[Rcppoctave-user] Apple Blues

[Dominick Samperi]

The biocLite windows binary install works (provided the user has Octave in
PATH).

The github (ref='develop') install works under Linux and Mac OS X
(Mavericks).

And by increasing the "biodiversity" (number of OS's supported) a hidden
bug was
uncovered and fixed (after 100 posts!).

Cheers,
Dominick


On Fri, Nov 8, 2013 at 4:42 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> True :D
> I thought of trying to get a neat sequence of flags without quote but
> clearly did not work.
> I updated the gh and myCRAN versions: they now contain your solution
> for -Wl and also use mkoctfile rather than octave-config to retrieve
> the include and linker flags.
>
> If possible, can anybody please try the windows binary from myCRAN:
>
> source('http://www.bioconductor.org/biocLite.R')
> biocLite('RcppOctave', siteRepos = 'http://web.cbio.uct.ac.za/~renaud/CRAN
> ')
>
> Thank you.
>
> Bests,
> Renaud
>
> On 7 November 2013 17:13, Dominick Samperi <djsamperi at gmail.com> wrote:
> > This solution yields:
> >
> > -Wl,-F/Library/Frameworks/R.framework/..,-framework R ...
> >
> > and the linker doesn't know that the last "R" belongs to the
> > -framework option.
> >
> > To fix, simply add the 'g' qualifier to the sed command in
> > configure.ac:
> >
> > R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/g'`
> >
> >
> > My original solution works because the -Wl,"whatever"
> > option causes mkoctfile to insert the string "whatever"
> > into the linker command line without parsing. If instead
> > mkoctfile used a form of exec(3) that expects tokenized
> > options, the sed solution would be necessary.
> >
> >
> >
> > On Thu, Nov 7, 2013 at 7:20 AM, Renaud Gaujoux
> > <renaud at mancala.cbio.uct.ac.za> wrote:
> >>
> >> I changed configure.ac into:
> >> R_LDFLAGS=`echo "-Wl,$R_LDFLAGS" | sed 's/ /,/'`
> >>
> >> as I read/saw that multiple options must be comma separated.
> >> This will break if the path to the R framework contains spaces though.
> >> Can you please try again:
> >>
> >> install_github('RcppOctave', 'renozao', ref = 'develop')
> >>
> >> Thanks.
> >>
> >> Bests,
> >> Renaud
> >>
> >> On 6 November 2013 22:37, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za
> >
> >> wrote:
> >> > Nice. It is indeed a better solution than changing the flags and their
> >> > values. The sed command did not work probably because I forgot to
> double
> >> > the
> >> > square brackets, which is necessary to correctly pass configure's
> first
> >> > string evaluation.
> >> > I will incorporate the change tomorrow.
> >> > Thanks!
> >> >
> >> > Bests,
> >> > Renaud
> >> >
> >> > On Wednesday, November 6, 2013, Dominick Samperi wrote:
> >> >>
> >> >> The reason we have been hacking away at '-F' vs '-L' instead of
> >> >> letting 'R CMD config' figure things out is that mkoctfile does not
> >> >> know about R frameworks ('-F' is invalid). But mkoctfile does have
> >> >> the -Wl,whatever option, which simply passes whatever down to
> >> >> the linker.
> >> >>
> >> >> I have attached a modified configure.ac that uses this option
> >> >> instead of using sed to hack the output of R CMD config --ldflags.
> >> >>
> >> >>
> >> >>
> >> >> On Wed, Nov 6, 2013 at 10:25 AM, Dominick Samperi <
> djsamperi at gmail.com>
> >> >> wrote:
> >> >>
> >> >> Hello Renaud,
> >> >>
> >> >> So, this R technical issue (reg.finalizer) was the crux of the
> problem
> >> >> all
> >> >> along. Good work!
> >> >>
> >> >> The '..' is still there and the build still fails without my hacked
> >> >> Makefile.in, but
> >> >> with this change everything works (no more install memory errors).
> >> >>
> >> >> The '..' in the output of R CMD config --ldflags is there for a
> >> >> purpose,
> >> >> because
> >> >> the R framework is under /Library/Frameworks, and not under
> >> >> /Library/Frameworks/R.framework. This is analogous to
> >> >> -L/usr/lib/mylibs -lfoo, where /usr/lib/mylibs may contain a
> collection
> >> >> of libraries (instead of frameworks), not just libfoo.so.
> >> >> (A Mac OS framework is analogous to an R package.)
> >> >>
> >> >> Make sure '..' is not in the path supplied to '-L' and everything
> >> >> should
> >> >> work.
> >> >>
> >> >> Cheers,
> >> >> Dominick
> >> >>
> >> >>
> >> >> On Wed, Nov 6, 2013 at 8:19 AM, Renaud Gaujoux
> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >> >>
> >> >> Hi,
> >> >>
> >> >> I made some changes available in the develop version, which should
> >> >> hopefully solve both issues:
> >> >>   * octave_end is now called on exit (via reg.finalizer: see my post
> >> >> on r-devel
> >> >> https://stat.ethz.ch/pipermail/r-devel/2013-November/067912.html)
> >> >>   * the extra dots are removed by the sed in configure.ac, but I
> think
> >> >> we still need to figure out why these dots are there...
> >> >>
> >> >> To test:
> >> >>
> >> >> devtools::install_github('RcppOctave', 'renozao', ref = 'develop')
> >> >>
> >> >> Thanks.
> >> >>
> >> >> Bests,
> >> >> Renaud
> >> >>
> >> >> On 6 November 2013 11:15, Renaud Gaujoux
> >> >> <renaud at mancala.cbio.uct.ac.za>
> >> >> wrote:
> >> >> > Couple of questions to understand what is going on:
> >> >> >
> >> >> >   * why does R CMD config --ldflags returns these extra '..' if
> they
> >> >> > are
> >> >> > incorrect?
> >> >> >   * why does the compilation work if the path is incorrect to R
> >> >> > library
> >> >> > is
> >> >> > incorrect?
> >> >> >   * why removing the dots should solve the malloc error?
> >> >> >
> >> >> >
> >> >> >
> >> >> > On 5 November 2013 16:38, Dominick Samperi <djsamperi at gmail.com>
> >> >> > wrote:
> >> >> >>
> >> >> >> R CMD config --ldflags
> >> >> >> yields
> >> >> >> -F/Library/Frameworks/R.framework/.. -framework R
> >> >> >>
> >> >> >> This needs to be hacked for mkoctfile to:
> >> >> >> -L/Library/Frameworks/R.framework/Libraries -lR
> >> >> >> (no '..')
> >> >> >>
> >> >> >> Applying this to the github source fixes it for
> >> >> >> Mac OS X Mavericks provided the --no-test-load
> >> >> >> and octave_end tricks are used.
> >> >> >>
> >> >> >>
> >> >> >> On Tue, Nov 5, 2013 at 9:04 AM, Renaud Gaujoux
> >> >> >> <renaud at mancala.cbio.uct.ac.za> wrote:
> >> >> >>>
> >> >> >>> Not sure where the extra '..' would come from.
> >> >> >>> Are you installing the latest version from github?
> >> >> >>>
> >> >> >>> devtools::install_github('RcppOctave', 'renozao')
> >> >> >>>
> >> >> >>>
> >> >> >>>
> >> >> >>> On 2 November 2013 07:00, Dominick Samperi <djsamperi at gmail.com>
> >> >> >>> wrote:
> >> >> >>>>
> >> >> >>>> It appears that octave_end is not called at all under Mac OS X.
> >> >> >>>> But
> >> >> >>>> it
> >> >> >>>> is also not called under Linux! I inserted Rprintf statements to
> >> >> >>>> check.
> >> >> >>>>
> >> >> >>>> Perhaps the explanation is that failing to call octave_end under
> >> >> >>>> Linux
> >> >> >>>> (or Windows?) is non-fatal, but this is fatal under Mac OS X? If
> >> >> >>>> this
> >> >> >>>> is so the Mac OS X behavior is less dangerous...
> >> >> >>>>
> >> >> >>>> If I do not use --no-test-load, I get the result in
> RcppOctave.log
> >> >> >>>> (attached)
> >
> >
>
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