RE: help with compiling octave-3.3.51

[Charles Yee]

Hi,

Thanks for sharing your experience with compiling octave-3.3.51.

I finally got octave-3.3.51 to compile (using lapack-3.2.2) and run without the segmentation fault. I had to resort to using Fedora Core 13.
It seems like the using gcc-4.4.4-2.fc13.x86_64 helped - something got linked in properly ( I am only guessing).  I had to compile and install lapack-3.2.2  (my installation of Fedora Core 13 did not have lapack and blas.

I can run octave-3.3.51 and do some simple vector addition as a test, which is great.

Unfortunately,  I tried installing the octave-java package - java-1.2.7.tar.gz - and that did not go well.

Below is the warnings and errors I got:

 pkg -verbose install java-1.2.7.tar.gz
__java__.cc: In function ‘std::string get_module_path(const std::string&, bool)’:
__java__.cc:223: error: ‘getcwd’ is not a member of ‘octave_env’
__java__.cc: In function ‘void initialize_jvm()’:
__java__.cc:385: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In function ‘octave_value get_array_elements(JNIEnv*, _jobject*, const octave_value_list&)’:
__java__.cc:612: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In function ‘octave_value set_array_elements(JNIEnv*, _jobject*, const octave_value_list&, const octave_value&)’:
__java__.cc:634: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In function ‘octave_value box(JNIEnv*, _jobject*, _jclass*)’:
__java__.cc:783: warning: deprecated conversion from string constant to ‘char*’
__java__.cc:848: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In function ‘int unbox(JNIEnv*, const octave_value&, jobject_ref&, jclass_ref&)’:
__java__.cc:988: warning: deprecated conversion from string constant to ‘char*’
__java__.cc:1052: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In function ‘int java_event_hook()’:
__java__.cc:1117: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In member function ‘octave_value octave_java::do_java_invoke(JNIEnv*, const std::string&, const octave_value_list&)’:
__java__.cc:1696: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In static member function ‘static octave_value octave_java::do_java_invoke(JNIEnv*, const std::string&, const std::string&, const octave_value_list&)’:
__java__.cc:1721: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In static member function ‘static octave_value octave_java::do_java_create(JNIEnv*, const std::string&, const octave_value_list&)’:
__java__.cc:1746: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In member function ‘octave_value octave_java::do_java_get(JNIEnv*, const std::string&)’:
__java__.cc:1767: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In static member function ‘static octave_value octave_java::do_java_get(JNIEnv*, const std::string&, const std::string&)’:
__java__.cc:1787: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In member function ‘octave_value octave_java::do_java_set(JNIEnv*, const std::string&, const octave_value&)’:
__java__.cc:1813: warning: deprecated conversion from string constant to ‘char*’
__java__.cc: In static member function ‘static octave_value octave_java::do_java_set(JNIEnv*, const std::string&, const std::string&, const octave_value&)’:
__java__.cc:1835: warning: deprecated conversion from string constant to ‘char*’
make: *** [__java__.oct] Error 1
mkdir (/tmp/oct-IZxkBk)
untar (java-1.2.7.tar.gz, /tmp/oct-IZxkBk)
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for mkoctfile... mkoctfile
retrieving compile and link flags from mkoctfile
checking for F77_FUNC... yes
checking for octave... octave
checking for OCTAVE_VERSION in Octave... 3.3.51
checking for octave_config_info('canonical_host_type') in Octave... x86_64-unknown-linux-gnu
checking for octave_config_info('SHLEXT') in Octave... so
checking whether ln -s works... yes
checking for ranlib... ranlib
checking for strip... strip
checking for java... /usr/local/jdk1.6.0_21/bin/java
checking for javac... /usr/local/jdk1.6.0_21/bin/javac
checking for jar... /usr/local/jdk1.6.0_21/bin/jar
checking for Java version... 1.6.0_21
configure: creating ./config.status
config.status: creating Makeconf
 
  "$prefix" is /usr/local/octave/3.3.51/share/octave/packages/java-1.2.7
  "$exec_prefix" is ${prefix}

octave commands will install into the following directories:
   m-files:   /usr/local/octave/3.3.51/share/octave/3.3.51/site/m/octave-forge
   oct-files: /usr/local/octave/3.3.51/libexec/octave/3.3.51/site/oct/x86_64-unknown-linux-gnu/octave-forge
   binaries:  /usr/local/octave/3.3.51/libexec/octave/3.3.51/site/exec/x86_64-unknown-linux-gnu
alternatives:
   m-files:   /usr/local/octave/3.3.51/share/octave/3.3.51/site/octave-forge-alternatives/m
   oct-files: /usr/local/octave/3.3.51/libexec/octave/3.3.51/site/octave-forge-alternatives/oct/x86_64-unknown-linux-gnu

shell commands will install into the following directories:
   binaries:  ${exec_prefix}/bin
   man pages: ${datarootdir}/man
   libraries: ${exec_prefix}/lib
   headers:   ${prefix}/include

octave-forge is configured with
   octave:      octave (version 3.3.51)
   mkoctfile:   mkoctfile for Octave 51
   java:        yes

find . -name NOINSTALL -print    # shows which toolboxes won't be installed

'make' returned the following error: make: Entering directory `/tmp/oct-IZxkBk/java-1.2.7/src'
if [ "Xamd64X" = "XX" ]; then \
                mkoctfile -DHAVE_OCTAVE_33 -v -DJAVAPKG_BUILD -I/usr/local/jdk1.6.0_21/include -I/usr/local/jdk1.6.0_21/include/linux -o __java__.oct __java__.cc ; \
        else \
                mkoctfile -DHAVE_OCTAVE_33 -v -DJAVAPKG_BUILD -DJAVA_ARCH=\\\"amd64\\\" -DJAVA_HOME=\\\"/usr/local/jdk1.6.0_21\\\" -I/usr/local/jdk1.6.0_21/include -I/usr/local/jdk1.6.0_21/include/linux -o __java__.oct __java__.cc ; \
        fi
g++ -c -fPIC -I/usr/local/octave/3.3.51/include/octave-3.3.51/octave/.. -I/usr/local/octave/3.3.51/include/octave-3.3.51/octave -I/usr/local/octave/3.3.51/include -I/usr/include/freetype2 -g -O2 -I/usr/local/jdk1.6.0_21/include -I/usr/local/jdk1.6.0_21/include/linux -DHAVE_OCTAVE_33 -DJAVAPKG_BUILD -DJAVA_ARCH=\"amd64\" -DJAVA_HOME=\"/usr/local/jdk1.6.0_21\" __java__.cc -o __java__.o
make: Leaving directory `/tmp/oct-IZxkBk/java-1.2.7/src'
error: called from `pkg>configure_make' in file /usr/local/octave/3.3.51/share/octave/3.3.51/m/pkg/pkg.m near line 1251, column 2
error: called from:
error:   /usr/local/octave/3.3.51/share/octave/3.3.51/m/pkg/pkg.m at line 712, column 5
error:   /usr/local/octave/3.3.51/share/octave/3.3.51/m/pkg/pkg.m at line 287, column 7
octave:3>


Any help with deciphering this would be greatly appreciated.
Thank you.

-Charles





-------------------------------------------------------------------


> Date: Thu, 8 Jul 2010 18:18:36 -0700
> From: address@hidden
> To: address@hidden
> Subject: RE: help with compiling octave-3.3.51
>
>
> Posting just to let you know you aren't alone in your struggles. I'm having
> quite a bit of difficulty building the current development sources on RH5
> myself, though some of that was due to the fact that I don't have root
> access so I've had to build a number of packages on my own. I could handle
> the numerous dependency problems but I'm at a loss battling against a
> segfault that seems identical to yours (though I suppose you can never be
> sure).
>
> I tried building BLAS and LAPACK without optimization, and I also still get
> the segfault. I'm trying LAPACK 3.2.1 to see if that helps.
>
> I don't have access to the machine at the moment, but for reference I'm
> using gcc 4.1.2 (which comes with RHEL5), and pretty much the latest of
> everything else which I downloaded and built myself. I can't remember
> everything involved, but I had to update flex and libtool, had to build git
> just to get gnulib (or libgnu, whatever it is), and I built the latest gperf
> and various optional stuff (qrupdate, hdf5, fltk, and I'm sure there are
> more). I can probably provide more detail later.
>
> Also, if you haven't noticed, you can do ./run-octave -g to run it through
> gdb, ./run-octave -valgrind to run memcheck, and strace as well (though I
> couldn't get that to work).
> --
> View this message in context: http://octave.1599824.n4.nabble.com/help-with-compiling-octave-3-3-51-tp2272804p2283017.html
> Sent from the Octave - General mailing list archive at Nabble.com.
> _______________________________________________
> Help-octave mailing list
> address@hidden
> https://www-old.cae.wisc.edu/mailman/listinfo/help-octave

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