[BioSQL-l] Some problem with installation DBD::mysql
Piotr Borowiec
piotrborowiec at g.pl
Tue Feb 16 11:14:29 UTC 2010
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=<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
>
>
--
Piotr Borowiec
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