Re: How to install Octave 4.0.1 on OS X Yosemite

[Ben Abbott]

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

make_symbolic_links.sh
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