[R-sig-Debian] Segfault from c2d4u binary of RandomFields

Dirk Eddelbuettel edd @end|ng |rom deb|@n@org
Sat Jan 8 23:10:51 CET 2022

On 8 January 2022 at 20:40, Ege Rubak wrote:
| Hi everyone,
| For some time the GitHub Action of spatstat.core has been failing due
| to a segfault when calling RandomFields (which calls RandomFieldsUtils
| which may be causing the acutal segfault):
| https://github.com/spatstat/spatstat.core/runs/4739596930?check_suite_focus=true#step:6:387
| I tried changing the action to install a source version of RandomField
| and RandomFieldsUtils over the binary c2d4u version and the action now
| continues smoothly without any segfault:
| https://github.com/spatstat/spatstat.core/runs/4749470559?check_suite_focus=true
| Does anyone know why the segfault only happens with the c2d4u version
| (Michael and Dirk are probably good guesses, but maybe someone else is
| listening out there and can take some workload off their shoulders...)
| I'm happy to investigate further and produce a more minimal
| reproducible example, but I will not go down the rabbit hole for now if
| someone already now knows what the problem is and how it should be
| fixed.
| A (not so minimal) reproducible example is to install both
| RandomFields, RandomFieldsUtils and spatstat.core from c2d4u and then
| run the following in R (this segfaults, so consider yourself warned):
| library(spatstat.core)
| example(kppm)

The geo stack is complicated. I have no pointers.  But on the Debian testing
machine (i.e. something "close" your Ubuntu setup) I use for Rcpp reverse
depends, I recently recompiled an entire stack "in bulk and anger" simply
because I could not pin-point where such a segfault came from.

What you could is try to mimick the Actions setup (by starting with a Ubuntu
20.04 container, Rocker has some as eg rocker/r-ubuntu:20.04 giving you a
head).  You can then start to replace .deb by .deb by hand-compiling and see
which one is 'guilty'. Michael could then rebuild that .deb.

Sadly I do not know of any other shortcuts.

Best, Dirk

https://dirk.eddelbuettel.com | @eddelbuettel | edd using debian.org

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