[Rcppoctave-user] Apple Blues

[Dominick Samperi]

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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