[Genome] Trouble building overlapSelect: previous message truncated

[Hiram Clawson]

Good Morning Cory:

Your system does not have the MySQL development system
installed.  With your rpm -qa command, you should see
something about a package: MySQL-devel-...

You need to get this installed properly.  You can't pull
in the .h files like that and expect it to work.

--Hiram

On 2007 Jan 15, , at 6:37 PM, Cory Y. McLean wrote:

> Dear Helpdesk,
>
>
> I am a student working with Gill Bejerano and am having trouble getting
> overlapSelect to compile.  When I type "make", I get the following 
> output:
>
> gcc -O  -o overlapSelect rowReader.o chromAnn.o selectTable.o 
> coordCols.o
> overlapSelect.o ../../lib/i686/jkhgap.a ../../lib/i686/jkweb.a
> -L/usr/lib/mysql/libmysqlclient.so.15 -lz -lm
> ./../lib/i686/jkhgap.a(jksql.o): In function `sqlEscapeString2':
> jksql.c:(.text+0x51b): undefined reference to `mysql_escape_string'
> ./../lib/i686/jkhgap.a(jksql.o): In function `sqlFieldCount':
> jksql.c:(.text+0x69a): undefined reference to `mysql_num_fields'
> ..
>
> etc.
>
> When I tried to follow the build and installation instructions I had 
> run
> into a problem running the "make compile" in the kent/src/hg 
> directory.  My
> MySQL include and library settings were incorrect:
>
> When I type mysql_config --libs, the output is:
> -L/usr/lib/mysql -lmysqlclient -lz -lcrypt -lnsl -lm -L/usr/lib -lssl
> -lcrypto
>
> Within the /usr/lib/mysql directory, the only entries are the following
> (libmysqlclient.a is missing):
> libmysqlclient_r.so.15      libmysqlclient.so.15      mysqlbug
> libmysqlclient_r.so.15.0.0  libmysqlclient.so.15.0.0  mysql_config
>
> where the *.so.15 entries are links to the respective .so.15.0.0 files.
>
> mysql_config --inc returns:
> -I/usr/include/mysql
>
> which is a directory that does not even exist on my machine!  I know 
> that
> MySQL is installed, from the output of running "rpm -qa | egrep -i 
> mysql":
> libdbi-dbd-mysql-0.8.1a-1.2.2
> mysql-server-5.0.22-2.1
> mysql-5.0.22-2.1
> perl-DBD-MySQL-3.0007-1.fc6
> MySQL-python-1.2.1-1
> mysql-connector-odbc-3.51.12-2.2
>
> I had previously hacked my way into building the components I needed
> (bedSort, chainSort) by pointing my MYSQLLIBS variable at
> /usr/lib/mysql/libmysqlclient_r.so.15 -lz, and pointing MYSQLINC to
> $HOME/mysql, a directory I created and populated with the following 
> files:
> errmsg.h     my_dbug.h    my_no_pthread.h  mysql_time.h     
> sql_common.h
> keycache.h   my_dir.h     my_pthread.h     mysql_version.h  
> sslopt-case.h
> m_ctype.h    my_getopt.h  my_semaphore.h   my_sys.h
> sslopt-longopts.h
> m_string.h   my_global.h  mysql_com.h      my_xml.h         
> sslopt-vars.h
> my_alloc.h   my_list.h    mysql_embed.h    raid.h           typelib.h
> my_config.h  my_net.h     mysql.h          readline.h
>
>
> One last thing:  My MACHTYPE is by default i686-redhat-linux-gnu, 
> though I
> changed it to "i686" to allow compilation to start, and the source 
> tree is
> located in $HOME/bin/i686/.
>
> Any ideas on how to get overlapSelect working would be greatly 
> appreciated!
>
> thanks,
> Cory McLean
> _______________________________________________
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> http://www.soe.ucsc.edu/mailman/listinfo/genome
>