[Rcppoctave-user] Apple Blues

[Dominick Samperi]

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).
>> >>>>
>> >>>> Also, I'm attaching RcppOctave/src/modules/Makefile.in
>> >>>> with a small edit (the sed script generates a path with an extra
>> '..').
>> >>>>
>> >>>>
>> >>>>
>> >>>> On Sat, Nov 2, 2013 at 12:19 AM, Renaud Gaujoux
>> >>>> <renaud at mancala.cbio.uct.ac.za> wrote:
>> >>>>>
>> >>>>>
>> >>>>>> The --no-test-load option is used because the embedded Octave
>> session
>> >>>>>> is not terminated properly at test time (during installation), and
>> the
>> >>>>>> embedded Octave session needs to be explicitly terminated before
>> >>>>>> leaving the R session using the 'octave_end' entry point.
>> >>>>>
>> >>>>>
>> >>>>> octave_end is normally called when the package is unloaded in
>> .onUnload
>> >>>>> as well as when the library is unloaded by in R_init_unload (or
>> something
>> >>>>> like that).
>> >>>>> There is no errors on Linux at load test.
>> >>>>> Can you please post the install logs showing the error?
>> >>>>>
>> >>>>> Thanks
>> >>>>
>> >>>>
>> >>>
>> >>
>> >
>>
>
>
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