[Rcppoctave-user] Apple Blues

[Renaud Gaujoux]

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)
>
>