[Rcppoctave-user] Apple Blues

[Renaud Gaujoux]

Ah, I forgot something:
  * running a full R CMD check --as-cran on Mac?
:D

On 8 November 2013 18:33, Renaud Gaujoux <renaud at mancala.cbio.uct.ac.za> wrote:
> Nice. Many thanks!
>
> ... and along the way we, or at least I, learnt that the hooks
> .onUnload and .onDetach are actually not called when R quits and that
> required cleanup procedures must be registered via reg.finalizer to be
> sure they are called.
>
> What is left:
>   * check if a Mac binary package works fine on machine different than
> the one it was built on.
>   * get CRAN building machines geared with Octave so that binary
> packages are available from CRAN. I will follow up with the CRAN
> maintainer on this.
>
> Bests,
> Renaud
>
>
>
> On 8 November 2013 16:23, Dominick Samperi <djsamperi at gmail.com> wrote:
>> 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)
>>> >
>>> >
>>
>>