[Rcpp-devel] RcppOctave on Windows: testing needed
renaud at mancala.cbio.uct.ac.za
Fri Oct 11 09:53:24 CEST 2013
Many thanks for this nice joint investigation work!
There certainly still are things to check and tweak to get the package run
smoothly and robustly on Mac (and Windows), but this is a great advance!
* a README file with instructions on how to build/install on these
platforms. I will post it here as well for comments.
* start another thread on rcppoctave-user to discuss Mac-specific
development and make information more easily accessible
* I want to update the version on CRAN with some other fixes, and will do
so keeping the Unix-only flag in the DESCRIPTION file, so that I don't need
to wait for the Windows/Mac building machines to get Octave-geared.
* the cross-platform capabilities development will carry on and be
available from the develop/ branch on github (+ r-forge and myCRAN). Any
further contribution to achieving this aim are obviously welcomed ;)
PS: ABI also means Acquired Brain Injury, which somehow makes sense in the
case of malfunctioning C++ libraries as well...
On 11 October 2013 06:51, Dominick Samperi <djsamperi at gmail.com> wrote:
> A few additional close out notes:
> 1. It turns out that Apple (and Homebrew) no longer support Fortran, so
> I had to specify an external Fortran compiler and options:
> $ export F77="/usr/local/bin/gfortran -arch x86_64"
> $ brew install octave --default-fortran-flags "-O2"
> 2. The fortran compiler can be obtained from AT&T (Simon Urbenek).
> 3. I think the build uses clang/clang++ and not gcc/g++
> (because Apple no longer supports the latter), so there
> is the potential for ABI problems when this version of
> Octave is used with RcppOctave.
> 4. I think brew can be instructed to use gcc/g++ by
> setting CC and CXX.
> On Thu, Oct 10, 2013 at 11:26 PM, Steve Lianoglou <
> lianoglou.steve at gene.com> wrote:
>> Just to close this out (for posterity again).
>> Dominick had pointed out to me off list that the octave formula isn't
>> in the default homebrew install, and to get it you've got to "tap"
>> their science repository by following the instructions here:
>> I had forgotten that I added those a while ago, so thanks again Dominick!
>> On Thu, Oct 10, 2013 at 12:44 PM, Steve Lianoglou
>> <lianoglou.steve at gene.com> wrote:
>> > Hi,
>> > On Thu, Oct 10, 2013 at 12:26 PM, Dominick Samperi <djsamperi at gmail.com>
>> >> The problem here is that Mac Ports installs a very old version of
>> >> Installing the latest version (3.6.4) from source seems to resolve the
>> >> issue. At least .O$version() works!
>> >> Installing Octave from source under MacOS takes some work due
>> >> to many dependencies, and the need for work-arounds for Apple
>> >> changes and deprecated features. See, for example:
>> >> http://wiki.octave.org/Octave_for_Mac
>> > Nice work!
>> > For the sake of future wanderers landing on this thread via google,
>> > these days the "preferred" package manager on OSX seems to be
>> > homebrew:
>> > http://brew.sh
>> > It's so good, Simon Urbanek doesn't hate it, yet ... which is not to
>> > say that he endorses it ;-)
>> > https://stat.ethz.ch/pipermail/r-sig-mac/2013-September/010303.html
>> > They've also got the latest octave on tap:
>> > $ brew info octave | head -n2
>> > octave: stable 3.6.4
>> > http://www.gnu.org/software/octave/index.html
>> > HTH,
>> > -steve
>> > --
>> > Steve Lianoglou
>> > Computational Biologist
>> > Bioinformatics and Computational Biology
>> > Genentech
>> Steve Lianoglou
>> Computational Biologist
>> Bioinformatics and Computational Biology
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