[BioSQL-l] Some problem with installation DBD::mysql
Piotr Borowiec
piotrborowiec at g.pl
Tue Feb 16 14:19:37 UTC 2010
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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