[Rcppoctave-user] Apple Blues

[Dominick Samperi]

With all suggested packages installed I managed to get R CMD check --as-cran
to run clean (no errors, warnings, or notes), but a few "non-standard"
directories
had to be removed, cleanup had to be run explicitly, and RcppOctave.Rnw had
to be modified to use tryCatch instead of try. The attached shell script
was used
to generate the clean check.


On Sat, Nov 9, 2013 at 2:21 AM, Renaud Gaujoux <
renaud at mancala.cbio.uct.ac.za> wrote:

> This NOTEs won't pass CRAN policy, but should really not appear. Did you
> run the check directly on the source tar.gz file or on the guthub directory
> where you tested compilation?
>
> Could you please try checking with all the suggested packages installed,
> otherwise unit tests will not run. It's actually strange that no error
> was thrown ar this step.
> Thanks.
>
> Bests,
> Renaud
>
>
> On Saturday, November 9, 2013, Dominick Samperi wrote:
>
>> I've attached the output of R CMD check --as-cran.
>> No errors, just a few NOTE's. (Suggested package
>> RUnit must be installed.)
>>
>> There has been a lot of discussion about "NOTE"
>> on r-revel, and it is not clear to me if this is considered
>> to be an error or just a warning. I don't know if CRAN
>> will accept a package with NOTE's...
>>
>>
>>
>> On Fri, Nov 8, 2013 at 5:53 PM, Renaud Gaujoux <
>> renaud at mancala.cbio.uct.ac.za> wrote:
>>
>> 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/ /,/'`
>> >>> >>
>> >>> >>
>>
>>
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