[R-pkg-devel] what is difference between Mac setup of rhub and CRAN

[Jan Wijffels]

Yes, that is exactly the problem I'm facing with that R package.
Anyone knows how do I find out which ABI issue it is & who should I contact
to try to find a solution?

Jan Wijffels
Statistician
www.bnosac.be  | +32 486 611708


On Thu, 31 Jan 2019 at 11:59, Gábor Csárdi <csardi.gabor using gmail.com> wrote:

> I can reproduce your problem, and indeed it seems that it is a
> compiler ABI incompatibility issue. I am not sure how it could be
> fixed, though.
>
> With the CRAN compiler it gets stuck here:
>
> ### Name: embed_articlespace
> ### Title: Build a Starspace model for learning the mapping between
> ###   sentences and articles (articlespace)
> ### Aliases: embed_articlespace
>
> ### ** Examples
>
> library(udpipe)
> data(brussels_reviews_anno, package = "udpipe")
> x <- subset(brussels_reviews_anno, language == "nl")
> x$token <- x$lemma
> x <- x[, c("doc_id", "sentence_id", "token")]
> set.seed(123456789)
> model <- embed_articlespace(x, early_stopping = 1,
>                             dim = 25, epoch = 25, minCount = 2,
>                             negSearchLimit = 1, maxNegSamples = 2)
> #> Start to initialize starspace model.
> #> Build dict from input file :
>
> /var/folders/59/0gkmw1yj2w7bf2dfc3jznv5w0000gn/T//RtmpL18Wso/textspace_1200026295f3c.txt
> #> Read 0M words
> #> Number of words in dictionary:  1274
> #> Number of labels in dictionary: 0
> #> Loading data from file :
>
> /var/folders/59/0gkmw1yj2w7bf2dfc3jznv5w0000gn/T//RtmpL18Wso/textspace_1200026295f3c.txt
> #> Total number of examples loaded : 470
> #> 2019-01-31 10:50:04 Start training epoch 1 with learning rate 0.01
>
> Gabor
>
> On Thu, Jan 31, 2019 at 10:34 AM Jan Wijffels <jwijffels using bnosac.be> wrote:
> >
> > Gabor. Thanks for the input. I unfortunately do not have a Mac at my
> disposal to check this at that would be indeed the most optimal solution to
> find out differences in the setups.
> >
> > Is there someone on this mailing list which can comment on the CRAN
> machines about MacOS to answer
> >
> > What can be a reason why a package fails on r-release-osx-x86_64 but
> checked fine on r-oldrel-osx-x86_64 as  the
> https://cran.r-project.org/web/checks/check_flavors.html seem to indicate
> they have the same setup? My package is using C++ code which relies on
> clang-3.3 or newer and relies on -pthread. The src/Makevars are at
> https://github.com/bnosac/ruimtehol/blob/master/src/Makevars
> >
> > Jan
> >
> > Jan Wijffels
> > Statistician
> > www.bnosac.be  | +32 486 611708
> >
> >
> > On Thu, 31 Jan 2019 at 11:26, Gábor Csárdi <csardi.gabor using gmail.com>
> wrote:
> >>
> >> See answers inline.
> >>
> >> On Thu, Jan 31, 2019 at 10:16 AM Jan Wijffels <jwijffels using bnosac.be>
> wrote:
> >> [...]
> >> > The package has C++ code which relies on clang-3.3 or newer and
> relies on -pthread. It has in it's src/Makevars (
> https://github.com/bnosac/ruimtehol/blob/master/src/Makevars)
> >> >
> >> > PKG_LIBS = -pthread
> >> > PKG_CPPFLAGS = -pthread
> >> >
> >> > Is that what you mean with linking to a system library?
> >>
> >> Possibly, yes.
> >>
> >> > What version of the compiler is running on rhub and how is it
> different from CRAN r-release-osx-x86_64 or even CRAN r-oldrel-osx-x86_64
> >>
> >> R-hub uses the standard system compiler in Xcode. CRAN checks use
> >> their custom built clang compiler. This is usually compatible with the
> >> system compiler, except for some rare ABI issues. You can download it
> >> at https://cran.r-project.org/bin/macosx/tools/  The check flavors
> >> page at https://cran.r-project.org/web/checks/check_flavors.html might
> >> be outdated, as it still shows clang 4.0.0. I don't know, I cannot
> >> speak for CRAN.
> >>
> >> > About CRAN (Question 2): What can be a reason why a package fails on
> r-release-osx-x86_64 but checked fine on r-oldrel-osx-x86_64
> >>
> >> Hard to say. I think you only have a real chance to fix this if you
> >> can reproduce it on your machine.
> >>
> >> Gabor
> >>
> >> [...]
>

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