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 :
===========================================================