg/proc_example3.pl > DBD-mysql-4.013/eg/proc_example1.pl > DBD-mysql-4.013/constants.h > DBD-mysql-4.013/t/ > DBD-mysql-4.013/t/85init_command.t > DBD-mysql-4.013/t/40listfields.t > DBD-mysql-4.013/t/40bindparam.t > DBD-mysql-4.013/t/mysql.mtest > DBD-mysql-4.013/t/41bindparam.t > DBD-mysql-4.013/t/76multi_statement.t > DBD-mysql-4.013/t/40nulls.t > DBD-mysql-4.013/t/32insert_error.t > DBD-mysql-4.013/t/40catalog.t > DBD-mysql-4.013/t/51bind_type_guessing.t > DBD-mysql-4.013/t/40bindparam2.t > DBD-mysql-4.013/t/41blobs_prepare.t > DBD-mysql-4.013/t/20createdrop.t > DBD-mysql-4.013/t/70takeimp.t > DBD-mysql-4.013/t/42bindparam.t > DBD-mysql-4.013/t/00base.t > DBD-mysql-4.013/t/55utf8.t > DBD-mysql-4.013/t/65types.t > DBD-mysql-4.013/t/40server_prepare_error.t > DBD-mysql-4.013/t/31insertid.t > DBD-mysql-4.013/t/29warnings.t > DBD-mysql-4.013/t/40types.t > DBD-mysql-4.013/t/10connect.t > DBD-mysql-4.013/t/lib.pl > DBD-mysql-4.013/t/mysql.dbtest > DBD-mysql-4.013/t/35limit.t > DBD-mysql-4.013/t/71impdata.t > DBD-mysql-4.013/t/40blobs.t > DBD-mysql-4.013/t/40server_prepare.t > DBD-mysql-4.013/t/40numrows.t > DBD-mysql-4.013/t/35prepare.t > DBD-mysql-4.013/t/40keyinfo.t > DBD-mysql-4.013/t/75supported_sql.t > DBD-mysql-4.013/t/60leaks.t > DBD-mysql-4.013/t/50commit.t > DBD-mysql-4.013/t/30insertfetch.t > DBD-mysql-4.013/t/50chopblanks.t > DBD-mysql-4.013/t/25lockunlock.t > DBD-mysql-4.013/t/80procs.t > DBD-mysql-4.013/MANIFEST > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > > CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > > Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. > > Cannot find the file 'mysql_config'! Your execution PATH doesn't seem > not contain the path to mysql_config. Resorting to guessed values! > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > > > PLEASE NOTE: > > For 'make test' to run properly, you must ensure that the > database user 'root' can connect to your MySQL server > and has the proper privileges that these tests require such > as 'drop table', 'create table', 'drop procedure', 'create procedure' > as well as others. > > mysql> grant all privileges on test.* to 'root'@'localhost' identified > by 's3kr1t'; > > You can also optionally set the user to run 'make test' with: > > perl Makefile.pl --testuser=username > > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Failed to determine directory of mysql.h. Use > > perl Makefile.PL --cflags=-I > > to set this directory. For details see the INSTALL.html file, > section "C Compiler flags" or type > > perl Makefile.PL --help > Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > CAPTTOFU/DBD-mysql-4.013.tar.gz > /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK > Running make test > Make had some problems, won't test > Running make install > Make had some problems, won't install > Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. > Falling back to other methods to determine prerequisites > Failed during this command: > CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO > '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 > cpan[1]> install DBD::mysql > CPAN: Storable loaded ok (v2.18) > Going to read /home/scati/.cpan/Metadata > Database was generated on Tue, 16 Feb 2010 07:53:49 GMT > Running install for module 'DBD::mysql' > CPAN: Data::Dumper loaded ok (v2.121_14) > 'YAML' not installed, falling back to Data::Dumper and Storable to > read prefs '/home/scati/.cpan/prefs' > Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > CPAN: Digest::SHA loaded ok (v5.45) > CPAN: Compress::Zlib loaded ok (v2.008) > Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > ok > Scanning cache /home/scati/.cpan/build for sizes > ............................................................................DONE > DBD-mysql-4.013/ > DBD-mysql-4.013/lib/ > DBD-mysql-4.013/lib/DBD/ > DBD-mysql-4.013/lib/DBD/mysql.pm > DBD-mysql-4.013/lib/DBD/mysql/ > DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm > DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod > DBD-mysql-4.013/lib/Bundle/ > DBD-mysql-4.013/lib/Bundle/DBD/ > DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm > DBD-mysql-4.013/mysql.xs > DBD-mysql-4.013/dbdimp.c > DBD-mysql-4.013/myld > DBD-mysql-4.013/INSTALL.html > DBD-mysql-4.013/Makefile.PL.embedded > DBD-mysql-4.013/TODO > DBD-mysql-4.013/README > DBD-mysql-4.013/MANIFEST.SKIP > DBD-mysql-4.013/ChangeLog > DBD-mysql-4.013/Makefile.PL > DBD-mysql-4.013/META.yml > DBD-mysql-4.013/dbdimp.h > DBD-mysql-4.013/eg/ > DBD-mysql-4.013/eg/prepare_memory_usage.pl > DBD-mysql-4.013/eg/proc_example2b.pl > DBD-mysql-4.013/eg/proc_example2.pl > DBD-mysql-4.013/eg/decimal_test.pl > DBD-mysql-4.013/eg/bug30033pg.pl > DBD-mysql-4.013/eg/proc_example2a.pl > DBD-mysql-4.013/eg/proc_example4.pl > DBD-mysql-4.013/eg/bug21028.pl > DBD-mysql-4.013/eg/bug14979.pl > DBD-mysql-4.013/eg/bug30033.pl > DBD-mysql-4.013/eg/issue21946.pl > DBD-mysql-4.013/eg/proc_example3.pl > DBD-mysql-4.013/eg/proc_example1.pl > DBD-mysql-4.013/constants.h > DBD-mysql-4.013/t/ > DBD-mysql-4.013/t/85init_command.t > DBD-mysql-4.013/t/40listfields.t > DBD-mysql-4.013/t/40bindparam.t > DBD-mysql-4.013/t/mysql.mtest > DBD-mysql-4.013/t/41bindparam.t > DBD-mysql-4.013/t/76multi_statement.t > DBD-mysql-4.013/t/40nulls.t > DBD-mysql-4.013/t/32insert_error.t > DBD-mysql-4.013/t/40catalog.t > DBD-mysql-4.013/t/51bind_type_guessing.t > DBD-mysql-4.013/t/40bindparam2.t > DBD-mysql-4.013/t/41blobs_prepare.t > DBD-mysql-4.013/t/20createdrop.t > DBD-mysql-4.013/t/70takeimp.t > DBD-mysql-4.013/t/42bindparam.t > DBD-mysql-4.013/t/00base.t > DBD-mysql-4.013/t/55utf8.t > DBD-mysql-4.013/t/65types.t > DBD-mysql-4.013/t/40server_prepare_error.t > DBD-mysql-4.013/t/31insertid.t > DBD-mysql-4.013/t/29warnings.t > DBD-mysql-4.013/t/40types.t > DBD-mysql-4.013/t/10connect.t > DBD-mysql-4.013/t/lib.pl > DBD-mysql-4.013/t/mysql.dbtest > DBD-mysql-4.013/t/35limit.t > DBD-mysql-4.013/t/71impdata.t > DBD-mysql-4.013/t/40blobs.t > DBD-mysql-4.013/t/40server_prepare.t > DBD-mysql-4.013/t/40numrows.t > DBD-mysql-4.013/t/35prepare.t > DBD-mysql-4.013/t/40keyinfo.t > DBD-mysql-4.013/t/75supported_sql.t > DBD-mysql-4.013/t/60leaks.t > DBD-mysql-4.013/t/50commit.t > DBD-mysql-4.013/t/30insertfetch.t > DBD-mysql-4.013/t/50chopblanks.t > DBD-mysql-4.013/t/25lockunlock.t > DBD-mysql-4.013/t/80procs.t > DBD-mysql-4.013/MANIFEST > CPAN: File::Temp loaded ok (v0.18) > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > > CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz > > Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. > > Cannot find the file 'mysql_config'! Your execution PATH doesn't seem > not contain the path to mysql_config. Resorting to guessed values! > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > > > PLEASE NOTE: > > For 'make test' to run properly, you must ensure that the > database user 'root' can connect to your MySQL server > and has the proper privileges that these tests require such > as 'drop table', 'create table', 'drop procedure', 'create procedure' > as well as others. > > mysql> grant all privileges on test.* to 'root'@'localhost' identified > by 's3kr1t'; > > You can also optionally set the user to run 'make test' with: > > perl Makefile.pl --testuser=username > > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. > Can't find mysql_config. Use --mysql_config option to specify where > mysql_config is located > Failed to determine directory of mysql.h. Use > > perl Makefile.PL --cflags=-I > > to set this directory. For details see the INSTALL.html file, > section "C Compiler flags" or type > > perl Makefile.PL --help > Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] > Warning (usually harmless): 'YAML' not installed, will not store > persistent state > CAPTTOFU/DBD-mysql-4.013.tar.gz > /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK > Running make test > Make had some problems, won't test > Running make install > Make had some problems, won't install > Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. > Falling back to other methods to determine prerequisites > Failed during this command: > CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO > '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 > > > -- > Piotr Borowiec > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From piotrborowiec at g.pl Tue Feb 16 11:14:29 2010 From: piotrborowiec at g.pl (Piotr Borowiec) Date: Tue, 16 Feb 2010 12:14:29 +0100 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> Message-ID: <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu 9.10. What should I check in first order? Thanks for advice @sgul.ac.uk>: > > Hi Piotr, > > this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. > > But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try > > perl Makefile.PL --mysql_config= > > regards > > adam > > > On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: > >> Hi! >> >> Last time I had a problem with loading_ncbi script so I decided to >> start with fresh biosql andy also Unix. When I want to install >> DBD::mysql module there is some mistakes. I`m not sure but maybe the >> version mysql is not correct. I already have 5.1 >> >> cpan[1]> install DBD::mysql >> CPAN: Storable loaded ok (v2.18) >> Going to read /home/scati/.cpan/Metadata >> ?Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >> Running install for module 'DBD::mysql' >> CPAN: Data::Dumper loaded ok (v2.121_14) >> 'YAML' not installed, falling back to Data::Dumper and Storable to >> read prefs '/home/scati/.cpan/prefs' >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> CPAN: Digest::SHA loaded ok (v5.45) >> CPAN: Compress::Zlib loaded ok (v2.008) >> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> ok >> Scanning cache /home/scati/.cpan/build for sizes >> ............................................................................DONE >> DBD-mysql-4.013/ >> DBD-mysql-4.013/lib/ >> DBD-mysql-4.013/lib/DBD/ >> DBD-mysql-4.013/lib/DBD/mysql.pm >> DBD-mysql-4.013/lib/DBD/mysql/ >> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >> DBD-mysql-4.013/lib/Bundle/ >> DBD-mysql-4.013/lib/Bundle/DBD/ >> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >> DBD-mysql-4.013/mysql.xs >> DBD-mysql-4.013/dbdimp.c >> DBD-mysql-4.013/myld >> DBD-mysql-4.013/INSTALL.html >> DBD-mysql-4.013/Makefile.PL.embedded >> DBD-mysql-4.013/TODO >> DBD-mysql-4.013/README >> DBD-mysql-4.013/MANIFEST.SKIP >> DBD-mysql-4.013/ChangeLog >> DBD-mysql-4.013/Makefile.PL >> DBD-mysql-4.013/META.yml >> DBD-mysql-4.013/dbdimp.h >> DBD-mysql-4.013/eg/ >> DBD-mysql-4.013/eg/prepare_memory_usage.pl >> DBD-mysql-4.013/eg/proc_example2b.pl >> DBD-mysql-4.013/eg/proc_example2.pl >> DBD-mysql-4.013/eg/decimal_test.pl >> DBD-mysql-4.013/eg/bug30033pg.pl >> DBD-mysql-4.013/eg/proc_example2a.pl >> DBD-mysql-4.013/eg/proc_example4.pl >> DBD-mysql-4.013/eg/bug21028.pl >> DBD-mysql-4.013/eg/bug14979.pl >> DBD-mysql-4.013/eg/bug30033.pl >> DBD-mysql-4.013/eg/issue21946.pl >> DBD-mysql-4.013/eg/proc_example3.pl >> DBD-mysql-4.013/eg/proc_example1.pl >> DBD-mysql-4.013/constants.h >> DBD-mysql-4.013/t/ >> DBD-mysql-4.013/t/85init_command.t >> DBD-mysql-4.013/t/40listfields.t >> DBD-mysql-4.013/t/40bindparam.t >> DBD-mysql-4.013/t/mysql.mtest >> DBD-mysql-4.013/t/41bindparam.t >> DBD-mysql-4.013/t/76multi_statement.t >> DBD-mysql-4.013/t/40nulls.t >> DBD-mysql-4.013/t/32insert_error.t >> DBD-mysql-4.013/t/40catalog.t >> DBD-mysql-4.013/t/51bind_type_guessing.t >> DBD-mysql-4.013/t/40bindparam2.t >> DBD-mysql-4.013/t/41blobs_prepare.t >> DBD-mysql-4.013/t/20createdrop.t >> DBD-mysql-4.013/t/70takeimp.t >> DBD-mysql-4.013/t/42bindparam.t >> DBD-mysql-4.013/t/00base.t >> DBD-mysql-4.013/t/55utf8.t >> DBD-mysql-4.013/t/65types.t >> DBD-mysql-4.013/t/40server_prepare_error.t >> DBD-mysql-4.013/t/31insertid.t >> DBD-mysql-4.013/t/29warnings.t >> DBD-mysql-4.013/t/40types.t >> DBD-mysql-4.013/t/10connect.t >> DBD-mysql-4.013/t/lib.pl >> DBD-mysql-4.013/t/mysql.dbtest >> DBD-mysql-4.013/t/35limit.t >> DBD-mysql-4.013/t/71impdata.t >> DBD-mysql-4.013/t/40blobs.t >> DBD-mysql-4.013/t/40server_prepare.t >> DBD-mysql-4.013/t/40numrows.t >> DBD-mysql-4.013/t/35prepare.t >> DBD-mysql-4.013/t/40keyinfo.t >> DBD-mysql-4.013/t/75supported_sql.t >> DBD-mysql-4.013/t/60leaks.t >> DBD-mysql-4.013/t/50commit.t >> DBD-mysql-4.013/t/30insertfetch.t >> DBD-mysql-4.013/t/50chopblanks.t >> DBD-mysql-4.013/t/25lockunlock.t >> DBD-mysql-4.013/t/80procs.t >> DBD-mysql-4.013/MANIFEST >> CPAN: File::Temp loaded ok (v0.18) >> Warning (usually harmless): 'YAML' not installed, will not store >> persistent state >> >> ?CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >> >> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >> not contain the path to mysql_config. Resorting to guessed values! >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> >> >> PLEASE NOTE: >> >> For 'make test' to run properly, you must ensure that the >> database user 'root' can connect to your MySQL server >> and has the proper privileges that these tests require such >> as 'drop table', 'create table', 'drop procedure', 'create procedure' >> as well as others. >> >> mysql> grant all privileges on test.* to 'root'@'localhost' identified >> by 's3kr1t'; >> >> You can also optionally set the user to run 'make test' with: >> >> perl Makefile.pl --testuser=username >> >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Failed to determine directory of mysql.h. Use >> >> ?perl Makefile.PL --cflags=-I >> >> to set this directory. For details see the INSTALL.html file, >> section "C Compiler flags" or type >> >> ?perl Makefile.PL --help >> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >> Warning (usually harmless): 'YAML' not installed, will not store >> persistent state >> ?CAPTTOFU/DBD-mysql-4.013.tar.gz >> ?/usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >> Running make test >> ?Make had some problems, won't test >> Running make install >> ?Make had some problems, won't install >> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >> Falling back to other methods to determine prerequisites >> Failed during this command: >> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >> cpan[1]> install DBD::mysql >> CPAN: Storable loaded ok (v2.18) >> Going to read /home/scati/.cpan/Metadata >> ?Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >> Running install for module 'DBD::mysql' >> CPAN: Data::Dumper loaded ok (v2.121_14) >> 'YAML' not installed, falling back to Data::Dumper and Storable to >> read prefs '/home/scati/.cpan/prefs' >> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> CPAN: Digest::SHA loaded ok (v5.45) >> CPAN: Compress::Zlib loaded ok (v2.008) >> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> ok >> Scanning cache /home/scati/.cpan/build for sizes >> ............................................................................DONE >> DBD-mysql-4.013/ >> DBD-mysql-4.013/lib/ >> DBD-mysql-4.013/lib/DBD/ >> DBD-mysql-4.013/lib/DBD/mysql.pm >> DBD-mysql-4.013/lib/DBD/mysql/ >> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >> DBD-mysql-4.013/lib/Bundle/ >> DBD-mysql-4.013/lib/Bundle/DBD/ >> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >> DBD-mysql-4.013/mysql.xs >> DBD-mysql-4.013/dbdimp.c >> DBD-mysql-4.013/myld >> DBD-mysql-4.013/INSTALL.html >> DBD-mysql-4.013/Makefile.PL.embedded >> DBD-mysql-4.013/TODO >> DBD-mysql-4.013/README >> DBD-mysql-4.013/MANIFEST.SKIP >> DBD-mysql-4.013/ChangeLog >> DBD-mysql-4.013/Makefile.PL >> DBD-mysql-4.013/META.yml >> DBD-mysql-4.013/dbdimp.h >> DBD-mysql-4.013/eg/ >> DBD-mysql-4.013/eg/prepare_memory_usage.pl >> DBD-mysql-4.013/eg/proc_example2b.pl >> DBD-mysql-4.013/eg/proc_example2.pl >> DBD-mysql-4.013/eg/decimal_test.pl >> DBD-mysql-4.013/eg/bug30033pg.pl >> DBD-mysql-4.013/eg/proc_example2a.pl >> DBD-mysql-4.013/eg/proc_example4.pl >> DBD-mysql-4.013/eg/bug21028.pl >> DBD-mysql-4.013/eg/bug14979.pl >> DBD-mysql-4.013/eg/bug30033.pl >> DBD-mysql-4.013/eg/issue21946.pl >> DBD-mysql-4.013/eg/proc_example3.pl >> DBD-mysql-4.013/eg/proc_example1.pl >> DBD-mysql-4.013/constants.h >> DBD-mysql-4.013/t/ >> DBD-mysql-4.013/t/85init_command.t >> DBD-mysql-4.013/t/40listfields.t >> DBD-mysql-4.013/t/40bindparam.t >> DBD-mysql-4.013/t/mysql.mtest >> DBD-mysql-4.013/t/41bindparam.t >> DBD-mysql-4.013/t/76multi_statement.t >> DBD-mysql-4.013/t/40nulls.t >> DBD-mysql-4.013/t/32insert_error.t >> DBD-mysql-4.013/t/40catalog.t >> DBD-mysql-4.013/t/51bind_type_guessing.t >> DBD-mysql-4.013/t/40bindparam2.t >> DBD-mysql-4.013/t/41blobs_prepare.t >> DBD-mysql-4.013/t/20createdrop.t >> DBD-mysql-4.013/t/70takeimp.t >> DBD-mysql-4.013/t/42bindparam.t >> DBD-mysql-4.013/t/00base.t >> DBD-mysql-4.013/t/55utf8.t >> DBD-mysql-4.013/t/65types.t >> DBD-mysql-4.013/t/40server_prepare_error.t >> DBD-mysql-4.013/t/31insertid.t >> DBD-mysql-4.013/t/29warnings.t >> DBD-mysql-4.013/t/40types.t >> DBD-mysql-4.013/t/10connect.t >> DBD-mysql-4.013/t/lib.pl >> DBD-mysql-4.013/t/mysql.dbtest >> DBD-mysql-4.013/t/35limit.t >> DBD-mysql-4.013/t/71impdata.t >> DBD-mysql-4.013/t/40blobs.t >> DBD-mysql-4.013/t/40server_prepare.t >> DBD-mysql-4.013/t/40numrows.t >> DBD-mysql-4.013/t/35prepare.t >> DBD-mysql-4.013/t/40keyinfo.t >> DBD-mysql-4.013/t/75supported_sql.t >> DBD-mysql-4.013/t/60leaks.t >> DBD-mysql-4.013/t/50commit.t >> DBD-mysql-4.013/t/30insertfetch.t >> DBD-mysql-4.013/t/50chopblanks.t >> DBD-mysql-4.013/t/25lockunlock.t >> DBD-mysql-4.013/t/80procs.t >> DBD-mysql-4.013/MANIFEST >> CPAN: File::Temp loaded ok (v0.18) >> Warning (usually harmless): 'YAML' not installed, will not store >> persistent state >> >> ?CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >> >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >> >> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >> not contain the path to mysql_config. Resorting to guessed values! >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> >> >> PLEASE NOTE: >> >> For 'make test' to run properly, you must ensure that the >> database user 'root' can connect to your MySQL server >> and has the proper privileges that these tests require such >> as 'drop table', 'create table', 'drop procedure', 'create procedure' >> as well as others. >> >> mysql> grant all privileges on test.* to 'root'@'localhost' identified >> by 's3kr1t'; >> >> You can also optionally set the user to run 'make test' with: >> >> perl Makefile.pl --testuser=username >> >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >> Can't find mysql_config. Use --mysql_config option to specify where >> mysql_config is located >> Failed to determine directory of mysql.h. Use >> >> ?perl Makefile.PL --cflags=-I >> >> to set this directory. For details see the INSTALL.html file, >> section "C Compiler flags" or type >> >> ?perl Makefile.PL --help >> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >> Warning (usually harmless): 'YAML' not installed, will not store >> persistent state >> ?CAPTTOFU/DBD-mysql-4.013.tar.gz >> ?/usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >> Running make test >> ?Make had some problems, won't test >> Running make install >> ?Make had some problems, won't install >> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >> Falling back to other methods to determine prerequisites >> Failed during this command: >> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >> >> >> -- >> Piotr Borowiec >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- Piotr Borowiec From awitney at sgul.ac.uk Tue Feb 16 11:24:08 2010 From: awitney at sgul.ac.uk (Adam Witney) Date: Tue, 16 Feb 2010 11:24:08 +0000 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> Message-ID: As i said you need to check if you have mysql_config installed. If not then for Ubuntu take a look at this: http://ubuntuforums.org/showthread.php?t=573286 adam On 16 Feb 2010, at 11:14, Piotr Borowiec wrote: > I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu > 9.10. What should I check in first order? > > Thanks for advice > > @sgul.ac.uk>: >> >> Hi Piotr, >> >> this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. >> >> But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try >> >> perl Makefile.PL --mysql_config= >> >> regards >> >> adam >> >> >> On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: >> >>> Hi! >>> >>> Last time I had a problem with loading_ncbi script so I decided to >>> start with fresh biosql andy also Unix. When I want to install >>> DBD::mysql module there is some mistakes. I`m not sure but maybe the >>> version mysql is not correct. I already have 5.1 >>> >>> cpan[1]> install DBD::mysql >>> CPAN: Storable loaded ok (v2.18) >>> Going to read /home/scati/.cpan/Metadata >>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>> Running install for module 'DBD::mysql' >>> CPAN: Data::Dumper loaded ok (v2.121_14) >>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>> read prefs '/home/scati/.cpan/prefs' >>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> CPAN: Digest::SHA loaded ok (v5.45) >>> CPAN: Compress::Zlib loaded ok (v2.008) >>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> ok >>> Scanning cache /home/scati/.cpan/build for sizes >>> ............................................................................DONE >>> DBD-mysql-4.013/ >>> DBD-mysql-4.013/lib/ >>> DBD-mysql-4.013/lib/DBD/ >>> DBD-mysql-4.013/lib/DBD/mysql.pm >>> DBD-mysql-4.013/lib/DBD/mysql/ >>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>> DBD-mysql-4.013/lib/Bundle/ >>> DBD-mysql-4.013/lib/Bundle/DBD/ >>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>> DBD-mysql-4.013/mysql.xs >>> DBD-mysql-4.013/dbdimp.c >>> DBD-mysql-4.013/myld >>> DBD-mysql-4.013/INSTALL.html >>> DBD-mysql-4.013/Makefile.PL.embedded >>> DBD-mysql-4.013/TODO >>> DBD-mysql-4.013/README >>> DBD-mysql-4.013/MANIFEST.SKIP >>> DBD-mysql-4.013/ChangeLog >>> DBD-mysql-4.013/Makefile.PL >>> DBD-mysql-4.013/META.yml >>> DBD-mysql-4.013/dbdimp.h >>> DBD-mysql-4.013/eg/ >>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>> DBD-mysql-4.013/eg/proc_example2b.pl >>> DBD-mysql-4.013/eg/proc_example2.pl >>> DBD-mysql-4.013/eg/decimal_test.pl >>> DBD-mysql-4.013/eg/bug30033pg.pl >>> DBD-mysql-4.013/eg/proc_example2a.pl >>> DBD-mysql-4.013/eg/proc_example4.pl >>> DBD-mysql-4.013/eg/bug21028.pl >>> DBD-mysql-4.013/eg/bug14979.pl >>> DBD-mysql-4.013/eg/bug30033.pl >>> DBD-mysql-4.013/eg/issue21946.pl >>> DBD-mysql-4.013/eg/proc_example3.pl >>> DBD-mysql-4.013/eg/proc_example1.pl >>> DBD-mysql-4.013/constants.h >>> DBD-mysql-4.013/t/ >>> DBD-mysql-4.013/t/85init_command.t >>> DBD-mysql-4.013/t/40listfields.t >>> DBD-mysql-4.013/t/40bindparam.t >>> DBD-mysql-4.013/t/mysql.mtest >>> DBD-mysql-4.013/t/41bindparam.t >>> DBD-mysql-4.013/t/76multi_statement.t >>> DBD-mysql-4.013/t/40nulls.t >>> DBD-mysql-4.013/t/32insert_error.t >>> DBD-mysql-4.013/t/40catalog.t >>> DBD-mysql-4.013/t/51bind_type_guessing.t >>> DBD-mysql-4.013/t/40bindparam2.t >>> DBD-mysql-4.013/t/41blobs_prepare.t >>> DBD-mysql-4.013/t/20createdrop.t >>> DBD-mysql-4.013/t/70takeimp.t >>> DBD-mysql-4.013/t/42bindparam.t >>> DBD-mysql-4.013/t/00base.t >>> DBD-mysql-4.013/t/55utf8.t >>> DBD-mysql-4.013/t/65types.t >>> DBD-mysql-4.013/t/40server_prepare_error.t >>> DBD-mysql-4.013/t/31insertid.t >>> DBD-mysql-4.013/t/29warnings.t >>> DBD-mysql-4.013/t/40types.t >>> DBD-mysql-4.013/t/10connect.t >>> DBD-mysql-4.013/t/lib.pl >>> DBD-mysql-4.013/t/mysql.dbtest >>> DBD-mysql-4.013/t/35limit.t >>> DBD-mysql-4.013/t/71impdata.t >>> DBD-mysql-4.013/t/40blobs.t >>> DBD-mysql-4.013/t/40server_prepare.t >>> DBD-mysql-4.013/t/40numrows.t >>> DBD-mysql-4.013/t/35prepare.t >>> DBD-mysql-4.013/t/40keyinfo.t >>> DBD-mysql-4.013/t/75supported_sql.t >>> DBD-mysql-4.013/t/60leaks.t >>> DBD-mysql-4.013/t/50commit.t >>> DBD-mysql-4.013/t/30insertfetch.t >>> DBD-mysql-4.013/t/50chopblanks.t >>> DBD-mysql-4.013/t/25lockunlock.t >>> DBD-mysql-4.013/t/80procs.t >>> DBD-mysql-4.013/MANIFEST >>> CPAN: File::Temp loaded ok (v0.18) >>> Warning (usually harmless): 'YAML' not installed, will not store >>> persistent state >>> >>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>> >>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>> not contain the path to mysql_config. Resorting to guessed values! >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> >>> >>> PLEASE NOTE: >>> >>> For 'make test' to run properly, you must ensure that the >>> database user 'root' can connect to your MySQL server >>> and has the proper privileges that these tests require such >>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>> as well as others. >>> >>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>> by 's3kr1t'; >>> >>> You can also optionally set the user to run 'make test' with: >>> >>> perl Makefile.pl --testuser=username >>> >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Failed to determine directory of mysql.h. Use >>> >>> perl Makefile.PL --cflags=-I >>> >>> to set this directory. For details see the INSTALL.html file, >>> section "C Compiler flags" or type >>> >>> perl Makefile.PL --help >>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>> Warning (usually harmless): 'YAML' not installed, will not store >>> persistent state >>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>> Running make test >>> Make had some problems, won't test >>> Running make install >>> Make had some problems, won't install >>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>> Falling back to other methods to determine prerequisites >>> Failed during this command: >>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>> cpan[1]> install DBD::mysql >>> CPAN: Storable loaded ok (v2.18) >>> Going to read /home/scati/.cpan/Metadata >>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>> Running install for module 'DBD::mysql' >>> CPAN: Data::Dumper loaded ok (v2.121_14) >>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>> read prefs '/home/scati/.cpan/prefs' >>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> CPAN: Digest::SHA loaded ok (v5.45) >>> CPAN: Compress::Zlib loaded ok (v2.008) >>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> ok >>> Scanning cache /home/scati/.cpan/build for sizes >>> ............................................................................DONE >>> DBD-mysql-4.013/ >>> DBD-mysql-4.013/lib/ >>> DBD-mysql-4.013/lib/DBD/ >>> DBD-mysql-4.013/lib/DBD/mysql.pm >>> DBD-mysql-4.013/lib/DBD/mysql/ >>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>> DBD-mysql-4.013/lib/Bundle/ >>> DBD-mysql-4.013/lib/Bundle/DBD/ >>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>> DBD-mysql-4.013/mysql.xs >>> DBD-mysql-4.013/dbdimp.c >>> DBD-mysql-4.013/myld >>> DBD-mysql-4.013/INSTALL.html >>> DBD-mysql-4.013/Makefile.PL.embedded >>> DBD-mysql-4.013/TODO >>> DBD-mysql-4.013/README >>> DBD-mysql-4.013/MANIFEST.SKIP >>> DBD-mysql-4.013/ChangeLog >>> DBD-mysql-4.013/Makefile.PL >>> DBD-mysql-4.013/META.yml >>> DBD-mysql-4.013/dbdimp.h >>> DBD-mysql-4.013/eg/ >>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>> DBD-mysql-4.013/eg/proc_example2b.pl >>> DBD-mysql-4.013/eg/proc_example2.pl >>> DBD-mysql-4.013/eg/decimal_test.pl >>> DBD-mysql-4.013/eg/bug30033pg.pl >>> DBD-mysql-4.013/eg/proc_example2a.pl >>> DBD-mysql-4.013/eg/proc_example4.pl >>> DBD-mysql-4.013/eg/bug21028.pl >>> DBD-mysql-4.013/eg/bug14979.pl >>> DBD-mysql-4.013/eg/bug30033.pl >>> DBD-mysql-4.013/eg/issue21946.pl >>> DBD-mysql-4.013/eg/proc_example3.pl >>> DBD-mysql-4.013/eg/proc_example1.pl >>> DBD-mysql-4.013/constants.h >>> DBD-mysql-4.013/t/ >>> DBD-mysql-4.013/t/85init_command.t >>> DBD-mysql-4.013/t/40listfields.t >>> DBD-mysql-4.013/t/40bindparam.t >>> DBD-mysql-4.013/t/mysql.mtest >>> DBD-mysql-4.013/t/41bindparam.t >>> DBD-mysql-4.013/t/76multi_statement.t >>> DBD-mysql-4.013/t/40nulls.t >>> DBD-mysql-4.013/t/32insert_error.t >>> DBD-mysql-4.013/t/40catalog.t >>> DBD-mysql-4.013/t/51bind_type_guessing.t >>> DBD-mysql-4.013/t/40bindparam2.t >>> DBD-mysql-4.013/t/41blobs_prepare.t >>> DBD-mysql-4.013/t/20createdrop.t >>> DBD-mysql-4.013/t/70takeimp.t >>> DBD-mysql-4.013/t/42bindparam.t >>> DBD-mysql-4.013/t/00base.t >>> DBD-mysql-4.013/t/55utf8.t >>> DBD-mysql-4.013/t/65types.t >>> DBD-mysql-4.013/t/40server_prepare_error.t >>> DBD-mysql-4.013/t/31insertid.t >>> DBD-mysql-4.013/t/29warnings.t >>> DBD-mysql-4.013/t/40types.t >>> DBD-mysql-4.013/t/10connect.t >>> DBD-mysql-4.013/t/lib.pl >>> DBD-mysql-4.013/t/mysql.dbtest >>> DBD-mysql-4.013/t/35limit.t >>> DBD-mysql-4.013/t/71impdata.t >>> DBD-mysql-4.013/t/40blobs.t >>> DBD-mysql-4.013/t/40server_prepare.t >>> DBD-mysql-4.013/t/40numrows.t >>> DBD-mysql-4.013/t/35prepare.t >>> DBD-mysql-4.013/t/40keyinfo.t >>> DBD-mysql-4.013/t/75supported_sql.t >>> DBD-mysql-4.013/t/60leaks.t >>> DBD-mysql-4.013/t/50commit.t >>> DBD-mysql-4.013/t/30insertfetch.t >>> DBD-mysql-4.013/t/50chopblanks.t >>> DBD-mysql-4.013/t/25lockunlock.t >>> DBD-mysql-4.013/t/80procs.t >>> DBD-mysql-4.013/MANIFEST >>> CPAN: File::Temp loaded ok (v0.18) >>> Warning (usually harmless): 'YAML' not installed, will not store >>> persistent state >>> >>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>> >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>> >>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>> not contain the path to mysql_config. Resorting to guessed values! >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> >>> >>> PLEASE NOTE: >>> >>> For 'make test' to run properly, you must ensure that the >>> database user 'root' can connect to your MySQL server >>> and has the proper privileges that these tests require such >>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>> as well as others. >>> >>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>> by 's3kr1t'; >>> >>> You can also optionally set the user to run 'make test' with: >>> >>> perl Makefile.pl --testuser=username >>> >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>> Can't find mysql_config. Use --mysql_config option to specify where >>> mysql_config is located >>> Failed to determine directory of mysql.h. Use >>> >>> perl Makefile.PL --cflags=-I >>> >>> to set this directory. For details see the INSTALL.html file, >>> section "C Compiler flags" or type >>> >>> perl Makefile.PL --help >>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>> Warning (usually harmless): 'YAML' not installed, will not store >>> persistent state >>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>> Running make test >>> Make had some problems, won't test >>> Running make install >>> Make had some problems, won't install >>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>> Falling back to other methods to determine prerequisites >>> Failed during this command: >>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>> >>> >>> -- >>> Piotr Borowiec >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> > > > > -- > Piotr Borowiec From cjfields at illinois.edu Tue Feb 16 13:26:24 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 16 Feb 2010 07:26:24 -0600 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> Message-ID: <101DFF66-EE65-49AB-A993-0B904F92F6DC@illinois.edu> Piotr, Adam, I can conform that is the problem. I ran into the exact issue when running tests on my local Ubuntu 9.10 setup, and installing the libmysqld-dev package fixed it. You can also install the DBD::mysql package as well (libdbd-mysql-perl). chris On Feb 16, 2010, at 5:24 AM, Adam Witney wrote: > > As i said you need to check if you have mysql_config installed. If not then for Ubuntu take a look at this: > > http://ubuntuforums.org/showthread.php?t=573286 > > adam > > > On 16 Feb 2010, at 11:14, Piotr Borowiec wrote: > >> I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu >> 9.10. What should I check in first order? >> >> Thanks for advice >> >> @sgul.ac.uk>: >>> >>> Hi Piotr, >>> >>> this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. >>> >>> But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try >>> >>> perl Makefile.PL --mysql_config= >>> >>> regards >>> >>> adam >>> >>> >>> On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: >>> >>>> Hi! >>>> >>>> Last time I had a problem with loading_ncbi script so I decided to >>>> start with fresh biosql andy also Unix. When I want to install >>>> DBD::mysql module there is some mistakes. I`m not sure but maybe the >>>> version mysql is not correct. I already have 5.1 >>>> >>>> cpan[1]> install DBD::mysql >>>> CPAN: Storable loaded ok (v2.18) >>>> Going to read /home/scati/.cpan/Metadata >>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>> Running install for module 'DBD::mysql' >>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>> read prefs '/home/scati/.cpan/prefs' >>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> CPAN: Digest::SHA loaded ok (v5.45) >>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> ok >>>> Scanning cache /home/scati/.cpan/build for sizes >>>> ............................................................................DONE >>>> DBD-mysql-4.013/ >>>> DBD-mysql-4.013/lib/ >>>> DBD-mysql-4.013/lib/DBD/ >>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>> DBD-mysql-4.013/lib/Bundle/ >>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>> DBD-mysql-4.013/mysql.xs >>>> DBD-mysql-4.013/dbdimp.c >>>> DBD-mysql-4.013/myld >>>> DBD-mysql-4.013/INSTALL.html >>>> DBD-mysql-4.013/Makefile.PL.embedded >>>> DBD-mysql-4.013/TODO >>>> DBD-mysql-4.013/README >>>> DBD-mysql-4.013/MANIFEST.SKIP >>>> DBD-mysql-4.013/ChangeLog >>>> DBD-mysql-4.013/Makefile.PL >>>> DBD-mysql-4.013/META.yml >>>> DBD-mysql-4.013/dbdimp.h >>>> DBD-mysql-4.013/eg/ >>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>> DBD-mysql-4.013/eg/proc_example2.pl >>>> DBD-mysql-4.013/eg/decimal_test.pl >>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>> DBD-mysql-4.013/eg/proc_example4.pl >>>> DBD-mysql-4.013/eg/bug21028.pl >>>> DBD-mysql-4.013/eg/bug14979.pl >>>> DBD-mysql-4.013/eg/bug30033.pl >>>> DBD-mysql-4.013/eg/issue21946.pl >>>> DBD-mysql-4.013/eg/proc_example3.pl >>>> DBD-mysql-4.013/eg/proc_example1.pl >>>> DBD-mysql-4.013/constants.h >>>> DBD-mysql-4.013/t/ >>>> DBD-mysql-4.013/t/85init_command.t >>>> DBD-mysql-4.013/t/40listfields.t >>>> DBD-mysql-4.013/t/40bindparam.t >>>> DBD-mysql-4.013/t/mysql.mtest >>>> DBD-mysql-4.013/t/41bindparam.t >>>> DBD-mysql-4.013/t/76multi_statement.t >>>> DBD-mysql-4.013/t/40nulls.t >>>> DBD-mysql-4.013/t/32insert_error.t >>>> DBD-mysql-4.013/t/40catalog.t >>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>> DBD-mysql-4.013/t/40bindparam2.t >>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>> DBD-mysql-4.013/t/20createdrop.t >>>> DBD-mysql-4.013/t/70takeimp.t >>>> DBD-mysql-4.013/t/42bindparam.t >>>> DBD-mysql-4.013/t/00base.t >>>> DBD-mysql-4.013/t/55utf8.t >>>> DBD-mysql-4.013/t/65types.t >>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>> DBD-mysql-4.013/t/31insertid.t >>>> DBD-mysql-4.013/t/29warnings.t >>>> DBD-mysql-4.013/t/40types.t >>>> DBD-mysql-4.013/t/10connect.t >>>> DBD-mysql-4.013/t/lib.pl >>>> DBD-mysql-4.013/t/mysql.dbtest >>>> DBD-mysql-4.013/t/35limit.t >>>> DBD-mysql-4.013/t/71impdata.t >>>> DBD-mysql-4.013/t/40blobs.t >>>> DBD-mysql-4.013/t/40server_prepare.t >>>> DBD-mysql-4.013/t/40numrows.t >>>> DBD-mysql-4.013/t/35prepare.t >>>> DBD-mysql-4.013/t/40keyinfo.t >>>> DBD-mysql-4.013/t/75supported_sql.t >>>> DBD-mysql-4.013/t/60leaks.t >>>> DBD-mysql-4.013/t/50commit.t >>>> DBD-mysql-4.013/t/30insertfetch.t >>>> DBD-mysql-4.013/t/50chopblanks.t >>>> DBD-mysql-4.013/t/25lockunlock.t >>>> DBD-mysql-4.013/t/80procs.t >>>> DBD-mysql-4.013/MANIFEST >>>> CPAN: File::Temp loaded ok (v0.18) >>>> Warning (usually harmless): 'YAML' not installed, will not store >>>> persistent state >>>> >>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>> >>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>> not contain the path to mysql_config. Resorting to guessed values! >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> >>>> >>>> PLEASE NOTE: >>>> >>>> For 'make test' to run properly, you must ensure that the >>>> database user 'root' can connect to your MySQL server >>>> and has the proper privileges that these tests require such >>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>> as well as others. >>>> >>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>> by 's3kr1t'; >>>> >>>> You can also optionally set the user to run 'make test' with: >>>> >>>> perl Makefile.pl --testuser=username >>>> >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Failed to determine directory of mysql.h. Use >>>> >>>> perl Makefile.PL --cflags=-I >>>> >>>> to set this directory. For details see the INSTALL.html file, >>>> section "C Compiler flags" or type >>>> >>>> perl Makefile.PL --help >>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>> Warning (usually harmless): 'YAML' not installed, will not store >>>> persistent state >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>> Running make test >>>> Make had some problems, won't test >>>> Running make install >>>> Make had some problems, won't install >>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>> Falling back to other methods to determine prerequisites >>>> Failed during this command: >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>> cpan[1]> install DBD::mysql >>>> CPAN: Storable loaded ok (v2.18) >>>> Going to read /home/scati/.cpan/Metadata >>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>> Running install for module 'DBD::mysql' >>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>> read prefs '/home/scati/.cpan/prefs' >>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> CPAN: Digest::SHA loaded ok (v5.45) >>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> ok >>>> Scanning cache /home/scati/.cpan/build for sizes >>>> ............................................................................DONE >>>> DBD-mysql-4.013/ >>>> DBD-mysql-4.013/lib/ >>>> DBD-mysql-4.013/lib/DBD/ >>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>> DBD-mysql-4.013/lib/Bundle/ >>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>> DBD-mysql-4.013/mysql.xs >>>> DBD-mysql-4.013/dbdimp.c >>>> DBD-mysql-4.013/myld >>>> DBD-mysql-4.013/INSTALL.html >>>> DBD-mysql-4.013/Makefile.PL.embedded >>>> DBD-mysql-4.013/TODO >>>> DBD-mysql-4.013/README >>>> DBD-mysql-4.013/MANIFEST.SKIP >>>> DBD-mysql-4.013/ChangeLog >>>> DBD-mysql-4.013/Makefile.PL >>>> DBD-mysql-4.013/META.yml >>>> DBD-mysql-4.013/dbdimp.h >>>> DBD-mysql-4.013/eg/ >>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>> DBD-mysql-4.013/eg/proc_example2.pl >>>> DBD-mysql-4.013/eg/decimal_test.pl >>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>> DBD-mysql-4.013/eg/proc_example4.pl >>>> DBD-mysql-4.013/eg/bug21028.pl >>>> DBD-mysql-4.013/eg/bug14979.pl >>>> DBD-mysql-4.013/eg/bug30033.pl >>>> DBD-mysql-4.013/eg/issue21946.pl >>>> DBD-mysql-4.013/eg/proc_example3.pl >>>> DBD-mysql-4.013/eg/proc_example1.pl >>>> DBD-mysql-4.013/constants.h >>>> DBD-mysql-4.013/t/ >>>> DBD-mysql-4.013/t/85init_command.t >>>> DBD-mysql-4.013/t/40listfields.t >>>> DBD-mysql-4.013/t/40bindparam.t >>>> DBD-mysql-4.013/t/mysql.mtest >>>> DBD-mysql-4.013/t/41bindparam.t >>>> DBD-mysql-4.013/t/76multi_statement.t >>>> DBD-mysql-4.013/t/40nulls.t >>>> DBD-mysql-4.013/t/32insert_error.t >>>> DBD-mysql-4.013/t/40catalog.t >>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>> DBD-mysql-4.013/t/40bindparam2.t >>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>> DBD-mysql-4.013/t/20createdrop.t >>>> DBD-mysql-4.013/t/70takeimp.t >>>> DBD-mysql-4.013/t/42bindparam.t >>>> DBD-mysql-4.013/t/00base.t >>>> DBD-mysql-4.013/t/55utf8.t >>>> DBD-mysql-4.013/t/65types.t >>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>> DBD-mysql-4.013/t/31insertid.t >>>> DBD-mysql-4.013/t/29warnings.t >>>> DBD-mysql-4.013/t/40types.t >>>> DBD-mysql-4.013/t/10connect.t >>>> DBD-mysql-4.013/t/lib.pl >>>> DBD-mysql-4.013/t/mysql.dbtest >>>> DBD-mysql-4.013/t/35limit.t >>>> DBD-mysql-4.013/t/71impdata.t >>>> DBD-mysql-4.013/t/40blobs.t >>>> DBD-mysql-4.013/t/40server_prepare.t >>>> DBD-mysql-4.013/t/40numrows.t >>>> DBD-mysql-4.013/t/35prepare.t >>>> DBD-mysql-4.013/t/40keyinfo.t >>>> DBD-mysql-4.013/t/75supported_sql.t >>>> DBD-mysql-4.013/t/60leaks.t >>>> DBD-mysql-4.013/t/50commit.t >>>> DBD-mysql-4.013/t/30insertfetch.t >>>> DBD-mysql-4.013/t/50chopblanks.t >>>> DBD-mysql-4.013/t/25lockunlock.t >>>> DBD-mysql-4.013/t/80procs.t >>>> DBD-mysql-4.013/MANIFEST >>>> CPAN: File::Temp loaded ok (v0.18) >>>> Warning (usually harmless): 'YAML' not installed, will not store >>>> persistent state >>>> >>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>> >>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>> not contain the path to mysql_config. Resorting to guessed values! >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> >>>> >>>> PLEASE NOTE: >>>> >>>> For 'make test' to run properly, you must ensure that the >>>> database user 'root' can connect to your MySQL server >>>> and has the proper privileges that these tests require such >>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>> as well as others. >>>> >>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>> by 's3kr1t'; >>>> >>>> You can also optionally set the user to run 'make test' with: >>>> >>>> perl Makefile.pl --testuser=username >>>> >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>> Can't find mysql_config. Use --mysql_config option to specify where >>>> mysql_config is located >>>> Failed to determine directory of mysql.h. Use >>>> >>>> perl Makefile.PL --cflags=-I >>>> >>>> to set this directory. For details see the INSTALL.html file, >>>> section "C Compiler flags" or type >>>> >>>> perl Makefile.PL --help >>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>> Warning (usually harmless): 'YAML' not installed, will not store >>>> persistent state >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>> Running make test >>>> Make had some problems, won't test >>>> Running make install >>>> Make had some problems, won't install >>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>> Falling back to other methods to determine prerequisites >>>> Failed during this command: >>>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>> >>>> >>>> -- >>>> Piotr Borowiec >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >>> >> >> >> >> -- >> Piotr Borowiec > > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/biosql-l From piotrborowiec at g.pl Tue Feb 16 14:19:37 2010 From: piotrborowiec at g.pl (Piotr Borowiec) Date: Tue, 16 Feb 2010 15:19:37 +0100 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: <101DFF66-EE65-49AB-A993-0B904F92F6DC@illinois.edu> References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> <101DFF66-EE65-49AB-A993-0B904F92F6DC@illinois.edu> Message-ID: <1c828cb91002160619xa82aedcj1578a74d6e2b329a@mail.gmail.com> HI, I`ve solved that problem, I installed libmysqlclient16-dev. So, that is a time to start script - load_ncbi_taxonomy.pl. I was puting in to terminal: sudo perl load_ncbi_taxonomy.pl etc. After that, there was another bug: 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 919. Use of uninitialized value in concatenation (.) or string at load_ncbi_taxonomy.pl line 921. So, I come back to same point. 2010/2/16 Chris Fields : > Piotr, Adam, > > I can conform that is the problem. ?I ran into the exact issue when running tests on my local Ubuntu 9.10 setup, and installing the libmysqld-dev package fixed it. ?You can also install the DBD::mysql package as well (libdbd-mysql-perl). > > chris > > On Feb 16, 2010, at 5:24 AM, Adam Witney wrote: > >> >> As i said you need to check if you have mysql_config installed. If not then for Ubuntu take a look at this: >> >> http://ubuntuforums.org/showthread.php?t=573286 >> >> adam >> >> >> On 16 Feb 2010, at 11:14, Piotr Borowiec wrote: >> >>> I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu >>> 9.10. What should I check in first order? >>> >>> Thanks for advice >>> >>> @sgul.ac.uk>: >>>> >>>> Hi Piotr, >>>> >>>> this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. >>>> >>>> But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try >>>> >>>> perl Makefile.PL --mysql_config= >>>> >>>> regards >>>> >>>> adam >>>> >>>> >>>> On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: >>>> >>>>> Hi! >>>>> >>>>> Last time I had a problem with loading_ncbi script so I decided to >>>>> start with fresh biosql andy also Unix. When I want to install >>>>> DBD::mysql module there is some mistakes. I`m not sure but maybe the >>>>> version mysql is not correct. I already have 5.1 >>>>> >>>>> cpan[1]> install DBD::mysql >>>>> CPAN: Storable loaded ok (v2.18) >>>>> Going to read /home/scati/.cpan/Metadata >>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>> Running install for module 'DBD::mysql' >>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>> read prefs '/home/scati/.cpan/prefs' >>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> ok >>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>> ............................................................................DONE >>>>> DBD-mysql-4.013/ >>>>> DBD-mysql-4.013/lib/ >>>>> DBD-mysql-4.013/lib/DBD/ >>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>> DBD-mysql-4.013/lib/Bundle/ >>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>> DBD-mysql-4.013/mysql.xs >>>>> DBD-mysql-4.013/dbdimp.c >>>>> DBD-mysql-4.013/myld >>>>> DBD-mysql-4.013/INSTALL.html >>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>> DBD-mysql-4.013/TODO >>>>> DBD-mysql-4.013/README >>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>> DBD-mysql-4.013/ChangeLog >>>>> DBD-mysql-4.013/Makefile.PL >>>>> DBD-mysql-4.013/META.yml >>>>> DBD-mysql-4.013/dbdimp.h >>>>> DBD-mysql-4.013/eg/ >>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>> DBD-mysql-4.013/constants.h >>>>> DBD-mysql-4.013/t/ >>>>> DBD-mysql-4.013/t/85init_command.t >>>>> DBD-mysql-4.013/t/40listfields.t >>>>> DBD-mysql-4.013/t/40bindparam.t >>>>> DBD-mysql-4.013/t/mysql.mtest >>>>> DBD-mysql-4.013/t/41bindparam.t >>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>> DBD-mysql-4.013/t/40nulls.t >>>>> DBD-mysql-4.013/t/32insert_error.t >>>>> DBD-mysql-4.013/t/40catalog.t >>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>> DBD-mysql-4.013/t/20createdrop.t >>>>> DBD-mysql-4.013/t/70takeimp.t >>>>> DBD-mysql-4.013/t/42bindparam.t >>>>> DBD-mysql-4.013/t/00base.t >>>>> DBD-mysql-4.013/t/55utf8.t >>>>> DBD-mysql-4.013/t/65types.t >>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>> DBD-mysql-4.013/t/31insertid.t >>>>> DBD-mysql-4.013/t/29warnings.t >>>>> DBD-mysql-4.013/t/40types.t >>>>> DBD-mysql-4.013/t/10connect.t >>>>> DBD-mysql-4.013/t/lib.pl >>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>> DBD-mysql-4.013/t/35limit.t >>>>> DBD-mysql-4.013/t/71impdata.t >>>>> DBD-mysql-4.013/t/40blobs.t >>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>> DBD-mysql-4.013/t/40numrows.t >>>>> DBD-mysql-4.013/t/35prepare.t >>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>> DBD-mysql-4.013/t/60leaks.t >>>>> DBD-mysql-4.013/t/50commit.t >>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>> DBD-mysql-4.013/t/80procs.t >>>>> DBD-mysql-4.013/MANIFEST >>>>> CPAN: File::Temp loaded ok (v0.18) >>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>> persistent state >>>>> >>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>> >>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> >>>>> >>>>> PLEASE NOTE: >>>>> >>>>> For 'make test' to run properly, you must ensure that the >>>>> database user 'root' can connect to your MySQL server >>>>> and has the proper privileges that these tests require such >>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>> as well as others. >>>>> >>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>> by 's3kr1t'; >>>>> >>>>> You can also optionally set the user to run 'make test' with: >>>>> >>>>> perl Makefile.pl --testuser=username >>>>> >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Failed to determine directory of mysql.h. Use >>>>> >>>>> perl Makefile.PL --cflags=-I >>>>> >>>>> to set this directory. For details see the INSTALL.html file, >>>>> section "C Compiler flags" or type >>>>> >>>>> perl Makefile.PL --help >>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>> persistent state >>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>> Running make test >>>>> Make had some problems, won't test >>>>> Running make install >>>>> Make had some problems, won't install >>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>> Falling back to other methods to determine prerequisites >>>>> Failed during this command: >>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>> cpan[1]> install DBD::mysql >>>>> CPAN: Storable loaded ok (v2.18) >>>>> Going to read /home/scati/.cpan/Metadata >>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>> Running install for module 'DBD::mysql' >>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>> read prefs '/home/scati/.cpan/prefs' >>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> ok >>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>> ............................................................................DONE >>>>> DBD-mysql-4.013/ >>>>> DBD-mysql-4.013/lib/ >>>>> DBD-mysql-4.013/lib/DBD/ >>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>> DBD-mysql-4.013/lib/Bundle/ >>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>> DBD-mysql-4.013/mysql.xs >>>>> DBD-mysql-4.013/dbdimp.c >>>>> DBD-mysql-4.013/myld >>>>> DBD-mysql-4.013/INSTALL.html >>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>> DBD-mysql-4.013/TODO >>>>> DBD-mysql-4.013/README >>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>> DBD-mysql-4.013/ChangeLog >>>>> DBD-mysql-4.013/Makefile.PL >>>>> DBD-mysql-4.013/META.yml >>>>> DBD-mysql-4.013/dbdimp.h >>>>> DBD-mysql-4.013/eg/ >>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>> DBD-mysql-4.013/constants.h >>>>> DBD-mysql-4.013/t/ >>>>> DBD-mysql-4.013/t/85init_command.t >>>>> DBD-mysql-4.013/t/40listfields.t >>>>> DBD-mysql-4.013/t/40bindparam.t >>>>> DBD-mysql-4.013/t/mysql.mtest >>>>> DBD-mysql-4.013/t/41bindparam.t >>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>> DBD-mysql-4.013/t/40nulls.t >>>>> DBD-mysql-4.013/t/32insert_error.t >>>>> DBD-mysql-4.013/t/40catalog.t >>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>> DBD-mysql-4.013/t/20createdrop.t >>>>> DBD-mysql-4.013/t/70takeimp.t >>>>> DBD-mysql-4.013/t/42bindparam.t >>>>> DBD-mysql-4.013/t/00base.t >>>>> DBD-mysql-4.013/t/55utf8.t >>>>> DBD-mysql-4.013/t/65types.t >>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>> DBD-mysql-4.013/t/31insertid.t >>>>> DBD-mysql-4.013/t/29warnings.t >>>>> DBD-mysql-4.013/t/40types.t >>>>> DBD-mysql-4.013/t/10connect.t >>>>> DBD-mysql-4.013/t/lib.pl >>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>> DBD-mysql-4.013/t/35limit.t >>>>> DBD-mysql-4.013/t/71impdata.t >>>>> DBD-mysql-4.013/t/40blobs.t >>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>> DBD-mysql-4.013/t/40numrows.t >>>>> DBD-mysql-4.013/t/35prepare.t >>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>> DBD-mysql-4.013/t/60leaks.t >>>>> DBD-mysql-4.013/t/50commit.t >>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>> DBD-mysql-4.013/t/80procs.t >>>>> DBD-mysql-4.013/MANIFEST >>>>> CPAN: File::Temp loaded ok (v0.18) >>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>> persistent state >>>>> >>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>> >>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> >>>>> >>>>> PLEASE NOTE: >>>>> >>>>> For 'make test' to run properly, you must ensure that the >>>>> database user 'root' can connect to your MySQL server >>>>> and has the proper privileges that these tests require such >>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>> as well as others. >>>>> >>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>> by 's3kr1t'; >>>>> >>>>> You can also optionally set the user to run 'make test' with: >>>>> >>>>> perl Makefile.pl --testuser=username >>>>> >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>> mysql_config is located >>>>> Failed to determine directory of mysql.h. Use >>>>> >>>>> perl Makefile.PL --cflags=-I >>>>> >>>>> to set this directory. For details see the INSTALL.html file, >>>>> section "C Compiler flags" or type >>>>> >>>>> perl Makefile.PL --help >>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>> persistent state >>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>> Running make test >>>>> Make had some problems, won't test >>>>> Running make install >>>>> Make had some problems, won't install >>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>> Falling back to other methods to determine prerequisites >>>>> Failed during this command: >>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>> >>>>> >>>>> -- >>>>> Piotr Borowiec >>>>> _______________________________________________ >>>>> BioSQL-l mailing list >>>>> BioSQL-l at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>> >>>> >>> >>> >>> >>> -- >>> Piotr Borowiec >> >> >> _______________________________________________ >> BioSQL-l mailing list >> BioSQL-l at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/biosql-l > > -- Piotr Borowiec From piotrborowiec at g.pl Tue Feb 16 14:32:40 2010 From: piotrborowiec at g.pl (Piotr Borowiec) Date: Tue, 16 Feb 2010 15:32:40 +0100 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: <78EE6F34-9BC7-4505-8858-6D9F3DBA2152@illinois.edu> References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> <101DFF66-EE65-49AB-A993-0B904F92F6DC@illinois.edu> <1c828cb91002160619xa82aedcj1578a74d6e2b329a@mail.gmail.com> <78EE6F34-9BC7-4505-8858-6D9F3DBA2152@illinois.edu> Message-ID: <1c828cb91002160632q5298839fje490e43b9e7034f@mail.gmail.com> Right, sorry for that. I was found answer http://bioperl.open-bio.org/SRC/bioperl-live/INSTALL.WIN So need to download, unzip and re-start script. 2010/2/16 Chris Fields : > That's not a bug. ?You need to use the --download option to retrieve the taxonomy files, they aren't included with the distribution. > > chris > > On Feb 16, 2010, at 8:19 AM, Piotr Borowiec wrote: > >> HI, I`ve solved that problem, I installed libmysqlclient16-dev. So, >> that is a time to start script - load_ncbi_taxonomy.pl. I was puting >> in to terminal: sudo perl load_ncbi_taxonomy.pl etc. After that, there >> was another bug: >> >> 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 919. >> Use of uninitialized value in concatenation (.) or string at >> load_ncbi_taxonomy.pl line 921. >> >> So, I come back to same point. >> >> 2010/2/16 Chris Fields : >>> Piotr, Adam, >>> >>> I can conform that is the problem. ?I ran into the exact issue when running tests on my local Ubuntu 9.10 setup, and installing the libmysqld-dev package fixed it. ?You can also install the DBD::mysql package as well (libdbd-mysql-perl). >>> >>> chris >>> >>> On Feb 16, 2010, at 5:24 AM, Adam Witney wrote: >>> >>>> >>>> As i said you need to check if you have mysql_config installed. If not then for Ubuntu take a look at this: >>>> >>>> http://ubuntuforums.org/showthread.php?t=573286 >>>> >>>> adam >>>> >>>> >>>> On 16 Feb 2010, at 11:14, Piotr Borowiec wrote: >>>> >>>>> I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu >>>>> 9.10. What should I check in first order? >>>>> >>>>> Thanks for advice >>>>> >>>>> @sgul.ac.uk>: >>>>>> >>>>>> Hi Piotr, >>>>>> >>>>>> this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. >>>>>> >>>>>> But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try >>>>>> >>>>>> perl Makefile.PL --mysql_config= >>>>>> >>>>>> regards >>>>>> >>>>>> adam >>>>>> >>>>>> >>>>>> On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: >>>>>> >>>>>>> Hi! >>>>>>> >>>>>>> Last time I had a problem with loading_ncbi script so I decided to >>>>>>> start with fresh biosql andy also Unix. When I want to install >>>>>>> DBD::mysql module there is some mistakes. I`m not sure but maybe the >>>>>>> version mysql is not correct. I already have 5.1 >>>>>>> >>>>>>> cpan[1]> install DBD::mysql >>>>>>> CPAN: Storable loaded ok (v2.18) >>>>>>> Going to read /home/scati/.cpan/Metadata >>>>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>>>> Running install for module 'DBD::mysql' >>>>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>>>> read prefs '/home/scati/.cpan/prefs' >>>>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> ok >>>>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>>>> ............................................................................DONE >>>>>>> DBD-mysql-4.013/ >>>>>>> DBD-mysql-4.013/lib/ >>>>>>> DBD-mysql-4.013/lib/DBD/ >>>>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>>>> DBD-mysql-4.013/lib/Bundle/ >>>>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>>>> DBD-mysql-4.013/mysql.xs >>>>>>> DBD-mysql-4.013/dbdimp.c >>>>>>> DBD-mysql-4.013/myld >>>>>>> DBD-mysql-4.013/INSTALL.html >>>>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>>>> DBD-mysql-4.013/TODO >>>>>>> DBD-mysql-4.013/README >>>>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>>>> DBD-mysql-4.013/ChangeLog >>>>>>> DBD-mysql-4.013/Makefile.PL >>>>>>> DBD-mysql-4.013/META.yml >>>>>>> DBD-mysql-4.013/dbdimp.h >>>>>>> DBD-mysql-4.013/eg/ >>>>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>>>> DBD-mysql-4.013/constants.h >>>>>>> DBD-mysql-4.013/t/ >>>>>>> DBD-mysql-4.013/t/85init_command.t >>>>>>> DBD-mysql-4.013/t/40listfields.t >>>>>>> DBD-mysql-4.013/t/40bindparam.t >>>>>>> DBD-mysql-4.013/t/mysql.mtest >>>>>>> DBD-mysql-4.013/t/41bindparam.t >>>>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>>>> DBD-mysql-4.013/t/40nulls.t >>>>>>> DBD-mysql-4.013/t/32insert_error.t >>>>>>> DBD-mysql-4.013/t/40catalog.t >>>>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>>>> DBD-mysql-4.013/t/20createdrop.t >>>>>>> DBD-mysql-4.013/t/70takeimp.t >>>>>>> DBD-mysql-4.013/t/42bindparam.t >>>>>>> DBD-mysql-4.013/t/00base.t >>>>>>> DBD-mysql-4.013/t/55utf8.t >>>>>>> DBD-mysql-4.013/t/65types.t >>>>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>>>> DBD-mysql-4.013/t/31insertid.t >>>>>>> DBD-mysql-4.013/t/29warnings.t >>>>>>> DBD-mysql-4.013/t/40types.t >>>>>>> DBD-mysql-4.013/t/10connect.t >>>>>>> DBD-mysql-4.013/t/lib.pl >>>>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>>>> DBD-mysql-4.013/t/35limit.t >>>>>>> DBD-mysql-4.013/t/71impdata.t >>>>>>> DBD-mysql-4.013/t/40blobs.t >>>>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>>>> DBD-mysql-4.013/t/40numrows.t >>>>>>> DBD-mysql-4.013/t/35prepare.t >>>>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>>>> DBD-mysql-4.013/t/60leaks.t >>>>>>> DBD-mysql-4.013/t/50commit.t >>>>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>>>> DBD-mysql-4.013/t/80procs.t >>>>>>> DBD-mysql-4.013/MANIFEST >>>>>>> CPAN: File::Temp loaded ok (v0.18) >>>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>>> persistent state >>>>>>> >>>>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>>>> >>>>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> >>>>>>> >>>>>>> PLEASE NOTE: >>>>>>> >>>>>>> For 'make test' to run properly, you must ensure that the >>>>>>> database user 'root' can connect to your MySQL server >>>>>>> and has the proper privileges that these tests require such >>>>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>>>> as well as others. >>>>>>> >>>>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>>>> by 's3kr1t'; >>>>>>> >>>>>>> You can also optionally set the user to run 'make test' with: >>>>>>> >>>>>>> perl Makefile.pl --testuser=username >>>>>>> >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Failed to determine directory of mysql.h. Use >>>>>>> >>>>>>> perl Makefile.PL --cflags=-I >>>>>>> >>>>>>> to set this directory. For details see the INSTALL.html file, >>>>>>> section "C Compiler flags" or type >>>>>>> >>>>>>> perl Makefile.PL --help >>>>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>>> persistent state >>>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>>>> Running make test >>>>>>> Make had some problems, won't test >>>>>>> Running make install >>>>>>> Make had some problems, won't install >>>>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>>>> Falling back to other methods to determine prerequisites >>>>>>> Failed during this command: >>>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >>>>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>>>> cpan[1]> install DBD::mysql >>>>>>> CPAN: Storable loaded ok (v2.18) >>>>>>> Going to read /home/scati/.cpan/Metadata >>>>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>>>> Running install for module 'DBD::mysql' >>>>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>>>> read prefs '/home/scati/.cpan/prefs' >>>>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> ok >>>>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>>>> ............................................................................DONE >>>>>>> DBD-mysql-4.013/ >>>>>>> DBD-mysql-4.013/lib/ >>>>>>> DBD-mysql-4.013/lib/DBD/ >>>>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>>>> DBD-mysql-4.013/lib/Bundle/ >>>>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>>>> DBD-mysql-4.013/mysql.xs >>>>>>> DBD-mysql-4.013/dbdimp.c >>>>>>> DBD-mysql-4.013/myld >>>>>>> DBD-mysql-4.013/INSTALL.html >>>>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>>>> DBD-mysql-4.013/TODO >>>>>>> DBD-mysql-4.013/README >>>>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>>>> DBD-mysql-4.013/ChangeLog >>>>>>> DBD-mysql-4.013/Makefile.PL >>>>>>> DBD-mysql-4.013/META.yml >>>>>>> DBD-mysql-4.013/dbdimp.h >>>>>>> DBD-mysql-4.013/eg/ >>>>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>>>> DBD-mysql-4.013/constants.h >>>>>>> DBD-mysql-4.013/t/ >>>>>>> DBD-mysql-4.013/t/85init_command.t >>>>>>> DBD-mysql-4.013/t/40listfields.t >>>>>>> DBD-mysql-4.013/t/40bindparam.t >>>>>>> DBD-mysql-4.013/t/mysql.mtest >>>>>>> DBD-mysql-4.013/t/41bindparam.t >>>>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>>>> DBD-mysql-4.013/t/40nulls.t >>>>>>> DBD-mysql-4.013/t/32insert_error.t >>>>>>> DBD-mysql-4.013/t/40catalog.t >>>>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>>>> DBD-mysql-4.013/t/20createdrop.t >>>>>>> DBD-mysql-4.013/t/70takeimp.t >>>>>>> DBD-mysql-4.013/t/42bindparam.t >>>>>>> DBD-mysql-4.013/t/00base.t >>>>>>> DBD-mysql-4.013/t/55utf8.t >>>>>>> DBD-mysql-4.013/t/65types.t >>>>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>>>> DBD-mysql-4.013/t/31insertid.t >>>>>>> DBD-mysql-4.013/t/29warnings.t >>>>>>> DBD-mysql-4.013/t/40types.t >>>>>>> DBD-mysql-4.013/t/10connect.t >>>>>>> DBD-mysql-4.013/t/lib.pl >>>>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>>>> DBD-mysql-4.013/t/35limit.t >>>>>>> DBD-mysql-4.013/t/71impdata.t >>>>>>> DBD-mysql-4.013/t/40blobs.t >>>>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>>>> DBD-mysql-4.013/t/40numrows.t >>>>>>> DBD-mysql-4.013/t/35prepare.t >>>>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>>>> DBD-mysql-4.013/t/60leaks.t >>>>>>> DBD-mysql-4.013/t/50commit.t >>>>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>>>> DBD-mysql-4.013/t/80procs.t >>>>>>> DBD-mysql-4.013/MANIFEST >>>>>>> CPAN: File::Temp loaded ok (v0.18) >>>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>>> persistent state >>>>>>> >>>>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>>>> >>>>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> >>>>>>> >>>>>>> PLEASE NOTE: >>>>>>> >>>>>>> For 'make test' to run properly, you must ensure that the >>>>>>> database user 'root' can connect to your MySQL server >>>>>>> and has the proper privileges that these tests require such >>>>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>>>> as well as others. >>>>>>> >>>>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>>>> by 's3kr1t'; >>>>>>> >>>>>>> You can also optionally set the user to run 'make test' with: >>>>>>> >>>>>>> perl Makefile.pl --testuser=username >>>>>>> >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>>> mysql_config is located >>>>>>> Failed to determine directory of mysql.h. Use >>>>>>> >>>>>>> perl Makefile.PL --cflags=-I >>>>>>> >>>>>>> to set this directory. For details see the INSTALL.html file, >>>>>>> section "C Compiler flags" or type >>>>>>> >>>>>>> perl Makefile.PL --help >>>>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>>> persistent state >>>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>>>> Running make test >>>>>>> Make had some problems, won't test >>>>>>> Running make install >>>>>>> Make had some problems, won't install >>>>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>>>> Falling back to other methods to determine prerequisites >>>>>>> Failed during this command: >>>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz ? ? ? ? ? ? ?: writemakefile NO >>>>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Piotr Borowiec >>>>>>> _______________________________________________ >>>>>>> BioSQL-l mailing list >>>>>>> BioSQL-l at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Piotr Borowiec >>>> >>>> >>>> _______________________________________________ >>>> BioSQL-l mailing list >>>> BioSQL-l at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>> >>> >> >> >> >> -- >> Piotr Borowiec > > -- Piotr Borowiec From cjfields at illinois.edu Tue Feb 16 14:24:51 2010 From: cjfields at illinois.edu (Chris Fields) Date: Tue, 16 Feb 2010 08:24:51 -0600 Subject: [BioSQL-l] Some problem with installation DBD::mysql In-Reply-To: <1c828cb91002160619xa82aedcj1578a74d6e2b329a@mail.gmail.com> References: <1c828cb91002160224l386ed04bt49c003abcceb8c1@mail.gmail.com> <1c828cb91002160314o73c685acv7b481e8a591a12fa@mail.gmail.com> <101DFF66-EE65-49AB-A993-0B904F92F6DC@illinois.edu> <1c828cb91002160619xa82aedcj1578a74d6e2b329a@mail.gmail.com> Message-ID: <78EE6F34-9BC7-4505-8858-6D9F3DBA2152@illinois.edu> That's not a bug. You need to use the --download option to retrieve the taxonomy files, they aren't included with the distribution. chris On Feb 16, 2010, at 8:19 AM, Piotr Borowiec wrote: > HI, I`ve solved that problem, I installed libmysqlclient16-dev. So, > that is a time to start script - load_ncbi_taxonomy.pl. I was puting > in to terminal: sudo perl load_ncbi_taxonomy.pl etc. After that, there > was another bug: > > 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 919. > Use of uninitialized value in concatenation (.) or string at > load_ncbi_taxonomy.pl line 921. > > So, I come back to same point. > > 2010/2/16 Chris Fields : >> Piotr, Adam, >> >> I can conform that is the problem. I ran into the exact issue when running tests on my local Ubuntu 9.10 setup, and installing the libmysqld-dev package fixed it. You can also install the DBD::mysql package as well (libdbd-mysql-perl). >> >> chris >> >> On Feb 16, 2010, at 5:24 AM, Adam Witney wrote: >> >>> >>> As i said you need to check if you have mysql_config installed. If not then for Ubuntu take a look at this: >>> >>> http://ubuntuforums.org/showthread.php?t=573286 >>> >>> adam >>> >>> >>> On 16 Feb 2010, at 11:14, Piotr Borowiec wrote: >>> >>>> I`m using MySQL server 5.1.37 and it works. I also workin on Ubuntu >>>> 9.10. What should I check in first order? >>>> >>>> Thanks for advice >>>> >>>> @sgul.ac.uk>: >>>>> >>>>> Hi Piotr, >>>>> >>>>> this is a problem with DBD::mysql rather than BioSQL, so you might be better checking on those lists. >>>>> >>>>> But it appears to be looking for mysql_config. Do you have that installed on your machine? I think it comes from one of the MySQL devel packages/rpm's (depending on which flavour of Unix you are using). If you have it and it is in a non standard place then try >>>>> >>>>> perl Makefile.PL --mysql_config= >>>>> >>>>> regards >>>>> >>>>> adam >>>>> >>>>> >>>>> On 16 Feb 2010, at 10:24, Piotr Borowiec wrote: >>>>> >>>>>> Hi! >>>>>> >>>>>> Last time I had a problem with loading_ncbi script so I decided to >>>>>> start with fresh biosql andy also Unix. When I want to install >>>>>> DBD::mysql module there is some mistakes. I`m not sure but maybe the >>>>>> version mysql is not correct. I already have 5.1 >>>>>> >>>>>> cpan[1]> install DBD::mysql >>>>>> CPAN: Storable loaded ok (v2.18) >>>>>> Going to read /home/scati/.cpan/Metadata >>>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>>> Running install for module 'DBD::mysql' >>>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>>> read prefs '/home/scati/.cpan/prefs' >>>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> ok >>>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>>> ............................................................................DONE >>>>>> DBD-mysql-4.013/ >>>>>> DBD-mysql-4.013/lib/ >>>>>> DBD-mysql-4.013/lib/DBD/ >>>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>>> DBD-mysql-4.013/lib/Bundle/ >>>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>>> DBD-mysql-4.013/mysql.xs >>>>>> DBD-mysql-4.013/dbdimp.c >>>>>> DBD-mysql-4.013/myld >>>>>> DBD-mysql-4.013/INSTALL.html >>>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>>> DBD-mysql-4.013/TODO >>>>>> DBD-mysql-4.013/README >>>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>>> DBD-mysql-4.013/ChangeLog >>>>>> DBD-mysql-4.013/Makefile.PL >>>>>> DBD-mysql-4.013/META.yml >>>>>> DBD-mysql-4.013/dbdimp.h >>>>>> DBD-mysql-4.013/eg/ >>>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>>> DBD-mysql-4.013/constants.h >>>>>> DBD-mysql-4.013/t/ >>>>>> DBD-mysql-4.013/t/85init_command.t >>>>>> DBD-mysql-4.013/t/40listfields.t >>>>>> DBD-mysql-4.013/t/40bindparam.t >>>>>> DBD-mysql-4.013/t/mysql.mtest >>>>>> DBD-mysql-4.013/t/41bindparam.t >>>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>>> DBD-mysql-4.013/t/40nulls.t >>>>>> DBD-mysql-4.013/t/32insert_error.t >>>>>> DBD-mysql-4.013/t/40catalog.t >>>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>>> DBD-mysql-4.013/t/20createdrop.t >>>>>> DBD-mysql-4.013/t/70takeimp.t >>>>>> DBD-mysql-4.013/t/42bindparam.t >>>>>> DBD-mysql-4.013/t/00base.t >>>>>> DBD-mysql-4.013/t/55utf8.t >>>>>> DBD-mysql-4.013/t/65types.t >>>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>>> DBD-mysql-4.013/t/31insertid.t >>>>>> DBD-mysql-4.013/t/29warnings.t >>>>>> DBD-mysql-4.013/t/40types.t >>>>>> DBD-mysql-4.013/t/10connect.t >>>>>> DBD-mysql-4.013/t/lib.pl >>>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>>> DBD-mysql-4.013/t/35limit.t >>>>>> DBD-mysql-4.013/t/71impdata.t >>>>>> DBD-mysql-4.013/t/40blobs.t >>>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>>> DBD-mysql-4.013/t/40numrows.t >>>>>> DBD-mysql-4.013/t/35prepare.t >>>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>>> DBD-mysql-4.013/t/60leaks.t >>>>>> DBD-mysql-4.013/t/50commit.t >>>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>>> DBD-mysql-4.013/t/80procs.t >>>>>> DBD-mysql-4.013/MANIFEST >>>>>> CPAN: File::Temp loaded ok (v0.18) >>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>> persistent state >>>>>> >>>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>>> >>>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> >>>>>> >>>>>> PLEASE NOTE: >>>>>> >>>>>> For 'make test' to run properly, you must ensure that the >>>>>> database user 'root' can connect to your MySQL server >>>>>> and has the proper privileges that these tests require such >>>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>>> as well as others. >>>>>> >>>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>>> by 's3kr1t'; >>>>>> >>>>>> You can also optionally set the user to run 'make test' with: >>>>>> >>>>>> perl Makefile.pl --testuser=username >>>>>> >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Failed to determine directory of mysql.h. Use >>>>>> >>>>>> perl Makefile.PL --cflags=-I >>>>>> >>>>>> to set this directory. For details see the INSTALL.html file, >>>>>> section "C Compiler flags" or type >>>>>> >>>>>> perl Makefile.PL --help >>>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>> persistent state >>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>>> Running make test >>>>>> Make had some problems, won't test >>>>>> Running make install >>>>>> Make had some problems, won't install >>>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>>> Falling back to other methods to determine prerequisites >>>>>> Failed during this command: >>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>>> cpan[1]> install DBD::mysql >>>>>> CPAN: Storable loaded ok (v2.18) >>>>>> Going to read /home/scati/.cpan/Metadata >>>>>> Database was generated on Tue, 16 Feb 2010 07:53:49 GMT >>>>>> Running install for module 'DBD::mysql' >>>>>> CPAN: Data::Dumper loaded ok (v2.121_14) >>>>>> 'YAML' not installed, falling back to Data::Dumper and Storable to >>>>>> read prefs '/home/scati/.cpan/prefs' >>>>>> Running make for C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> CPAN: Digest::SHA loaded ok (v5.45) >>>>>> CPAN: Compress::Zlib loaded ok (v2.008) >>>>>> Checksum for /home/scati/.cpan/sources/authors/id/C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> ok >>>>>> Scanning cache /home/scati/.cpan/build for sizes >>>>>> ............................................................................DONE >>>>>> DBD-mysql-4.013/ >>>>>> DBD-mysql-4.013/lib/ >>>>>> DBD-mysql-4.013/lib/DBD/ >>>>>> DBD-mysql-4.013/lib/DBD/mysql.pm >>>>>> DBD-mysql-4.013/lib/DBD/mysql/ >>>>>> DBD-mysql-4.013/lib/DBD/mysql/GetInfo.pm >>>>>> DBD-mysql-4.013/lib/DBD/mysql/INSTALL.pod >>>>>> DBD-mysql-4.013/lib/Bundle/ >>>>>> DBD-mysql-4.013/lib/Bundle/DBD/ >>>>>> DBD-mysql-4.013/lib/Bundle/DBD/mysql.pm >>>>>> DBD-mysql-4.013/mysql.xs >>>>>> DBD-mysql-4.013/dbdimp.c >>>>>> DBD-mysql-4.013/myld >>>>>> DBD-mysql-4.013/INSTALL.html >>>>>> DBD-mysql-4.013/Makefile.PL.embedded >>>>>> DBD-mysql-4.013/TODO >>>>>> DBD-mysql-4.013/README >>>>>> DBD-mysql-4.013/MANIFEST.SKIP >>>>>> DBD-mysql-4.013/ChangeLog >>>>>> DBD-mysql-4.013/Makefile.PL >>>>>> DBD-mysql-4.013/META.yml >>>>>> DBD-mysql-4.013/dbdimp.h >>>>>> DBD-mysql-4.013/eg/ >>>>>> DBD-mysql-4.013/eg/prepare_memory_usage.pl >>>>>> DBD-mysql-4.013/eg/proc_example2b.pl >>>>>> DBD-mysql-4.013/eg/proc_example2.pl >>>>>> DBD-mysql-4.013/eg/decimal_test.pl >>>>>> DBD-mysql-4.013/eg/bug30033pg.pl >>>>>> DBD-mysql-4.013/eg/proc_example2a.pl >>>>>> DBD-mysql-4.013/eg/proc_example4.pl >>>>>> DBD-mysql-4.013/eg/bug21028.pl >>>>>> DBD-mysql-4.013/eg/bug14979.pl >>>>>> DBD-mysql-4.013/eg/bug30033.pl >>>>>> DBD-mysql-4.013/eg/issue21946.pl >>>>>> DBD-mysql-4.013/eg/proc_example3.pl >>>>>> DBD-mysql-4.013/eg/proc_example1.pl >>>>>> DBD-mysql-4.013/constants.h >>>>>> DBD-mysql-4.013/t/ >>>>>> DBD-mysql-4.013/t/85init_command.t >>>>>> DBD-mysql-4.013/t/40listfields.t >>>>>> DBD-mysql-4.013/t/40bindparam.t >>>>>> DBD-mysql-4.013/t/mysql.mtest >>>>>> DBD-mysql-4.013/t/41bindparam.t >>>>>> DBD-mysql-4.013/t/76multi_statement.t >>>>>> DBD-mysql-4.013/t/40nulls.t >>>>>> DBD-mysql-4.013/t/32insert_error.t >>>>>> DBD-mysql-4.013/t/40catalog.t >>>>>> DBD-mysql-4.013/t/51bind_type_guessing.t >>>>>> DBD-mysql-4.013/t/40bindparam2.t >>>>>> DBD-mysql-4.013/t/41blobs_prepare.t >>>>>> DBD-mysql-4.013/t/20createdrop.t >>>>>> DBD-mysql-4.013/t/70takeimp.t >>>>>> DBD-mysql-4.013/t/42bindparam.t >>>>>> DBD-mysql-4.013/t/00base.t >>>>>> DBD-mysql-4.013/t/55utf8.t >>>>>> DBD-mysql-4.013/t/65types.t >>>>>> DBD-mysql-4.013/t/40server_prepare_error.t >>>>>> DBD-mysql-4.013/t/31insertid.t >>>>>> DBD-mysql-4.013/t/29warnings.t >>>>>> DBD-mysql-4.013/t/40types.t >>>>>> DBD-mysql-4.013/t/10connect.t >>>>>> DBD-mysql-4.013/t/lib.pl >>>>>> DBD-mysql-4.013/t/mysql.dbtest >>>>>> DBD-mysql-4.013/t/35limit.t >>>>>> DBD-mysql-4.013/t/71impdata.t >>>>>> DBD-mysql-4.013/t/40blobs.t >>>>>> DBD-mysql-4.013/t/40server_prepare.t >>>>>> DBD-mysql-4.013/t/40numrows.t >>>>>> DBD-mysql-4.013/t/35prepare.t >>>>>> DBD-mysql-4.013/t/40keyinfo.t >>>>>> DBD-mysql-4.013/t/75supported_sql.t >>>>>> DBD-mysql-4.013/t/60leaks.t >>>>>> DBD-mysql-4.013/t/50commit.t >>>>>> DBD-mysql-4.013/t/30insertfetch.t >>>>>> DBD-mysql-4.013/t/50chopblanks.t >>>>>> DBD-mysql-4.013/t/25lockunlock.t >>>>>> DBD-mysql-4.013/t/80procs.t >>>>>> DBD-mysql-4.013/MANIFEST >>>>>> CPAN: File::Temp loaded ok (v0.18) >>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>> persistent state >>>>>> >>>>>> CPAN.pm: Going to build C/CA/CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 82. >>>>>> >>>>>> Cannot find the file 'mysql_config'! Your execution PATH doesn't seem >>>>>> not contain the path to mysql_config. Resorting to guessed values! >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> >>>>>> >>>>>> PLEASE NOTE: >>>>>> >>>>>> For 'make test' to run properly, you must ensure that the >>>>>> database user 'root' can connect to your MySQL server >>>>>> and has the proper privileges that these tests require such >>>>>> as 'drop table', 'create table', 'drop procedure', 'create procedure' >>>>>> as well as others. >>>>>> >>>>>> mysql> grant all privileges on test.* to 'root'@'localhost' identified >>>>>> by 's3kr1t'; >>>>>> >>>>>> You can also optionally set the user to run 'make test' with: >>>>>> >>>>>> perl Makefile.pl --testuser=username >>>>>> >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Can't exec "mysql_config": No such file or directory at Makefile.PL line 464. >>>>>> Can't find mysql_config. Use --mysql_config option to specify where >>>>>> mysql_config is located >>>>>> Failed to determine directory of mysql.h. Use >>>>>> >>>>>> perl Makefile.PL --cflags=-I >>>>>> >>>>>> to set this directory. For details see the INSTALL.html file, >>>>>> section "C Compiler flags" or type >>>>>> >>>>>> perl Makefile.PL --help >>>>>> Warning: No success on command[/usr/bin/perl Makefile.PL INSTALLDIRS=site] >>>>>> Warning (usually harmless): 'YAML' not installed, will not store >>>>>> persistent state >>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz >>>>>> /usr/bin/perl Makefile.PL INSTALLDIRS=site -- NOT OK >>>>>> Running make test >>>>>> Make had some problems, won't test >>>>>> Running make install >>>>>> Make had some problems, won't install >>>>>> Could not read '/home/scati/.cpan/build/DBD-mysql-4.013-3mdpDW/META.yml'. >>>>>> Falling back to other methods to determine prerequisites >>>>>> Failed during this command: >>>>>> CAPTTOFU/DBD-mysql-4.013.tar.gz : writemakefile NO >>>>>> '/usr/bin/perl Makefile.PL INSTALLDIRS=site' returned status 512 >>>>>> >>>>>> >>>>>> -- >>>>>> Piotr Borowiec >>>>>> _______________________________________________ >>>>>> BioSQL-l mailing list >>>>>> BioSQL-l at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/biosql-l >>>>> >>>>> >>>> >>>> >>>> >>>> -- >>>> Piotr Borowiec >>> >>> >>> _______________________________________________ >>> BioSQL-l mailing list >>> BioSQL-l at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/biosql-l >> >> > > > > -- > Piotr Borowiec From mysarapa at cyf-kr.edu.pl Tue Feb 16 16:59:10 2010 From: mysarapa at cyf-kr.edu.pl (Krzysztof Sarapata) Date: Tue, 16 Feb 2010 17:59:10 +0100 Subject: [BioSQL-l] some problems with loading GenBank Message-ID: <006401caaf29$5c0c9990$2f0c9c95@rubin> Hi I've loaded GenBank file into bioSQL structure with "load_seqdatabase.pl" script. Is it correct that each entity (qualifier) from FEATURES even "db_xref" e.g. FEATURES Location/Qualifiers source 1..257719 /organism="Homo sapiens" /mol_type="genomic DNA" /db_xref="taxon:9606" /chromosome="1" ..... /db_xref="GeneID:100287102" is put into "Seqfeature Qualifier Value" table, if we have exactly table "Dbxref"? Why value of this qualifier (db_xref) isn't put into "Dbxref" table? With regards Krzysztof Sarapata From hlapp at drycafe.net Thu Feb 18 18:18:52 2010 From: hlapp at drycafe.net (Hilmar Lapp) Date: Thu, 18 Feb 2010 13:18:52 -0500 Subject: [BioSQL-l] some problems with loading GenBank In-Reply-To: <006401caaf29$5c0c9990$2f0c9c95@rubin> References: <006401caaf29$5c0c9990$2f0c9c95@rubin> Message-ID: <9334383A-BB0D-4AE3-9536-762C4123964F@drycafe.net> Hi Krzysztof - your question really is about the BioPerl object- relational mapping to BioSQL, and I see you have posted your question to the BioPerl list already. Roy's answer there is correct - where stuff ends up depends solely on the object-relational mapping (which put feature tag/value pairs into feature_qualifier_value) and the structure of the sequence object in BioPerl. You can easily manipulate the destination of stuff by manipulating the BioPerl object itself to have the representation you want. If there are certain feature tags that have a special meaning to you (such as being dbxrefs), pull them out of feature tag/values and add them back in as Bio::Annotation::DBLink annotation on the sequence (or the feature). Writing a SeqProcessor will allow you to do that seamlessly; i.e., you do not need to change BioPerl itself, since load_seqdatabase.pl allows you to specify the SeqProcessors you want to employ. -hilmar On Feb 16, 2010, at 11:59 AM, Krzysztof Sarapata wrote: > Hi > > > > I've loaded GenBank file into bioSQL structure with > "load_seqdatabase.pl" script. > > Is it correct that each entity (qualifier) from FEATURES even > "db_xref" e.g. > > > > FEATURES Location/Qualifiers > > source 1..257719 > > /organism="Homo sapiens" > > /mol_type="genomic DNA" > > /db_xref="taxon:9606" > > /chromosome="1" > > ..... > > /db_xref="GeneID:100287102" > > > > is put into "Seqfeature Qualifier Value" table, if we have exactly > table "Dbxref"? > > Why value of this qualifier (db_xref) isn't put into "Dbxref" table? > > > > With regards > > Krzysztof Sarapata > > _______________________________________________ > 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 : ===========================================================