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Re: Problem with installing general package on TACC
|
From: |
Sergei Steshenko |
|
Subject: |
Re: Problem with installing general package on TACC |
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Date: |
Mon, 3 Dec 2012 20:22:37 -0800 (PST) |
----- Original Message -----
> From: solarisx <address@hidden>
> To: address@hidden
> Cc:
> Sent: Tuesday, December 4, 2012 3:02 AM
> Subject: Problem with installing general package on TACC
>
> Hi,
>
> Ranger has the Octave installed, but I don't see any packages installed. I
> tried installing the general package in Octave but get the following error.
> Has anyone tried installing this package before?
>
> PS. I have loaded the hdf5 module.
>
> Thanks,
>
>
> octave:1> pkg install -local general-1.3.2.tar.gz
> In file included from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov.h:43,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/oct-obj.h:34,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov-fcn.h:32,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov-builtin.h:28,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/defun-int.h:28,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/defun-dld.h:30,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/oct.h:36,
> from __exit__.cc:16:
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/oct-hdf5.h:27:18:
> hdf5.h: No such file or directory
> In file included from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov.h:58,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/oct-obj.h:34,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov-fcn.h:32,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov-builtin.h:28,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/defun-int.h:28,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/defun-dld.h:30,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/oct.h:36,
> from __exit__.cc:16:
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov-base.h:628:
> error: `hid_t' has not been declared
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov-base.h:628:
> error: ISO C++ forbids declaration of `loc_id' with no type
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov-base.h:631:
> error: `hid_t' has not been declared
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov-base.h:631:
> error: ISO C++ forbids declaration of `loc_id' with no type
> In file included from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/oct-obj.h:34,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov-fcn.h:32,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov-builtin.h:28,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/defun-int.h:28,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/defun-dld.h:30,
> from
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/oct.h:36,
> from __exit__.cc:16:
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov.h:1052:
> error: `hid_t' has not been declared
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov.h:1053:
> error: ISO C++ forbids declaration of `loc_id' with no type
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov.h:1055:
> error: `hid_t' has not been declared
> /opt/apps/octave/3.6.1/include/octave-3.6.1/octave/../octave/ov.h:1056:
> error: ISO C++ forbids declaration of `loc_id' with no type
> make: *** [__exit__.oct] Error 1
> 'make' returned the following error: make: Entering directory
> `/tmp/oct-GB3iXd/general/src'
> /opt/apps/octave/3.6.1/bin/mkoctfile-3.6.1 __exit__.cc
> make: Leaving directory `/tmp/oct-GB3iXd/general/src'
> error: called from `pkg>configure_make' in file
> /opt/apps/octave/3.6.1/share/octave/3.6.1/m/pkg/pkg.m near line 1385, column
> 9
> error: called from:
> error: /opt/apps/octave/3.6.1/share/octave/3.6.1/m/pkg/pkg.m at line 827,
> column 5
> error: /opt/apps/octave/3.6.1/share/octave/3.6.1/m/pkg/pkg.m at line 383,
> column 9
>
>
>
>
> --
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> http://octave.1599824.n4.nabble.com/Problem-with-installing-general-package-on-TACC-tp4647518.html
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The core problem is indicated by
hdf5.h: No such file or directory
message.
The point is that the compiler needs to know search paths for .h files involved
in (the) package compilation. So, you need to set CXXFLAGS, CPPFLAGS either
manually or through 'pkg-config'.
The same applies to library search path for linker, i.e. after resolving the
missing .h files problem you can encounter linking problems.
The issue can be complicated also because package building often requires
'mkoctfile'. The latter is a shell script which sets certain paths.
You'll probably need to look into the script. The point is that if you set
certain environment variables from outside, the script respects your choice,
but _discards_ its own settings (rather than combining what you want and what
it had "in mind").
So, if you set certain environment variables from outside, you resolve your
immediate problems, but you may break what's needed for compiling and linking
with Octave proper stuff.
I.e. by setting certain environment variables from outside you'll need to
respect your needs and to reproduce what's originally set in the script.
...
I am able to build and install 76 packages at the moment, so I had my fair (or
probably fare) share of stepping on various rakes. The above analysis and
recommendations are from personal experience.
Regards,
Sergei.
>