<div dir="ltr">Dear Andreas, <div><br></div><div>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. </div><div><br></div><div>Do you know of any other issues with RGL? Maybe a problem with libglu dependencies?</div><div>For what it's worth, these are the pkg installed on my system:</div><div>libglu1-mesa:amd64 <br></div><div><div>libglu1-mesa:i386 </div><div>libglu1-mesa-dev </div></div><div><br></div><div>In the log you posted, I cannot see libglu1-mesa-dev. Sorry, this is mostly guesswork here..</div><div><br></div><div>Can you try installing the package from R directly rather than via apt?</div><div><br></div><div>Cheers</div><div>Thibaut</div><div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><div><div><br>--<br>Dr Thibaut Jombart<br>Lecturer, Department of Infectious Disease Epidemiology, <span style="font-size:12.8px">Imperial College London</span></div></div><div><span style="font-size:12.8px">Head of RECON: </span><span style="font-size:12.8px"><a href="http://repidemicsconsortium.org" target="_blank">repidemicsconsortium.org</a></span><br></div></div><div><a href="http://sites.google.com/site/thibautjombart/" style="font-size:12.8px" target="_blank">sites.google.com/site/thibautjombart/</a><br></div><div><a href="http://github.com/thibautjombart" target="_blank">github.com/thibautjombart</a></div>Twitter: <a href="http://twitter.com/TeebzR" target="_blank">@TeebzR</a><br></div><div dir="ltr">+44(0)20 7594 3658</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
<br><div class="gmail_quote">On 8 December 2016 at 19:09, Andreas Tille <span dir="ltr"><<a href="mailto:andreas@an3as.eu" target="_blank">andreas@an3as.eu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Thibaut,<br>
<br>
thanks a lot for the pointer to a potential solution of the problem.<br>
<br>
On Fri, Dec 02, 2016 at 11:41:09PM +0100, Andreas Tille wrote:<br>
><br>
> It would be quite convenient to have a downloadable tarball from CRAN<br>
> mirror since this fits the usual workflow. If this is not possible I'd<br>
> consider<br>
><br>
> <a href="https://github.com/thibautjombart/treescape/commit/bbd3f0e9c627f04daf21725c02ab8e7c69d61f8f" rel="noreferrer" target="_blank">https://github.com/<wbr>thibautjombart/treescape/<wbr>commit/<wbr>bbd3f0e9c627f04daf21725c02ab8e<wbr>7c69d61f8f</a><br>
><br>
> as a patch to the packaging.<br>
<br>
I tried to find the essential change of this patch ignoring all<br>
autogenerated files I considered (possibly wrongly) the follwing<br>
patch:<br>
<br>
<a href="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" rel="noreferrer" target="_blank">https://anonscm.debian.org/<wbr>viewvc/debian-med/trunk/<wbr>packages/R/r-cran-treescape/<wbr>trunk/debian/patches/0001-<wbr>fixing-issue-with-new-release-<wbr>of-ape.patch?view=markup</a><br>
<br>
I uploaded the package including the patch but the problematic build<br>
issue remains. While I admit that I have no idea about R internals<br>
nor what ape is doing I somehow can not understand in how far the<br>
error:<br>
<br>
...<br>
** preparing package for lazy loading<br>
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'<br>
Warning in rgl.init(initValue, onlyNULL) :<br>
RGL: unable to open X11 display<br>
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE<br>
Error: segfault from C stack overflow<br>
* removing '/«PKGBUILDDIR»/debian/r-cran-<wbr>treescape/usr/lib/R/site-<wbr>library/treescape'<br>
...<br>
<br>
should be related. The full build log is available online<br>
<br>
<a href="https://buildd.debian.org/status/fetch.php?pkg=r-cran-treescape&arch=i386&ver=1.10.17-2&stamp=1481212918" rel="noreferrer" target="_blank">https://buildd.debian.org/<wbr>status/fetch.php?pkg=r-cran-<wbr>treescape&arch=i386&ver=1.10.<wbr>17-2&stamp=1481212918</a><br>
<br>
the critical part is quite at the end.<br>
<br>
Kind regards<br>
<span class="HOEnZb"><font color="#888888"><br>
Andreas.<br>
<br>
--<br>
<a href="http://fam-tille.de" rel="noreferrer" target="_blank">http://fam-tille.de</a><br>
</font></span></blockquote></div><br></div>