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

Chris Fields cjfields at illinois.edu
Tue Feb 16 14:24:51 UTC 2010 

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 <cjfields at 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=<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
>> 
>> 
> 
> 
> 
> -- 
> Piotr Borowiec

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