[Bioperl-l] libgd

[James Thompson]

Ryan,

If you don't need gcc-utils, you can try uninstalling that package and then
instsalling your gd-devel packages. That would be a quick and easy fix, but
hoping for that may be a bit unlikely. I can't imagine why utilities for a 
compiler would need libgd, but that's just me.

Another option is to use the Bioperl RPM from http://biolinux.org/bioperl.html,
IIRC it contains a 2.0.x version of the GD library in it. You may want to try
this on a testing system before risking a production system, but for what it's
worth I've successfully used the RPM on RedHat 9.0 and Fedora Core 2. 

Best of luck solving your problem.

Cheers,

James Thompson

On Fri, 7 Jan 2005, Ryan Golhar wrote:

> Hi all,
> 
> Not sure where this should be posted, so forgive me if I'm posting it in
> the wrong place.
> 
> I'm trying to use Bioperl with RedHat Enterprise Linux v3.  RedHat
> provides gd v1.8, however bioperl requires > 2.something.  
> 
> So, I downloaded gd 2.0.33 and rebuilt it using a spec file I found from
> verion 2.0.16 (I think).  
> 
> When I tried upgrading the package using:
> [root at hydrogen i386]# rpm -Uvh gd-2.0.33-1.i386.rpm
> gd-devel-2.0.33-1.i386.rpm
> 
> I get the error:
> error: Failed dependencies:
>         libgd.so.1.8 is needed by (installed) glibc-utils-2.3.2-95.30
> 
> If I do a 'ls -lp /usr/lib/libgd*', I get:
> 
> -rw-r--r--    1 root     root       212978 Jun 17  2003 /usr/lib/libgd.a
> lrwxrwxrwx    1 root     root           14 Jan  7 13:23
> /usr/lib/libgd.so -> libgd.so.1.8.4
> lrwxrwxrwx    1 root     root           14 Jan  7 13:23
> /usr/lib/libgd.so.1 -> libgd.so.1.8.4
> lrwxrwxrwx    1 root     root           14 Jan  7 13:23
> /usr/lib/libgd.so.1.8 -> libgd.so.1.8.4
> -rwxr-xr-x    1 root     root       183332 Jun 17  2003
> /usr/lib/libgd.so.1.8.4
> 
> 
> If I do a 'rpm -qpl gd-2.0.33-1.i386.rpm', I get:
> 
> /usr/lib/libgd.so.1
> /usr/lib/libgd.so.1.8
> /usr/lib/libgd.so.2
> /usr/lib/libgd.so.2.0.0
> /usr/share/doc/gd-2.0.33
> /usr/share/doc/gd-2.0.33/README-JPEG.TXT
> /usr/share/doc/gd-2.0.33/README.TXT
> /usr/share/doc/gd-2.0.33/entities.html
> /usr/share/doc/gd-2.0.33/index.html
> 
> Here is the spec file I'm using (minus some unnecessary stuff).  Any
> ideas?
> 
> Summary: A graphics library for quick creation of PNG, GIF or JPEG
> images.
> Name: gd
> Version: 2.0.33
> Release: 1
> URL: http://www.boutell.com/gd/
> Source0: http://www.boutell.com/gd/http/gd-%{version}.tar.gz
> License: BSD-style
> Group: System Environment/Libraries
> BuildRoot: %{_tmppath}/%{name}-root
> Prereq: /sbin/ldconfig
> BuildPrereq: freetype-devel, libjpeg-devel, libpng-devel, zlib-devel
> %define shlibver %(echo %{version} | cut -f-2 -d.)
> 
> %prep
> %setup -q
> 
> %build
> ./configure --prefix=$RPM_BUILD_ROOT/usr
> make
> 
> %install
> [ "$RPM_BUILD_ROOT" != "/" ] && rm -fr $RPM_BUILD_ROOT
> make install
> (cd $RPM_BUILD_ROOT/usr/lib && ln -s libgd.so.2.0.0 libgd.so.1)
> (cd $RPM_BUILD_ROOT/usr/lib && ln -s libgd.so.2.0.0 libgd.so.1.8)
> rm -rf $RPM_BUILD_ROOT%{_libdir}/libgd.la
> 
> %clean
> [ "$RPM_BUILD_ROOT" != "/" ] && rm -fr $RPM_BUILD_ROOT
> 
> %post -p /sbin/ldconfig
> 
> %postun -p /sbin/ldconfig
> 
> %files
> %defattr(-,root,root)
> %doc README.TXT README-JPEG.TXT index.html entities.html
> %{_libdir}/*.so.*
> 
> %files progs
> %defattr(-,root,root)
> %{_bindir}/*
> 
> %files devel
> %defattr(-,root,root)
> %{_includedir}/*
> %{_libdir}/*.so
> %{_libdir}/*.a
> 
> 
> -----
> Ryan Golhar
> Computational Biologist
> The Informatics Institute at
> The University of Medicine & Dentistry of NJ
> 
> Phone: 973-972-5034
> Fax: 973-972-7412
> Email: golharam at umdnj.edu
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l