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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>
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> Genome maillist - [email protected]
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