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Old 10-18-2008, 01:40 AM
John R Pierce
 
Default octave

trying to install octave from epel onto centos 5.2, and getting
dependency errors. only place I could find this RPM was in epel, which
I 'thought' ran on native rhel5/centos5 without requiring any other
repos, but I guess I'm wrong?!?


google tells me libhdf5 is some sot of 'heirarchial data format'
library, whatever that means.



# yum install octave
Loading "fastestmirror" plugin
Loading "priorities" plugin
Loading mirror speeds from cached hostfile
* epel: mirror.hmc.edu
* pgdg83: yum.pgsqlrpms.org
* rpmforge: ftp-stud.fht-esslingen.de
* base: mirror.nic.uoregon.edu
* updates: mirror.hmc.edu
* centosplus: centos-distro.cavecreek.net
* addons: mirrors.cat.pdx.edu
* extras: centos-distro.cavecreek.net
Excluding Packages from CentOS-5 - Base
Finished
Excluding Packages from CentOS-5 - Updates
Finished
1541 packages excluded due to repository priority protections
Setting up Install Process
Parsing package install arguments
Resolving Dependencies
--> Running transaction check
---> Package octave.i386 6:3.0.1-2.el5 set to be updated
--> Processing Dependency: libcamd.so.2 for package: octave
--> Processing Dependency: libumfpack.so.5 for package: octave
--> Processing Dependency: libcolamd.so.2 for package: octave
--> Processing Dependency: libfftw3.so.3 for package: octave
--> Processing Dependency: libccolamd.so.2 for package: octave
--> Processing Dependency: libblas.so.3 for package: octave
--> Processing Dependency: libglpk.so.0 for package: octave
--> Processing Dependency: libcholmod.so.1 for package: octave
--> Processing Dependency: libamd.so.2 for package: octave
--> Processing Dependency: gnuplot for package: octave
--> Processing Dependency: libcxsparse.so.2 for package: octave
--> Processing Dependency: libhdf5.so.0 for package: octave
--> Processing Dependency: liblapack.so.3 for package: octave
--> Processing Dependency: libqhull.so.5 for package: octave
--> Running transaction check
---> Package glpk.i386 0:4.20-2.el5 set to be updated
---> Package octave.i386 6:3.0.1-2.el5 set to be updated
--> Processing Dependency: libhdf5.so.0 for package: octave
---> Package qhull.i386 0:2003.1-7.el5 set to be updated
---> Package lapack.i386 0:3.0-37.el5 set to be updated
---> Package gnuplot.i386 0:4.0.0-12 set to be updated
---> Package fftw3.i386 0:3.1.1-1.el5.rf set to be updated
---> Package blas.i386 0:3.0-37.el5 set to be updated
---> Package suitesparse.i386 0:3.1.0-1.el5 set to be updated
--> Finished Dependency Resolution
Error: Missing Dependency: libhdf5.so.0 is needed by package octave


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Old 10-18-2008, 04:33 AM
"John"
 
Default octave

>>Error: Missing Dependency: libhdf5.so.0 is needed by package octave

JohnStanley Writes:
yum whatprovides libhdf5.so.0
Loading "fastestmirror" plugin
Loading mirror speeds from cached hostfile
* base: ftp.linux.ncsu.edu
* updates: styx.biochem.wfubmc.edu
* addons: mirror.atlantic.net
* extras: pubmirrors.reflected.net
base 100% |=========================| 1.1 kB 00:00
updates 100% |=========================| 951 B 00:00
addons 100% |=========================| 951 B 00:00
extras 100% |=========================| 1.1 kB 00:00
No Matches found

The package is not in the CentOS Distro. You will have to look elsewhere to
find it. A good start would be google to find it and remember the
whatprovides command to find what libs go with the package you need. CentOS
and RHEL Versions 5 with Point releases 1,2, and 3 you can try this one
here.
http://rpm.pbone.net/index.php3/stat/4/idpl/4123486/com/hdf5-1.6.5-7.fc6.i38
6.rpm.html

"OR"

This one is for EPEL 5 on there site.
http://rpm.pbone.net/index.php3/stat/4/idpl/8177721/com/hdf5-1.6.7-1.el5.i38
6.rpm.html

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Old 10-18-2008, 07:58 AM
John R Pierce
 
Default octave

John wrote:

This one is for EPEL 5 on there site.
http://rpm.pbone.net/index.php3/stat/4/idpl/8177721/com/hdf5-1.6.7-1.el5.i38
6.rpm.html




I installed the hdf5 package off EPEL (via yum install hdf5) and my yum
install octave still fails with the same error.


Error: Missing Dependency: libhdf5.so.0 is needed by package octave

when I look at that hdf5 package, I see...

# rpm -ql hdf5
/usr/bin/gif2h5
/usr/bin/h52gif
/usr/bin/h52gifgentst
/usr/bin/h5cc
/usr/bin/h5copy
/usr/bin/h5debug
/usr/bin/h5diff
/usr/bin/h5dump
/usr/bin/h5import
/usr/bin/h5jam
/usr/bin/h5ls
/usr/bin/h5mkgrp
/usr/bin/h5redeploy
/usr/bin/h5repack
/usr/bin/h5repart
/usr/bin/h5stat
/usr/bin/h5unjam
/usr/lib/libhdf5.settings
/usr/lib/libhdf5.so.5
/usr/lib/libhdf5.so.5.0.0
/usr/lib/libhdf5_hl.so.0
/usr/lib/libhdf5_hl.so.0.0.0
/usr/share/doc/hdf5-1.8.0
/usr/share/doc/hdf5-1.8.0/COPYING
/usr/share/doc/hdf5-1.8.0/README.txt


libhdf5.so.5 and .5.0.0 and _hl.so.0 != what octave is looking for. I
know EPEL isn't a CentOS project, IIRC, its a Fedora/RH projecct but
this isn't looking good.



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Old 10-18-2008, 10:05 AM
"John"
 
Default octave

I installed the hdf5 package off EPEL (via yum install hdf5) and my yum
install octave still fails with the same error.

Error: Missing Dependency: libhdf5.so.0 is needed by package octave

when I look at that hdf5 package, I see...

# rpm -ql hdf5
/usr/bin/gif2h5
/usr/bin/h52gif
/usr/bin/h52gifgentst
/usr/bin/h5cc
/usr/bin/h5copy
/usr/bin/h5debug
/usr/bin/h5diff
/usr/bin/h5dump
/usr/bin/h5import
/usr/bin/h5jam
/usr/bin/h5ls
/usr/bin/h5mkgrp
/usr/bin/h5redeploy
/usr/bin/h5repack
/usr/bin/h5repart
/usr/bin/h5stat
/usr/bin/h5unjam
/usr/lib/libhdf5.settings
/usr/lib/libhdf5.so.5
/usr/lib/libhdf5.so.5.0.0
/usr/lib/libhdf5_hl.so.0
/usr/lib/libhdf5_hl.so.0.0.0
/usr/share/doc/hdf5-1.8.0
/usr/share/doc/hdf5-1.8.0/COPYING
/usr/share/doc/hdf5-1.8.0/README.txt


libhdf5.so.5 and .5.0.0 and _hl.so.0 != what octave is looking for. I
know EPEL isn't a CentOS project, IIRC, its a Fedora/RH projecct but
this isn't looking good.

JohnStanley Writes:
That's strange because the both links I give you to them have on the down
load page this;
Provides :
libhdf5.so.0
libhdf5_hl.so.0
Hdf5

Maybe try running "rpm --rebuilddb" or "ldconfig" or "yum clean-all" (bad or
old yum headers can cause that)and then try the install again. Aonother
thing to check may is your priorities for yum. Lastly it could just simply
be the way the rpm was packaged. As in the developer has it going into a
none standard directory or the other way around like Octave is looking for
the lib in the wrong place. You could also take the two hdf rpms and compare
the directory structure.

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Old 10-20-2008, 01:48 PM
Tony Schreiner
 
Default octave

On Oct 18, 2008, at 3:58 AM, John R Pierce wrote:


John wrote:

This one is for EPEL 5 on there site.
http://rpm.pbone.net/index.php3/stat/4/idpl/8177721/com/
hdf5-1.6.7-1.el5.i38

6.rpm.html




I installed the hdf5 package off EPEL (via yum install hdf5) and my
yum install octave still fails with the same error.


Error: Missing Dependency: libhdf5.so.0 is needed by package octave

when I look at that hdf5 package, I see...

# rpm -ql hdf5
/usr/bin/gif2h5
/usr/bin/h52gif
....



/usr/share/doc/hdf5-1.8.0/README.txt


libhdf5.so.5 and .5.0.0 and _hl.so.0 != what octave is looking
for. I know EPEL isn't a CentOS project, IIRC, its a Fedora/RH
projecct but this isn't looking good.





Just to reassure you. I've had no problems with octave and hdf5
( both from epel ).


From what you've written, I don't think this it the problem, but
just to be sure: are you running x86_64 and have installed i386 hdf5?


Tony Schreiner
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Old 10-20-2008, 03:59 PM
John R Pierce
 
Default octave

Tony Schreiner wrote:
Just to reassure you. I've had no problems with octave and hdf5 ( both
from epel ).


From what you've written, I don't think this it the problem, but just
to be sure: are you running x86_64 and have installed i386 hdf5?


no, its i386

OH. looking again (having put this aside since last week)

# yum list hdf5
....
hdf5.i386 1.8.0-1.el5.rf
installed


looks like I got hdf5 from rpmforge :-/

ok,
# yum remove hdf5
# yum --disablerepo=rpmforge install octave octave-forge hdf5

has sorted it out. grrrrrr. once again epel does not play well with
others ((


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