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

Chris Fields cjfields at illinois.edu
Tue Feb 16 13:26:24 UTC 2010 

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=<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
> 
> 
> _______________________________________________
> BioSQL-l mailing list
> BioSQL-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biosql-l

More information about the BioSQL-l mailing list