Re: How to install Octave 4.0.1 on OS X Yosemite

On Thu, Apr 28, 2016 at 4:32 AM, Ben Abbott <address@hidden> wrote:

On Apr 27, 2016, at 11:35 PM, Sunil Shah <address@hidden> wrote:

On Wed, Apr 27, 2016 at 7:11 PM, Ben Abbott <address@hidden> wrote:
On Apr 27, 2016, at 10:03 PM, Sunil Shah <address@hidden> wrote:

On Wed, Apr 27, 2016 at 6:56 PM, Ben Abbott <address@hidden> wrote:
On Apr 27, 2016, at 9:29 PM, Sunil Shah <address@hidden> wrote:

On Wed, Apr 27, 2016 at 6:25 PM, Sunil Shah <address@hidden> wrote:
On Wed, Apr 27, 2016 at 6:01 PM, Ben Abbott <address@hidden> wrote:
*** Sunil, please respond at the bottom of the email so that others can read along after this thread is archived ***

On Apr 27, 2016, at 8:52 PM, Sunil Shah <address@hidden> wrote:

> On Wed, Apr 27, 2016 at 5:23 PM, Ben Abbott <address@hidden> wrote:
>
>> > On Apr 27, 2016, at 7:58 PM, Sunil Shah <address@hidden> wrote:
>> >
>> > On Fri, Apr 15, 2016 at 5:25 PM, Ben Abbott <address@hidden> wrote:
>> >> On Apr 15, 2016, at 11:07 AM, Sunil Shah <address@hidden> wrote:
>> >>
>> >> Hi Ben,
>> >>
>> >> Can you post how to build 4.0.1 on the latest Yosemite release using Fink? I have been using Fink octave packages with altas.
>> >>
>> >> Thanks,
>> >
>> > I’ll assume you are using the released sources (you could also build from the developer’s sources).
>> >
>> > (1) Goto the sources at https://www.gnu.org/software/octave/download.html. You may be prompted to login. Just select “guest” and skit the username/password.
>> > (2) When a Finder window opens with the tar-balls, locate octave-4.0.1.tar.gz and copy it to the location where you’d like to build octave.
>> > (3) Double click on the archive. It will unpack in to a folder called octave-4.0.1.
>> > (4) Place the files attached to this email in the folder.
>> > (5) To ensure you have all the needed dependencies, open a Terminal window and enter "fink install octave382-atlas-qtmac-dev”
>> > (6) You’ll need to remove Fink’s Octave before trying to run the one you’ll compile (“fink remove octave382-atlas-qtmac-dev”)
>> > (7) My scripts assume you have gcc5 installed, “fink install gcc5”
>> > (8) From the Terminal window cd into octave-4.0.1 and type “chmod 755 ./fink_*.sh”. This marks the two scripts as executable.
>> > (9) From the Terminal window type “./fink_configure_octave_noX11_v1.sh” to configure the octave build. This might take a few minutes. If any errors are encountered, please tell us what the error.
>> > (10) Build Octave by typing “./fink_make_octave.sh”. If any errors occur, please tell us what the error was. My script configured octave's build was configured to install into /sw/local. This is done to ensure that it doesn’t conflict with anything else.
>> > (11) To install octave type “make install” in a Terminal window and from the octave-4.0.1 folder.
>> > (12) If you decide to uninstall, type “make uninstall” for the octave-4.0.1 folder where you build octave.
>> > (13) To run octave, type “/sw/local/bin/octave &” from a Terminal window.
>> >
>> > Once all the above is completed, we can help you setup an icon to click on to launch Octave.
>> >
>> > Ben
>> >
>> > Hi Ben,
>> >
>> > In following your instructions on octave 4.0.1 on fink, it worked fine till step 7).
>> >
>> > When I issued fink install gcc5, it failed. I saw that on fink mailing list, others had a similar problem (though for gcc 5.2.0.2). The latest gcc5 in fink is gcc 5.3.0.1. So I am trying the remedy in the mailing list, to remove fink's make and retrying gcc5 install.
>> >
>> > https://sourceforge.net/p/fink/mailman/message/34537356/
>> >
>> > I suppose if that works, should I reinstall fink make before proceeding with your steps 8)-12) ?
>> >
>> > Thanks,
>> >
>> > Sunil
>>
>> Opps, I actually don’t have gcc5 installed :-(
>>
>> I do have gcc5-compiler & gcc5-shlibs installed.
>>
>> $ fink list gcc5
>> Scanning package description files..........
>> Information about 9327 packages read in 68 seconds.
>> gcc5 5.3.0-1 GNU Compiler Collection Version 5
>> i gcc5-compiler 5.3.0-1 Compiler Binaries for gcc5
>> i gcc5-shlibs 5.3.0-1 Shared libraries for gcc5
>> liboctave364-gcc5 [virtual package]
>> liboctave364-gcc5-dev [virtual package]
>> liboctave382-gcc5 [virtual package]
>> liboctave382-gcc5-dev [virtual package]
>>
>> So (7) should be …
>>
>> (7) My scripts assume you have gfortran from gcc5 installed, “fink install gcc5-compiler gcc5-shlibs”
>>
>> You should be able to pick up from (7) and continue (you don’t need repeat the earlier steps).
>>
>> Ben
>
> Thanks, Alex and Ben.
>
> Here is the state of my installed packages.
>
> fink list -i -t gcc5
>
> Scanning package description files..........
> Information about 9087 packages read in 2 seconds.
> (i) gcc5-compiler 5.3.0-1 Compiler Binaries for gcc5
> (i) gcc5-shlibs 5.3.0-1 Shared libraries for gcc5
> p liboctave382-gcc5 [virtual package]
>
> fink list -i -t make
>
> Scanning package description files..........
> Information about 9087 packages read in 1 seconds.
> i automake1.14-core 1.14.1-2 GNU Standards-compliant Makefile generator
> i automake1.15 1.15-1 GNU Standards-compliant Makefile generator
> i automake1.15-core 1.15-1 GNU Standards-compliant Makefile generator
> p automaken [virtual package]
> (i) cmake 3.5.1-1 Cross-platform Make
> i extutils-makemaker-pm5182 7.06-1 Perl module to create a module Makefile
> p extutils-makemaker-pm5182-bin [virtual package]
> p locale-maketext-lexicon-pm5182 [virtual package]
> p locale-maketext-pm5182 [virtual package]
> p locale-maketext-simple-pm5182 [virtual package]
>
> Questions:
>
> 1) Since I do not have fink make, should I install it before the next steps?
>
> 2) Should I install / update gcc5-compiler and gcc5-shlibs ?
>
> Sunil

I see that you already have the required gcc5 packages installed. If you have also run "fink install octave382-atlas-qtmac-dev” then you have all the dependencies covered.

Ben

Ben,

I did run your steps 5) and 6) - i.e. installed and removed octave382-atlas-qtmac-dev.

I take it I do not need to update gcc5-compiler and gcc5-shlibs to a newer version.

Sunil

Ben,

On step 9) I did have to remove the ^M from the file.

There isn’t a ^M in the file I attached. Did you open the file in an editor before using it? Perhaps an editor whose standard format isn’t plain text?

Ben

Must be my gmail download of attachment.

Here is the output of 9) - Is it ok?

configure:

Octave is now configured for x86_64-apple-darwin

Source directory: .
Installation prefix: /sw/local
C compiler: /sw/var/lib/fink/path-prefix-clang/cc -D_THREAD_SAFE -pthread -Wall -W -Wshadow -Wformat -Wpointer-arith -Wmissing-prototypes -Wstrict-prototypes -Wwrite-strings -Wcast-align -Wcast-qual -v -O3 -MD -D_THREAD_SAFE
C++ compiler: /sw/var/lib/fink/path-prefix-libcxx/c++ -D_THREAD_SAFE -pthread -Wall -W -Wshadow -Wold-style-cast -Wformat -Wpointer-arith -Wwrite-strings -Wcast-align -Wcast-qual -g -O2
Fortran compiler: /sw/bin/gfortran-fsf-5 -O3
Fortran libraries: -L/sw/lib/gcc5/lib -lgfortran
Lex libraries:
LIBS: -lm -lm -lgl2ps

AMD CPPFLAGS:
AMD LDFLAGS:
AMD libraries: -lamd
ARPACK CPPFLAGS:
ARPACK LDFLAGS:
ARPACK libraries: -larpack
BLAS libraries: -ltatlas
CAMD CPPFLAGS:
CAMD LDFLAGS:
CAMD libraries: -lcamd
CARBON libraries: -Wl,-framework -Wl,Carbon
CCOLAMD CPPFLAGS:
CCOLAMD LDFLAGS:
CCOLAMD libraries: -lccolamd
CHOLMOD CPPFLAGS:
CHOLMOD LDFLAGS:
CHOLMOD libraries: -lcholmod
COLAMD CPPFLAGS:
COLAMD LDFLAGS:
COLAMD libraries: -lcolamd
CURL CPPFLAGS:
CURL LDFLAGS:
CURL libraries: -lcurl
CXSPARSE CPPFLAGS:
CXSPARSE LDFLAGS:
CXSPARSE libraries: -lcxsparse
DL libraries: -ldl
FFTW3 CPPFLAGS:
FFTW3 LDFLAGS:
FFTW3 libraries: -lfftw3_threads -lfftw3
FFTW3F CPPFLAGS:
FFTW3F LDFLAGS:
FFTW3F libraries: -lfftw3f_threads -lfftw3f
FLTK CPPFLAGS:
FLTK LDFLAGS:
FLTK libraries:
fontconfig CPPFLAGS: -I/sw/include
fontconfig libraries: -L/sw/lib -lfontconfig
FreeType2 CPPFLAGS: -I/sw/include/freetype2
FreeType2 libraries: -L/sw/lib -lfreetype
GLPK CPPFLAGS:
GLPK LDFLAGS:
GLPK libraries: -lglpk
HDF5 CPPFLAGS:
HDF5 LDFLAGS:
HDF5 libraries: -lhdf5
Java home: /System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home
Java JVM path: /Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Libraries
Java CPPFLAGS: -I/System/Library/Java/JavaVirtualMachines/1.6.0.jdk/Contents/Home/include -I/System/Library/Frameworks/JavaVM.framework/Home/include -I/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Headers -I/System/Library/Frameworks/JavaVM.framework/Versions/Current/Headers
Java libraries: -framework JavaVM
LAPACK libraries: -ltatlas
LLVM CPPFLAGS:
LLVM LDFLAGS:
LLVM libraries:
Magick++ CPPFLAGS: -I/sw/include/GraphicsMagick
Magick++ LDFLAGS: -L/sw/lib/graphicsmagick1322
Magick++ libraries: -lGraphicsMagick++ -lGraphicsMagick
OPENGL libraries: -L/sw/lib -lfontconfig -Wl,-framework -Wl,OpenGL
OSMesa CPPFLAGS:
OSMesa LDFLAGS:
OSMesa libraries:
PCRE CPPFLAGS: -I/sw/include
PCRE libraries: -L/sw/lib/libpcre1 -lpcre
PortAudio CPPFLAGS:
PortAudio LDFLAGS:
PortAudio libraries:
PTHREAD flags: -D_THREAD_SAFE -pthread
PTHREAD libraries:
QHULL CPPFLAGS: -I/sw/include/libqhull
QHULL LDFLAGS:
QHULL libraries: -lqhull
QRUPDATE CPPFLAGS:
QRUPDATE LDFLAGS:
QRUPDATE libraries: -lqrupdate
Qt CPPFLAGS: -I/sw/lib/qt4-mac/include/QtCore -I/sw/lib/qt4-mac/include/QtGui -I/sw/lib/qt4-mac/include/QtNetwork -I/sw/lib/qt4-mac/include -I/sw/lib/qt4-mac/include/QtOpenGL
Qt LDFLAGS: -F/sw/lib/qt4-mac/lib
Qt libraries: -Wl,-framework,QtCore -Wl,-framework,QtGui -Wl,-framework,QtNetwork -Wl,-framework,QtOpenGL -lqscintilla2
READLINE libraries: -lreadline
Sndfile CPPFLAGS:
Sndfile LDFLAGS:
Sndfile libraries:
TERM libraries: -lncurses
UMFPACK CPPFLAGS:
UMFPACK LDFLAGS:
UMFPACK libraries: -lumfpack
X11 include flags:
X11 libraries:
Z CPPFLAGS:
Z LDFLAGS:
Z libraries: -lz

Default pager: less
gnuplot: gnuplot

Build Octave GUI: yes
JIT compiler for loops: no
Build Java interface: yes
Do internal array bounds checking: no
Build static libraries: no
Build shared libraries: yes
Dynamic Linking: yes (dlopen)
Include support for GNU readline: yes
64-bit array dims and indexing: no
OpenMP SMP multithreading: no
Build cross tools: no

configure: WARNING:

I wasn't able to find a suitable style for declaring a push-pull
parser in a bison input file so I'm disabling bison.

configure: WARNING:

I didn't find bison, or the version of bison that I found does not
support all the features that are required, but it's only a problem
if you need to reconstruct parse.cc, which is the case if you're
building from VCS sources.

configure: WARNING:

I didn't find icotool, but it's only a problem if you need to
reconstruct octave-logo.ico, which is the case if you're building from
VCS sources.

configure: WARNING: --without-fltk specified. Native graphics will be disabled.
configure: WARNING: OSMesa library not found. Offscreen rendering with OpenGL will be disabled.
configure: WARNING:
configure: WARNING: I didn't find the necessary libraries to compile native
configure: WARNING: graphics. It isn't necessary to have native graphics,
configure: WARNING: but you will need to have gnuplot installed or you won't
configure: WARNING: be able to use any of Octave's plotting commands
configure: WARNING:
configure:
configure: NOTE: Libraries or auxiliary programs may be skipped if they are
configure: NOTE: not found OR if they are missing required features on your
configure: NOTE: system.

I don’t have a copy of what I usually see, but it looks ok to me. Please continue.

Ben

Make check

Summary:

PASS 12976
FAIL 27
XFAIL 25
SKIPPED 74

Is that expected?

That’s about what I get. The failures are mostly trivial (round off errors and such)

How do install packages - control, signal ?

Do I use fink install or octave command package install?

Thanks

Fink’s install will not work since it requires Octave 3.8.2 as a dependency and will not be binary compatible.

The procedure you used for building Octave is intended for developers. Some of Octave’s packages will require special tweaking to install under Mac OS X. I rarely use Octave’s packages and won’t be any help in getting them to work if anything special is needed.

What I do know is that you must install octave first. This is risky and you’ll be on your own if something goes wrong. In any event, you’ll need to attached script to be placed in the folder with Octave’s sources.

sudo make install
chmod 755 make_symbolic_links.sh
./make_symbolic_links.sh

If you later install an updated version (4.0.2?) you’ll need to modify this script to work with the new version (the other scripts may need maintenance as well).

Now you can try to install the control package using Octave’s pkg command.

Ben

Hi Ben,

I do need control and signal packages. I also need mkoctfile to work for my own code. These did work with octave 3.8.2, however, since I removed octave382-atlas-qtmac-dev, I my installed version 3.8.2 will not let me do mkoctfile.

1) Will octave 4.0.1 allow me to run mkoctfile ? If yes, do I need anything special? Do I need to install 4.0.1 with make install to allow mkoctfile to work, or can I try out the version in the build directory?

2) If 4.0.1 does not allow me to do mkoctfile or install control and signal packages, I need to reinstall octave382-atlas-qtmac-dev. If I do so, do I need to remove any packages I have installed as a result of building 4.0.1? I have not yet installed it.

Thanks,

Sunil

From:	Sunil Shah
Subject:	Re: How to install Octave 4.0.1 on OS X Yosemite
Date:	Thu, 28 Apr 2016 13:12:17 -0700