Do you have the mysql client libs installed? These are required. It has nothing to do with firewall.
In other words, the paths your are giving in $MYSQLLIBS and $MYSQLINC need to point to real things at exist on your system. The only minor thing is that with MYSQLLIBS="/usr/lib/mysql/libmysqlclient.a -lz" we have tacked on the -lz for the zlib dependency. -Galt ----- Original Message ----- From: "Shraddha Pai" <[email protected]> To: "Galt Barber" <[email protected]> Cc: [email protected] Sent: Wednesday, March 3, 2010 6:25:53 PM GMT -08:00 US/Canada Pacific Subject: RE: [Genome] Source code compile failing 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. > > > > > ______________________________________________________________________ > This email has been scanned by the CAMH Email Security System. > ______________________________________________________________________ > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome ______________________________________________________________________ This email has been scanned by the CAMH Email Security System. ______________________________________________________________________ ______________________________________________________________________ This email has been scanned by the CAMH Email Security System. ______________________________________________________________________ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
