Re: How to install Octave 4.0.1 on OS X Yosemite

On Thu, Apr 28, 2016 at 1:18 PM, Alexander Hansen <address@hidden> wrote:

On Apr 28, 2016, at 13:12, Sunil Shah <address@hidden> wrote:

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

A 4.0.1 build should install mkoctfile. Fink’s Octave packaging separates the runtime and build-time portions because we need different Octave runtime versions to coexist to avoid having updates break people’s currently installed Octave Forge packages.

—akh

Thanks.

After installing octave 4.0.1, and setting the symbolic links per Ben, I was able to run mkoctfile on that version. I do however get the following warnings:

mkoctfile helloworld.cc

Apple LLVM version 7.3.0 (clang-703.0.29)

Target: x86_64-apple-darwin15.4.0

Thread model: posix

InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

clang: warning: argument unused during compilation: '-pthread'

"/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld" -demangle -dynamic -archx86_64 -bundle -bundle_loader /sw/local/bin/octave-4.0.1 -macosx_version_min 10.11.0 -o helloworld.oct -L/sw/local/lib/octave/4.0.1 -L/sw/local/lib -L/sw/lib/qt4-mac/lib -L/sw/lib -L/sw/lib -L/sw/lib -L/sw/lib/libpcre1 -L/sw/lib/gcc5/lib helloworld.o -loctinterp -loctave -framework QtNetwork -framework QtCore -framework QtGui -framework QtCore -dead_strip_dylibs -framework JavaVM -framework JavaVM -lfreetype -lhdf5 -lz -lfftw3_threads -lfftw3 -lfftw3f_threads -lfftw3f -lfontconfig -framework OpenGL -framework Carbon -framework JavaVM -ltatlas -lcurl -lcholmod -lumfpack -lamd -lcamd -lcolamd -lccolamd -lcxsparse -larpack -lqrupdate -lfftw3_threads -lfftw3 -lfftw3f_threads -lfftw3f -ltatlas -ltatlas -lreadline -lncurses -lpcre -ldl -lgfortran -lm -lm -lgl2ps -lc++ -lSystem /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/7.3.0/lib/darwin/libclang_rt.osx.a -F/sw/lib/qt4-mac/lib -F/sw/lib/qt4-mac/lib -F/sw/lib/qt4-mac/lib -F/sw/lib/qt4-mac/lib

Are the warning expected? Alex, are there other flags with mkoctfile to ensure that the right compilers and run times libs are used in octave 4.0.1?

Can I use fink to reinstall octave382-atlas-qtmac-dev? That way both versions will be fully useable on the machine.

Thanks,

Sunil

From:	Alexander Hansen
Subject:	Re: How to install Octave 4.0.1 on OS X Yosemite
Date:	Thu, 28 Apr 2016 13:58:14 -0700