[Debian-med-packaging] Bug#845753: Treescape fails to build on i386 and armhf architecture

[Thibaut Jombart]

Dear Andreas,

unfortunately it looks like a rgl error, which I cannot help with. There
was a problem triggered by a change in the ape package, but this is now
fixed and on CRAN (the package update went through yesterday). I think it
was a separate issue anyway.

Do you know of any other issues with RGL? Maybe a problem with libglu
dependencies?
For what it's worth, these are the pkg installed on my system:
libglu1-mesa:amd64
libglu1-mesa:i386
libglu1-mesa-dev

In the log you posted, I cannot see libglu1-mesa-dev. Sorry, this is mostly
guesswork here..

Can you try installing the package from R directly rather than via apt?

Cheers
Thibaut



--
Dr Thibaut Jombart
Lecturer, Department of Infectious Disease Epidemiology, Imperial College
London
Head of RECON: repidemicsconsortium.org
sites.google.com/site/thibautjombart/
github.com/thibautjombart
Twitter: @TeebzR <http://twitter.com/TeebzR>
+44(0)20 7594 3658

On 8 December 2016 at 19:09, Andreas Tille <andreas at an3as.eu> wrote:

> Hi Thibaut,
>
> thanks a lot for the pointer to a potential solution of the problem.
>
> On Fri, Dec 02, 2016 at 11:41:09PM +0100, Andreas Tille wrote:
> >
> > It would be quite convenient to have a downloadable tarball from CRAN
> > mirror since this fits the usual workflow.  If this is not possible I'd
> > consider
> >
> >    https://github.com/thibautjombart/treescape/commit/
> bbd3f0e9c627f04daf21725c02ab8e7c69d61f8f
> >
> > as a patch to the packaging.
>
> I tried to find the essential change of this patch ignoring all
> autogenerated files I considered (possibly wrongly) the follwing
> patch:
>
>      https://anonscm.debian.org/viewvc/debian-med/trunk/
> packages/R/r-cran-treescape/trunk/debian/patches/0001-
> fixing-issue-with-new-release-of-ape.patch?view=markup
>
> I uploaded the package including the patch but the problematic build
> issue remains.  While I admit that I have no idea about R internals
> nor what ape is doing I somehow can not understand in how far the
> error:
>
> ...
> ** preparing package for lazy loading
> Creating a generic function for 'toJSON' from package 'jsonlite' in
> package 'googleVis'
> Warning in rgl.init(initValue, onlyNULL) :
>   RGL: unable to open X11 display
> Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
> Error: segfault from C stack overflow
> * removing '/«PKGBUILDDIR»/debian/r-cran-treescape/usr/lib/R/site-
> library/treescape'
> ...
>
> should be related.  The full build log is available online
>
>   https://buildd.debian.org/status/fetch.php?pkg=r-cran-
> treescape&arch=i386&ver=1.10.17-2&stamp=1481212918
>
> the critical part is quite at the end.
>
> Kind regards
>
>      Andreas.
>
> --
> http://fam-tille.de
>
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