python - Debugging the error "gcc: error: x86_64-linux-gnu-gcc: No such file or directory"

Question

I'm trying to build: https://github.com/kanzure/nanoengineer

But it looks like it errors out on:

gcc -DHAVE_CONFIG_H -I. -I../.. -I/usr/include/python2.7   -std=c99 x86_64-linux-gnu-gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -MT libstructcompare_a-structcompare.o -MD -MP -MF .deps/libstructcompare_a-structcompare.Tpo -c -o libstructcompare_a-structcompare.o `test -f 'structcompare.c' || echo './'`structcompare.c
gcc: error: x86_64-linux-gnu-gcc: No such file or directory

x86_64-linux-gnu-gcc definitely exists in /usr/bin (It's a symlink) and the target definitely exists as well. It looks to me like the Makefile wasn't generated correctly, perhaps there is a flag that should be passed before specifying x86_64-linux-gnu-gcc? I am unsure as well what specifying x86_64-linux-gnu-gcc is supposed to accomplish.

Finally, this makefile was generated by configure, so once we narrow down the cause of the error, I'll have to figure out what files to modify in order to fix this. (I'm a CMake kind of guy myself, but of course I didn't choose the build system for this project.) My OS is Debian.

I've tried building this branch as well: https://github.com/kanzure/nanoengineer/branches/kirka-updates

If you can try getting this to build on your system, I would greatly appreciate it! Thanks!

Answer 1

After a fair amount of work, I was able to get it to build on Ubuntu 12.04 x86 and Debian 7.4 x86_64. I wrote up a guide below. Can you please try following it to see if it resolves the issue?

If not please let me know where you get stuck.

Install Common Dependencies

sudo apt-get install build-essential autoconf libtool pkg-config python-opengl python-imaging python-pyrex python-pyside.qtopengl idle-python2.7 qt4-dev-tools qt4-designer libqtgui4 libqtcore4 libqt4-xml libqt4-test libqt4-script libqt4-network libqt4-dbus python-qt4 python-qt4-gl libgle3 python-dev

Install NumArray 1.5.2

wget http://goo.gl/6gL0q3 -O numarray-1.5.2.tgz
tar xfvz numarray-1.5.2.tgz
cd numarray-1.5.2
sudo python setup.py install

Install Numeric 23.8

wget http://goo.gl/PxaHFW -O numeric-23.8.tgz
tar xfvz numeric-23.8.tgz
cd Numeric-23.8
sudo python setup.py install

Install HDF5 1.6.5

wget ftp://ftp.hdfgroup.org/HDF5/releases/hdf5-1.6/hdf5-1.6.5.tar.gz
tar xfvz hdf5-1.6.5.tar.gz
cd hdf5-1.6.5
./configure --prefix=/usr/local
sudo make 
sudo make install

Install Nanoengineer

git clone https://github.com/kanzure/nanoengineer.git
cd nanoengineer
./bootstrap
./configure
make
sudo make install

Troubleshooting

On Debian Jessie, you will receive the error message that cant pants mentioned. There seems to be an issue in the automake scripts. x86_64-linux-gnu-gcc is inserted in CFLAGS and gcc will interpret that as a name of one of the source files. As a workaround, let's create an empty file with that name. Empty so that it won't change the program and that very name so that compiler picks it up. From the cloned nanoengineer directory, run this command to make gcc happy (it is a hack yes, but it does work) ...

touch sim/src/x86_64-linux-gnu-gcc

If you receive an error message when attemping to compile HDF5 along the lines of: "error: call to ‘__open_missing_mode’ declared with attribute error: open with O_CREAT in second argument needs 3 arguments", then modify the file perform/zip_perf.c, line 548 to look like the following and then rerun make...

output = open(filename, O_RDWR | O_CREAT, S_IRUSR|S_IWUSR);

If you receive an error message about Numeric/arrayobject.h not being found when building Nanoengineer, try running

export CPPFLAGS=-I/usr/local/include/python2.7
./configure
make
sudo make install

If you receive an error message similar to "TRACE_PREFIX undeclared", modify the file sim/src/simhelp.c lines 38 to 41 to look like this and re-run make:

#ifdef DISTUTILS
static char tracePrefix[] = "";
#else
static char tracePrefix[] = "";

If you receive an error message when trying to launch NanoEngineer-1 that mentions something similar to "cannot import name GL_ARRAY_BUFFER_ARB", modify the lines in the following files

/usr/local/bin/NanoEngineer1_0.9.2.app/program/graphics/drawing/setup_draw.py
/usr/local/bin/NanoEngineer1_0.9.2.app/program/graphics/drawing/GLPrimitiveBuffer.py
/usr/local/bin/NanoEngineer1_0.9.2.app/program/prototype/test_drawing.py

that look like this:

from OpenGL.GL import GL_ARRAY_BUFFER_ARB
from OpenGL.GL import GL_ELEMENT_ARRAY_BUFFER_ARB

to look like this:

from OpenGL.GL.ARB.vertex_buffer_object import GL_ARRAY_BUFFER_AR
from OpenGL.GL.ARB.vertex_buffer_object import GL_ELEMENT_ARRAY_BUFFER_ARB

I also found an additional troubleshooting text file that has been removed, but you can find it here

Answer 2

You just need to enter this command:

sudo apt-get install gcc

Answer 3

the error can be due to one of several missing package. Below command will install several packages like g++, gcc, etc.

sudo apt-get install build-essential

Answer 4

apt-get install python-dev

...solved the problem for me.

Answer 5

sudo apt-get -y install python-software-properties && \
sudo apt-get -y install software-properties-common && \
sudo apt-get -y install gcc make build-essential libssl-dev libffi-dev python-dev

You need the libssl-dev and libffi-dev if especially you are trying to install python's cryptography libraries or python libs that depend on it(eg ansible)

Answer 6

What worked for me is : sudo apt-get install python3-dev build-essential gcc libpq-dev

Answer 7

I was getting the error “gcc: error: x86_64-linux-gnu-gcc: No such file or directory” as I was trying to build a simple c-extension module to run in Python. I tried all the things above to no avail, and finally realized that I had an error in my module.c code! So I thought it would be helpful to add that, if you are getting this error message but you have python-dev and everything correctly installed, you should look for issues in your code.