Good Morning Shraddha:
Now that you have the source tree locally, you can follow the
build instructions in the file:
src/product/README.building.source
Note the export command following the setting of the environment
variables. Also, how to use the mysql_config command to find out
exactly where in your system the libraries may be installed.
Typical build problems are also discussed in this README file.
You may want to add your name to the genome-mirror mail list
where queries about maintaining a mirror site are often
discussed:
https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror
--Hiram
> 3. Create the following shell environment variables:
> MYSQLINC=/usr/include/mysql
> MYSQLLIBS="/usr/lib/mysql/libmysqlclient.a -lz"
> export MYSQLINC MYSQLLIBS
> Your setting may vary depending upon where your
> mysql is installed. The above example is typical.
> If your system does not have this set of include files
> or this static client.a file, you may need to install
> the mysql-devel package to obtain the mysql development
> environment. (http://dev.mysql.com/downloads/)
> With that package installed, this command:
> mysql_config --libs
> will display the appropriate libraries to link with
> for your system configuration. And:
> mysql_config --include
> will display the appropriate MYSQLINC directory.
> The -lz requires a link to the libraries installed in the
> zlib-devel rpm.
Shraddha Pai wrote:
> Hi Galt,
> That fixed the hgSuggest.c error - thanks!
> I now have another problem.
>
> When I type the "make install" command, I am told that MYSQLLIBS and MYSQLINC
> is not defined, whereas you can see from the "echo" command that it is.
>
> p...@paitemp:/usr/local/kent/src/hg# sudo make install DESTDIR=/mydisk2/UCSC
> CGI_BIN=/mydisk2/cgi-bin/ucsc
> ERROR: missing MYSQLLIBS or MYSQLINC definitions in environment
> these are typically,
> for bash shell users:
> $ export MYSQLLIBS="/usr/lib/mysql/libmysqlclient.a -lz"
> $ export MYSQLINC=/usr/include/mysql
> for csh/tcsh shell users:
> % setenv MYSQLLIBS "/usr/lib/mysql/libmysqlclient.a -lz"
> % setenv MYSQLINC /usr/include/mysql
> See also: http://genome.ucsc.edu/admin/jk-install.html
> make: *** [hgLib] Error 255
> p...@paitemp:/usr/local/kent/src/hg# echo $MYSQLLIBS
> /usr/lib -lmysqlclient -lz
> p...@paitemp:/usr/local/kent/src/hg# echo $MYSQLINC
> /usr/include/mysql
> r...@paitemp:/usr/local/kent/src/hg#
> <<<
>
> I get the same error if
> MYSQLLIBS = "/usr/lib/libmysqlclient.a -lz" or
> MYSQLLIBS = "-lmysqlclient -lz" ---> this param was suggested in the
> Debian/Ubuntu build script here
> (http://genomewiki.ucsc.edu/index.php/Source_tree_compilation_on_Debian/Ubuntu).
> I'm not sure if the shared library option is necessary in my case because I
> plan to install it on a machine internal to a firewall.
>
> Thanks again,
> Shraddha
>
>
> -----Original Message-----
> From: Galt Barber [mailto:[email protected]]
> Sent: Wed 3/3/2010 6:56 PM
> To: Shraddha Pai
> Cc: [email protected]
> Subject: Re: [Genome] Source code compile failing
>
>
> Please patch src/hg/hgSuggest/hgSuggest.c as follows:
>
> retrieving revision 1.2
> diff -r1.2 hgSuggest.c
> 74c74
> < safef(previous, sizeof(previous), row[0]);
> ---
> > safef(previous, sizeof(previous), "%s", row[0]);
>
> We have patched our main branch but it will take a while
> to hit the public release (a few days to a couple of weeks).
>
> -Galt
>
> Shraddha Pai wrote:
>> Hi all,
>> I'd like to install a local copy of the genome browser.
>> I'm following instructions from here:
>> http://genome.ucsc.edu/admin/jk-install.html
>>
>> When I try to type "make compile" or "make $DIRS" (from the Debian
>> instructions here:
>> http://genomewiki.ucsc.edu/index.php/Source_tree_compilation_on_Debian/Ubunt
>> u), I get the following error:
>>
>> ( cd hgSuggest && echo hgSuggest && make compile)
>> hgSuggest
>> make[1]: Entering directory `/usr/local/kent/src/hg/hgSuggest'
>> gcc -O -g -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized
>> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64
>> -Wall -Werror -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc
>> -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -o
>> hgSuggest.o -c hgSuggest.c
>> cc1: warnings being treated as errors
>> hgSuggest.c: In function รข:
>> hgSuggest.c:74: error: format not a string literal and no format arguments
>> make[1]: *** [hgSuggest.o] Error 1
>> make[1]: Leaving directory `/usr/local/kent/src/hg/hgSuggest'
>> make: *** [hgSuggest.compile] Error 2
>> r...@paitemp:/usr/local/kent/src/hg#
>> <<<
>>
>> What am I doing wrong?
>> - I've created ~/bin/x86_64 (my $MACHTYPE)
>> - Here are my environment variables:
>>> echo $MYSQLLIBS
>> -lmysqlclient -lz
>>> echo $MYSQLINC
>> /usr/include/mysql
>>> echo $MACHTYPE
>> x86_64
>>> echo $DIRS
>> SCRIPTS=/usr/local/bin CGI_BIN=/usr/lib/cgi-bin DOCUMENTROOT=/var/www/genome
>> BINDIR=/usr/local/bin ENCODE_PIPELINE_BIN=/usr/local/bin
>>
>> Other info:
>> - My machine runs Ubuntu 9.10.
>> - I've installed mysql-client mysql-server libmysqlclient-dev and apache2
>>
>> Is there a binary for Ubuntu that I can just download and use?
>>
>> Thanks so much,
>> Shraddha
>>
>> ------------------------------------------------------
>> Shraddha Pai
>> Postdoctoral fellow, Petronis lab
>> The Krembil Family Epigenetics Research Laboratory
>> Centre for Addiction and Mental Health
>> 250 College Street, Toronto, ON.
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