bugGNU Octave - Bugs: bug #45406, netcdf package install fails

 
 

bug #45406: netcdf package install fails

Submitter:  None
Submitted:  Thu 25 Jun 2015 12:36:41 PM UTC
   
 
Category:  Octave Package Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Build Failure
Status:  Invalid / Not an Octave Bug Assigned to:  None
Originator Name:  Greg King Originator Email:  -email is unavailable-
Open/Closed:  * Closed Release:  * 3.8.2
Operating System:  * Mac OS Fixed Release:  None
Planned Release:  None
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Tue 20 Sep 2016 01:28:26 AM UTC, comment #7: 

Hi,

I encountered a problem when I tried to install the netcdf package to octave on my macbook (os x 10.9.5). I got similar error messages like Greg’s. I am hoping to get advice from you here.
 
I defined PATH and LD_LIBRARY_PATH by adding export PATH="/opt/local/bin:$PATH"
export LD_LIBRARY_PATH=“/opt/local/lib:$LD_LIBRARY_PATH" to the end of the ./bash_profile. They should correspond to the libraries, which are /opt/local/bin/nc-config, and -L/opt/local/lib -lnetcdf -lhdf5_hl -lhdf5 -ldl -lm -lz -lcurl, respectively. Despite of this setting, the installation still fails.

I am not sure what I can do to solve this problem. I would be very appreciated if anyone can help me out. Thank you very much.

Yi-Hui

My error message is here:
mkdir (/var/tmp/oct-oKDJX5)
untar (/Users/yihuiw/netcdf-1.0.11.tar.gz, /var/tmp/oct-oKDJX5)
checking for gcc... /usr/local/octave/3.8.0/bin/gcc-mp-4.7
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in `/var/tmp/oct-oKDJX5/netcdf/src':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details

pkg: error running the configure script for netcdf.
error: called from 'configure_make' in file /usr/local/octave/3.8.0/share/octave/3.8.0/m/pkg/private/configure_make.m near line 72, column 9
error: called from:
error:   /usr/local/octave/3.8.0/share/octave/3.8.0/m/pkg/private/install.m at line 199, column 5
error:   /usr/local/octave/3.8.0/share/octave/3.8.0/m/pkg/pkg.m at line 394, column 9

Yi-Hui Wang <yihuiwang>
Thu 30 Jul 2015 09:20:55 PM UTC, comment #6: 

to the bug tracking maintainers:
Can this be closed now?

Alexander Barth <abarth>
Thu 16 Jul 2015 02:29:25 PM UTC, comment #5: 

I created .bash_profile and included the information you have in your wiki.  As I am not so experience with linux, I copied the info exactly, which of course did not work.  So you probably should put in a warning. 

Anyway, I discovered that "/path/to/netcdf" and "/path/to/hdf5" should both be replaced with "/usr/local".  Homebrew provides links to the netcdf and hdf5 libs and include files in /usr/local to the ones in the Cellar.

After doing that, I sourced bash_profile and launched the octave gui. 
From the gui I executed ...

pkg install -verbose -forge -auto netcdf

and netcdf was built and installed without error.  I checked the installation with...

pkg load netcdf

and then tested with

test_netcdf

ALL OK.  Thanks!
greg

Greg King <gking>
Wed 15 Jul 2015 08:22:04 AM UTC, comment #4: 

Hello

I did an uninstall of all versions of netcdf (there was an older version, but it seems to have had no effect on the current problem). And uninstalled hdf5.   Then I reinstalled netcdf and hdf5.

I then checked and there is only one nc-config. 
The link in /usr/local/bin points to this...
/usr/local/Cellar/netcdf/4.3.3.1/bin/nc-config

The output from nc-config --all (below) was unchanged from before I did the above re-installs. It does not point to the hdf5 in the Cellar.  The output follows


This netCDF 4.3.3.1 has been built with the following features:

  --cc        -> clang
  --cflags    ->  -I/usr/local/Cellar/netcdf/4.3.3.1/include
  --libs      -> -L/usr/local/Cellar/netcdf/4.3.3.1/lib -lnetcdf

  --has-c++   -> no
  --cxx       ->
  --has-c++4  -> yes
  --cxx4      -> clang++

  --fc        -> /usr/local/bin/gfortran
  --fflags    -> -I/usr/local/Cellar/netcdf/4.3.3.1/include
  --flibs     -> -L/usr/local/Cellar/netcdf/4.3.3.1/lib -lnetcdff -L/usr/local/Cellar/netcdf/4.3.3.1/lib -lnetcdf -lnetcdf
  --has-f90   -> no

  --has-dap   -> yes
  --has-nc2   -> yes
  --has-nc4   -> yes
  --has-hdf5  -> yes
  --has-hdf4  -> no
  --has-pnetcdf-> no

  --prefix    -> /usr/local/Cellar/netcdf/4.3.3.1
  --includedir-> /usr/local/Cellar/netcdf/4.3.3.1/include
  --version   -> netCDF 4.3.3.1

Greg King <gking>
Tue 14 Jul 2015 08:18:56 PM UTC, comment #3: 

Sorry for my late reply, but for some reasons I do not get notification from the bug tracker.

What is the output of "nc-config --all"?

The --cflags should include "/usr/local/Cellar/hdf5/1.8.14/include" for instance and --libs should include the location of the HDF5 library (libhdf5*).

Can you also check if you have multiple scripts called nc-config on your system?


More info on nc-config:
http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-install/nc_002dconfig.html

https://www.unidata.ucar.edu/software/netcdf/workshops/2012/utilities/Nc-config.html


Alexander Barth <abarth>
Fri 03 Jul 2015 09:30:20 AM UTC, comment #2: 

the command>

 brew install hdf5

confirms that hdf5 is installed.
Further search shows that brew installed hdf5 here...

 /usr/local/Cellar/hdf5/1.8.14/

and hdf5.h is in subfolder "include"

This suggests to me that there is a missing link somewhere, though I am not sure what to look for and where.

Greg King <gking>
Thu 02 Jul 2015 08:57:30 PM UTC, comment #1: 


netcdf 4 and octave depend on HDF5. Do you have HDF5 installed (libs and headers)?

Alexander Barth <abarth>
Thu 25 Jun 2015 12:36:41 PM UTC, original submission:  

I just installed octave on mac osx Yosemite, using homebrew.

Octave install was okay. The version homebrew installed was 3.8.2.

I then tried to install the netcdf package from the octave gui. That failed.  The output is below.

What to do??

greg king

pkg install -forge netcdf
warning: creating installation directory /Users/gking/octave
In file included from _netcdf_.cc:17:
In file included from /usr/local/Cellar/octave/3.8.2_1/include/octave-3.8.2/octave/../octave/oct.h:36:
In file included from /usr/local/Cellar/octave/3.8.2_1/include/octave-3.8.2/octave/defun-dld.h:30:
In file included from /usr/local/Cellar/octave/3.8.2_1/include/octave-3.8.2/octave/defun-int.h:28:
In file included from /usr/local/Cellar/octave/3.8.2_1/include/octave-3.8.2/octave/ov-builtin.h:28:
In file included from /usr/local/Cellar/octave/3.8.2_1/include/octave-3.8.2/octave/ov-fcn.h:32:
In file included from /usr/local/Cellar/octave/3.8.2_1/include/octave-3.8.2/octave/oct-obj.h:34:
In file included from /usr/local/Cellar/octave/3.8.2_1/include/octave-3.8.2/octave/ov.h:42:
/usr/local/Cellar/octave/3.8.2_1/include/octave-3.8.2/octave/oct-hdf5.h:27:10: fatal error: 'hdf5.h' file
      not found
#include <hdf5.h>
         ^
1 error generated.
make: * [__netcdf__.oct] Error 1
/usr/local/Cellar/octave/3.8.2_1/bin/mkoctfile-3.8.2 -DHAVE_OCTAVE_ -v -I/usr/local/Cellar/netcdf/4.3.3.1/include _netcdf_.cc -L/usr/local/Cellar/netcdf/4.3.3.1/lib -lnetcdf
clang++ -c  -fPIC -I/usr/local/Cellar/octave/3.8.2_1/include/octave-3.8.2/octave/.. -I/usr/local/Cellar/octave/3.8.2_1/include/octave-3.8.2/octave -I/usr/local/Cellar/octave/3.8.2_1/include  -I/Library/Java/JavaVirtualMachines/jdk1.8.0_40.jdk/Contents/Home/include -I/Library/Java/JavaVirtualMachines/jdk1.8.0_40.jdk/Contents/Home/include/darwin -D_REENTRANT -D_THREAD_SAFE -pthread   -I/usr/local/Cellar/netcdf/4.3.3.1/include  -DHAVE_OCTAVE_ _netcdf_.cc -o _netcdf_.o

pkg: error running `make' for the netcdf package.
error: called from 'configure_make' in file /usr/local/Cellar/octave/3.8.2_1/share/octave/3.8.2/m/pkg/private/configure_make.m near line 82, column 9
error: called from:
error:   /usr/local/Cellar/octave/3.8.2_1/share/octave/3.8.2/m/pkg/private/install.m at line 199, column 5
error:   /usr/local/Cellar/octave/3.8.2_1/share/octave/3.8.2/m/pkg/pkg.m at line 394, column 9

>>

Anonymous

 

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