Good Afternoon Yuan Zhidong:
It is unclear how you were able to build the hgTables cgi binary
and now it can not find the library it was linked with.
Did you have to use the -lssl linker argument because your MySQL
libraries required that ? Do you know if you have a libssl.so.6
file on your system in /lib/libssl.so.6 ?
To find your binaries, set your shell environment PATH variable
to include /root/bin/x86_64/getRnaPred
Please read the installation documents in the source tree README files:
src/product/README.*
I would *highly* recommend that you work on your system as
a normal user rather than as user root. You can easily disable
your entire computer while working as root.
See also: http://en.wikipedia.org/wiki/Shell_variable
and: http://en.wikipedia.org/wiki/Root_user
--Hiram
zhidong yuan wrote:
> Dear Sir,
>
> When I compile kent source,I met some problems and I can't open local Genome
> browser and can't run utilities,such as following:
>
> [Tue Jul 14 07:40:49 2009] [error] [client 127.0.0.1]
> /var/www/cgi-bin/hgTables: error while loading shared libraries:
> libssl.so.6: cannot open shared object file: No such file or directory,
> referer: http://localhost/
> [Tue Jul 14 07:40:49 2009] [error] [client 127.0.0.1] Premature end of
> script headers: hgTables, referer: http://localhost/
>
> [Tue Jul 14 07:56:47 2009] [error] [client 127.0.0.1]
> /var/www/cgi-bin/hgGateway: error while loading shared libraries:
> libssl.so.6: cannot open shared object file: No such file or directory,
> referer: http://localhost/index.html
> [Tue Jul 14 07:56:47 2009] [error] [client 127.0.0.1] Premature end of
> script headers: hgGateway, referer: http://localhost/index.html
>
>
> [r...@localhost getRnaPred]#
> make
> gcc -O -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64
> -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc
> -I../../../inc -I../../../../inc -I../../../../../inc -o getRnaPred.o -c
> getRnaPred.c
> gcc -O -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o
> /root/bin/x86_64/getRnaPred getRnaPred.o ../../lib/x86_64/jkhgap.a
> ../../lib/x86_64/jkweb.a -lm /usr/lib64/mysql/libmysqlclient.a -lz -lcrypto
> -lssl -lm -lnsl
> strip /root/bin/x86_64/getRnaPred
> [r...@localhost getRnaPred]# getRnaPred
> bash: getRnaPred: command not found
>
>
> [r...@localhost bedIntersect]# make
> gcc -O -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_x86_64
> -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -I../inc -I../../inc
> -I../../../inc -I../../../../inc -I../../../../../inc -o bedIntersect.o -c
> bedIntersect.c
> gcc -O -Wall -Wformat -Wimplicit -Wreturn-type -Wuninitialized -o
> /root/bin/x86_64/bedIntersect bedIntersect.o ../../lib/x86_64/jkhgap.a
> ../../lib/x86_64/jkweb.a -lm
>
> [r...@localhost yzd]# bedIntersect
> bash: bedIntersect: command not found
>
> Compile kent source as following :
>
> OS Information
> OS: Linux 2.6.27.25-170.2.72.fc10.x86_64 x86_64
> System: Fedora release 10 (Cambridge)
> KDE: 4.2.4 (KDE 4.2.4)
>
> others
> Apache/2.2.11 (Unix) DAV/2 mod_ssl/2.2.11 OpenSSL/0.9.8g Apache/2.2.0
> (Fedora)
> MySQL version: 5.0.77
>
>
> 1.CVS Access to Browser Code
> export CVSROOT=:pserver:[email protected]:/cbse
>
> cvs login
> Logging in to :pserver:[email protected]:2401/cbse
> CVS password: genome
> cvs co -P -rbeta kent
>
>
> 2.
>
> [r...@localhost]# yum list mysql*
>
> [r...@localhost]# yum install mysql*
>
> MACHTYPE=x86_64
> export MACHTYPE
> $ mkdir -p ~/bin/${MACHTYPE}
>
> 3.Configure Apache serverand environment settings
>
> Add the following somewhere in /etc/httpd/conf/httpd.conf
>
> XBitHack on
> <Directory /var/www/html>
> Options +Includes
> </Directory>
>
> export MYSQLINC='/usr/include/mysql'
> export MYSQLLIBS='/usr/lib64/mysql/libmysqlclient.a -lz -lcrypto -lssl
> -lm -lnsl'
> export MYSQLDATA="/var/lib/mysql"
> export GLOBAL_CONFIG_FILE=/var/www/cgi-bin/hg.conf
> export WEBROOT="/var/www/html"
> export CGI_BIN="/var/www/cgi-bin"
>
> 4.
> $ cd kent/src
> $ make libs
>
>
> 5.To continue building the CGI binaries
> $ cd kent/src/hg
> $ make compile
> # make install DESTDIR=/var/www CGI_BIN=/cgi-bin DOCUMENTROOT=/html
>
> How to fix these problems? Please help me!Thank you in advance!
>
> Yuan Zhidong
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