unable to install netcdf package

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unable to install netcdf package

Andrew Friedman
Hi all,

I am unable to install the netcdf package for Octave 4.2.1.

I receive the following error message:
—————————————————————————————————————————————
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"
  ^
/usr/bin/ld: cannot find -lGraphicsMagick++
/usr/bin/ld: cannot find -lGraphicsMagick
/usr/bin/ld: cannot find -lqrupdate
collect2: error: ld returned 1 exit status
configure: error: Could not run /usr/bin/mkoctfile-4.2.1
checking for gcc... gcc -std=gnu11
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... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu11 accepts -g... yes
checking for gcc -std=gnu11 option to accept ISO C89... none needed
checking for mkoctfile... /usr/bin/mkoctfile-4.2.1
checking for octave-config... /usr/bin/octave-config-4.2.1

pkg: error running the configure script for netcdf.
error: called from
    configure_make at line 78 column 9
    install at line 192 column 7
    pkg at line 394 column 9
————————————————————————————————————

Additional information: I am running scientific linux, and I do not have root access.

Thanks for any suggestions,
Andrew

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Re: unable to install netcdf package

Andreas Weber-6
Am 10.02.2018 um 01:08 schrieb Andrew Friedman:
> I am unable to install the netcdf package for Octave 4.2.1.
> ...
> octave:1> pkg install -forge netcdf
> /usr/bin/ld: cannot find -lGraphicsMagick++
> /usr/bin/ld: cannot find -lGraphicsMagick
> /usr/bin/ld: cannot find -lqrupdate
> ...
> Additional information: I am running scientific linux, and I do not have root access.

I never used "scientific linux" but from what I've read the wiki parts
for RHEL/CentOS can be used.

Have you installed octave via some package manager (yum?), then you
should also install netcdf this way. If it's not available you have to
install the octave-devel-* packages (via yum) which provides mkoctfile
and libs needed to build forge packages.


Obviously you also have to install the dependencies yourself. configure
tells you which one are needed but aren't found:

> /usr/bin/ld: cannot find -lGraphicsMagick++
> /usr/bin/ld: cannot find -lGraphicsMagick
> /usr/bin/ld: cannot find -lqrupdate

go and install these development libaries with yum, I guess they are
named libgraphicsmagick....-dev and so on.

Good luck and happy hacking
-- Andy


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Re: unable to install netcdf package

Andrew Friedman
> Have you installed octave via some package manager (yum?), then you
> should also install netcdf this way. If it's not available you have to
> install the octave-devel-* packages (via yum) which provides mkoctfile
> and libs needed to build forge packages.

> Obviously you also have to install the dependencies yourself. configure
> tells you which one are needed but aren't found:

> > /usr/bin/ld: cannot find -lGraphicsMagick++
> > /usr/bin/ld: cannot find -lGraphicsMagick
> > /usr/bin/ld: cannot find -lqrupdate

Unfortunately I'm on a shared system where I don't have permission to
install yum, or to install these libraries in the standard locations.

I was able to download and install qrupdate and GraphicsMagick in
/$HOME/lib/
However, the octave-forge installer still doesn't locate these directories
during the package installation, even after adding $HOME/lib/ to $PATH and
$LD_LIBRARY_PATH.

Are there other settings I should modify so that the libraries are
recognized? Or perhaps try a different way to install the packages than from
within octave?

Thanks for any suggestions - I'm still quite new to linux and software
installation.
-Andrew



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Re: unable to install netcdf package

Andrew Friedman
Hi all,

I have downloaded the netcdf package from octave-forge and am attempting to
build from source.

Following previous suggestions, I have installed the necessary dependency
libraries, but the package installer seems unable to locate them.

Does anyone know how I can specify where to find dependencies in
non-standard locations?

Thanks, Andrew



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