bugGNU Octave - Bugs: bug #50629, can't install netcdf package...

 
 

bug #50629: can't install netcdf package anymore

Submitter:  None
Submitted:  Fri 24 Mar 2017 09:12:18 PM UTC
   
 
Category:  Octave Package Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Installation Failure
Status:  Works For Me Assigned to:  None
Originator Name:  grg Originator Email:  -email is unavailable-
Open/Closed:  * Closed Release:  * 4.2.1
Operating System:  * GNU/Linux Fixed Release:  None
Planned Release:  None
* Mandatory Fields

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Tue 28 Mar 2017 06:57:21 PM UTC, comment #4: 

Giorgio - installing the netcdf package uses the nc-config program to list the necessary include and library paths for building. You may have a broken nc-config utility installed or remnants of another system.

I think it's safe to close this bug as working, confirmed by Dmitri. If you need help figuring out how to fix your system or install packages, please use one of the support options listed here: http://www.octave.org/support

Mike Miller <mtmiller>
Group Member
Tue 28 Mar 2017 05:48:20 AM UTC, comment #3: 

I can confirm that netcdf compiles and installs
against octave-4.2.1 on Fedora 25.

octave:1> pkg install -forge netcdf
In file included from /usr/include/octave-4.2.1/octave/../octave/config.h:6:0,
                 from conftest.cc:1:
/usr/include/octave-4.2.1/octave/../octave/config-64.h:28:2: warning: #warning "config.h has been deprecated; there is no need to include it directly" [-Wcpp]
 #warning "config.h has been deprecated; there is no need to include it directly"
  ^~~~~~~
For information about changes from previous versions of the netcdf package, run 'news netcdf'.
octave:2>


Dmitri.
--

Dmitri A. Sergatskov <dasergatskov>
Tue 28 Mar 2017 05:37:47 AM UTC, comment #2: 

Hi Mike,

thanks for your response.

the directory

/home/swdev/ocssw/build/lib3

does not exist on our system and it is not something I have added myself...

Do you have a clue where this directory is coming from in the
configuration of the pkg netcdf?

Also, I do not know how and where to specify that I want to use the
Fedora library: could you help with that?

Thanks a lot!

grg


Giorgio <grg>
Sat 25 Mar 2017 08:04:54 PM UTC, comment #1: 

It looks like you built the netcdf library yourself, under /home/swdev/ocssw/build/lib3, and you built it as a static library instead of a shared library. Can you fix this or use the netcdf distributed with Fedora, and see if the problem is resolved?

Mike Miller <mtmiller>
Group Member
Fri 24 Mar 2017 09:12:18 PM UTC, original submission:  

Hi there,

since I installed octave-4.2.1 on my fedora 24 machine I cannot install anymore the octave-forge package netcdf.

This is how to reproduce the problem:


octave:2> pkg install -forge netcdf
In file included from conftest.cc:1:0:
/usr/local/include/octave-4.2.1/octave/../octave/config.h:28:2: warning: #warning "config.h has been deprecated; there is no need to include it directly" [-Wcpp]
 #warning "config.h has been deprecated; there is no need to include it directly"
  ^~~~~~~
/usr/bin/ld: /usr/lib/gcc/x86_64-redhat-linux/6.3.1/crtbeginT.o: relocation R_X86_64_32 against `__TMC_END__' can not be used when making a shared object; recompile with -fPIC
/usr/lib/gcc/x86_64-redhat-linux/6.3.1/crtbeginT.o: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
make: *** [__netcdf__.oct] Error 1
make: Entering directory '/tmp/oct-WBle36/netcdf/src'
/usr/local/bin/mkoctfile-4.2.1 -DHAVE_OCTAVE_ -v -I/home/swdev/ocssw/build/lib3/include __netcdf__.cc -L/home/swdev/ocssw/build/lib3/lib -L/home/swdev/ocssw/build/lib3/lib -static -lnetcdf -lhdf5_hl -lhdf5 -lsz -lm -lz
g++ -c  -fPIC -I/usr/local/include/octave-4.2.1/octave/.. -I/usr/local/include/octave-4.2.1/octave -I/usr/local/include  -pthread -fopenmp -g -O2  -static  -I/home/swdev/ocssw/build/lib3/include  -DHAVE_OCTAVE_ __netcdf__.cc -o __netcdf__.o
g++ -I/usr/local/include/octave-4.2.1/octave/.. -I/usr/local/include/octave-4.2.1/octave -I/usr/local/include  -pthread -fopenmp -g -O2 -shared -Wl,-Bsymbolic  -static -o __netcdf__.oct  __netcdf__.o   -L/home/swdev/ocssw/build/lib3/lib -L/home/swdev/ocssw/build/lib3/lib -lnetcdf -lhdf5_hl -lhdf5 -lsz -lm -lz -L/usr/local/lib/octave/4.2.1 -L/usr/local/lib -loctinterp -loctave
Makefile:24: recipe for target '__netcdf__.oct' failed
make: Leaving directory '/tmp/oct-WBle36/netcdf/src'

pkg: error running `make' for the netcdf package.
error: called from
    configure_make at line 95 column 9
    install at line 192 column 7
    pkg at line 394 column 9
octave:2>


Please help!
thanks a lot
grg

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    Follow 4 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2019-02-26 mtmiller Carbon-CopyRemoved 80942 -
    2017-03-28 mtmiller StatusNeed Info Works For Me
        Open/ClosedOpen Closed
    2017-03-25 mtmiller StatusNone Need Info

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