[BioSQL-l] Some problem with installation DBD::mysql

Adam Witney awitney at sgul.ac.uk
Tue Feb 16 10:40:57 UTC 2010 

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=<path>

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<dir>
> 
> 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<dir>
> 
> 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

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