[BioSQL-l] Some problem with installation DBD::mysql
Adam Witney
awitney at sgul.ac.uk
Tue Feb 16 11:24:08 UTC 2010
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=<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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