fatal error: jni.h: No such file or directory

[mart-e]

Hello,

The install of javabridge-1.0.7 via pip fails. Done on Archlinux x86_64.
Seems like an issue with the version of numpy being incompatible.

gcc -pthread -fno-strict-aliasing -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -DNDEBUG -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/lib/jvm/java-7-openjdk/include -I/usr/lib/jvm/java-7-openjdk/include/linux -I/usr/include/python2.7 -c _javabridge.c -o build/temp.linux-x86_64-2.7/_javabridge.o

In file included from /usr/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1761:0,
                 from /usr/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17,
                 from /usr/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                 from _javabridge.c:346:

/usr/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]

 #warning "Using deprecated NumPy API, disable it by " \
  ^

_javabridge.c:348:17: fatal error: jni.h: No such file or directory

 #include "jni.h"
                 ^

compilation terminated.

error: command 'gcc' failed with exit status 1

Thanks

[LeeKamentsky]

I think the numpy warning is a red herring. We're using a deprecated, but still supported API for something. The real problem is that "jni.h" is not on your include path. The compiler is looking for it in:

/usr/lib/jvm/java-7-openjdk/include
/usr/lib/jvm/java-7-openjdk/include/linux

I am pretty sure that jni.h should be in /usr/lib/jvm/java-7-openjdk/include, could you check that for me? Do you have the JDK installed?

[mart-e]

@LeeKamentsky you are right, I was missing the jdk (only jre).
I have installed it and now I have indeed the file at /usr/lib/jvm/java-7-openjdk/include/jni.h but I still get the same error :-/

[LeeKamentsky]

You still get the "fatal error: jni.h: No such file or directory" error? Is the GCC invocation still:

gcc -pthread -fno-strict-aliasing -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -DNDEBUG -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/usr/lib/jvm/java-7-openjdk/include -I/usr/lib/jvm/java-7-openjdk/include/linux -I/usr/include/python2.7 -c _javabridge.c -o build/temp.linux-x86_64-2.7/_javabridge.o

Distutils is adding /usr/lib/jvm/java-7-openjdk/include to the #include path, so it is surprising that gcc would not find jni.h

[mart-e]

No actually the command is now
gcc -pthread -fno-strict-aliasing -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -DNDEBUG -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector --param=ssp-buffer-size=4 -fPIC -I/usr/lib/python2.7/site-packages/numpy/core/include -I/include -I/include/linux -I/usr/include/python2.7 -c _javabridge.c -o build/temp.linux-x86_64-2.7/_javabridge.o.
Notice the -I/include -I/include/linux (which, of course, can not succeed)

[LeeKamentsky]

Interesting. I'm looking at the code that figures this out (https://github.com/CellProfiler/python-javabridge/blob/master/javabridge/locate.py). Could you do the following for me in a shell?

readlink -f `(type -p java)`

I am guessing that it reports "/usr/bin/java" and that's not what it does for me (/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/bin/java). If that turns out to be the case maybe @ljosa can figure it out. Anyway, you can get around this by exporting JAVA_HOME before installing:

export JAVA_HOME=/usr/lib/jvm/java-7-openjdk
pip install javabridge

Not a fix, but a work-around that I'm betting works for you.

[mart-e]

Almost :)

$ readlink -f `(type -p java)`
/usr/lib/java-common-wrapper
$ cat /usr/lib/java-common-wrapper
#!/bin/bash
exec "${JAVA_HOME:-/usr/lib/jvm/java-default-runtime}/bin/${0##*/}" "$@"

I guess it's Archlinux magic somehow.
Anyway after I exported the JAVA_HOME (as root, it took me sometime to figure out why it did not work when exporting as regular user), I was able to install it with pip.
Victory 👍

IMO, we can close the issue but let me know if you wish to investigate on how to improve the setup.py (or we can consider it as a configuration issue on my side)

[LeeKamentsky]

Thanks for hanging in there Martin. I'll leave this open for now and let my Unix guru colleague, Vebjorn handle it. We might close this out by making the installation fail more gracefully with a more helpful error message, detecting the absence of jni.h in the expected location and suggesting to the user that they define JAVA_HOME manually.

[abujed]

Hello, I'm also getting hung up on the jni.h issue reported above. I'm trying it on both 64 and 32 bit hosts. (both running ubuntu 14.04.1 and as far as I know I've installed all of the prereqs)
the readlink command gives me:
32 bit host - /usr/lib/jvm/java-7-openjdk-i386/jre/bin/java
64 bit hosts - /usr/lib/jvm/java-7-openjdk-amd64/jre/bin/java
I did the export JAVA_HOME according to the appropriate jdk found in /usr/lib/jvm/:
export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-i386
export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
then ran: pip install javabridge (sudo-ing didn't give me any advantage :-p)

Any help (or a boot in the right direction if this has been answered elsewhere) would be appreciated.
thanks!

[ljosa]

@abujed, I can't reproduce your problem. Here's what I did; see if what you did is different in any way:

1. Started with a clean Ubuntu 14.04.1 machine.
2. apt-get update
3. apt-get install openjdk-7-jdk python-pip python-numpy python-dev -y
4. pip install javabridge
5. Ran the first "Hello world" script in the documentation.

Feel free to reopen the issue if necessary.

[ljosa]

@mart-e, sorry to keep you waiting so long. I lost track of this issue.

I couldn't reproduce your problem. This is what I did; see if you did something different:

1. Started with a clean Arch Linux machine. (Not sure what version—whatever's in the base/arch Docker image.)
2. Synchronized the package database and upgraded packages: pacman -Syu --ignore filesystem
3. Installed dependencies: pacman -S jdk7-openjdk python2-pip python2-numpy base-devel
4. Installed the javabridge: pip2 install javabridge
5. Ran the first "Hello world" script in the documentation.

Feel free to reopen the issue if necessary.

[abujed]

Vebjorn,
wow thank you for your very quick response and the time you took to test.
Forgive me, I thought my installation was clean, turns out it was just
mostly clean. I started completely fresh, following your instructions
and I also cannot reproduce my error on a perfectly clean machine, it works
fine.

Now I just have to figure out how to use it :-D

Thank you again and my apologies for taking your time.
v/r
abujed

On Wed, Nov 5, 2014 at 12:58 PM, Vebjorn Ljosa notifications@github.com
wrote:

@abujed https://github.com/abujed, I can't reproduce your problem.
Here's what I did; see if what you did is different in any way:

1. Started with a clean Ubuntu 14.04.1 machine.
2. apt-get install openjdk-7-jdk python-pip python-numpy python-dev -y
3. export JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
4. pip install javabridge
5. Ran the first "Hello world" script in the documentation
   http://pythonhosted.org//javabridge/hello.html.

—
Reply to this email directly or view it on GitHub
CellProfiler#28 (comment)
.

[ljosa]

Glad to help.

[LeeKamentsky]

Good going Abujed, hope that you find Javabridge useful and maybe fun. And your struggles, I'm sure by posting them here, others will google for them, read your post and go from to 😻 without bothering us.