Compilation error on linux/ubuntu: gsl/gsl_vector.h: No such file or directory

[jvollme]

Hi,
I'm trying to install CONCOCT-0.4.0 on a Linux (Ubuntu 14.04) system using Anaconda.
gsl1.16-4 is installed (and so are all the dependancies listed in the CONCOCT-installation-instructions)
However, when I try to run the installer-script within the conda-environment, i get the following error:

"gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ic-concoct -I/home/john/anaconda/envs/concoct_env/include/python2.7 -c c-concoct/vbgmmmodule.c -o build/temp.linux-x86_64-2.7/c-concoct/vbgmmmodule.o
c-concoct/vbgmmmodule.c:10:28: fatal error: gsl/gsl_vector.h: No such file or directory
#include <gsl/gsl_vector.h>
^
compilation terminated.
error: command 'gcc' failed with exit status 1"

I tried reinstalling gsl, by running:
"conda install -c https://conda.binstar.org/trent gsl"
but that didn't help.
Could you give me any suggestions on how to carry on from here?

[alneberg]

Hi @jvollme,

I think this is indeed a problem with gs not being properly installed or configured. Did you try installing it using apt-get as well?

Thanks for reporting,
Johannes

[jvollme]

OK, I reinstalled gsl with apt-get, including the binary, library and development packages, and now it works! It seems that I apparently only had the binary and library packages installed previously, and that was the problem.
Also, since I am not yet familiar with Anaconca, I thought that perhaps you have to install everything from within the conda-environment using "conda install", but happily this is not the case.
Thanks,
John

[alneberg]

Great you got it working and thanks for sharing your solution!

Dont hesitate to let us know if you're experiencing any other problems down
the road.

Cheers,
Johannes
Den 7 nov 2014 09:04 skrev "jvollme" notifications@github.com:

OK, I reinstalled gsl with apt-get, including the binary, library and
development packages, and now it works! It seems that I apparently only had
the binary and library packages installed previously, and that was the
problem.
Also, since I am not yet familiar with Anaconca, I thought that perhaps
you have to install everything from within the conda-environment using
"conda install", but happily this is not the case.
Thanks,
John

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#117 (comment).

[aimirza]

conda install -c nlesc gcc worked for me.
I had the same problem. It seems that gcc is not installed. I cannot install using apt-get because I do not have sudo privileges. Fortunately, you can install gcc via conda.

[jonoave]

Hello,

I´m having the same issue as well. I tried as suggested by @aimirza
conda install -c nlesc gcc

but the error remains.

Edit to update:
The original suggestion by the poster worked for me:
conda install -c https://conda.binstar.org/trent gsl

Edit to add, thanks @alneberg for your reply. I tried the method used by the OP and it worked, so I didn´t try your suggestion.

[alneberg]

Hi @jonoave, I think this error is due to the gnu scientific library (gsl) is not installed.

Could you try to install gsl through conda, i.e. using https://anaconda.org/conda-forge/gsl

Otherwise, can you post your error log. Also, if you have sudo privileges, you can try to use the other solution above.