From g.h.m.van.valkenhoef at rug.nl  Wed Dec 16 12:06:51 2015
From: g.h.m.van.valkenhoef at rug.nl (Gert van Valkenhoef)
Date: Wed, 16 Dec 2015 12:06:51 +0100
Subject: [Rd] Mystifying SEGFAULT on 3.2.3 but not 3.2.2
Message-ID: <CAGB9c4B3KFGWd371+7DJb84zKw3X3L28qtSyappPY9CZA57y2w@mail.gmail.com>

Dear R developers,

(Apologies about previous incomplete e-mail, I fat-fingered a keyboard
shortcut)??

I recently upgraded to 3.2.3 and am getting mystifying errors with my
in-development code (available at
https://github.com/gertvv/gemtc/tree/feature/regression). Every few hundred
LPs that I solve using the rcdd package will result in a SEGFAULT in the
garbage collector (address 0x10, cause 'memory not mapped') or an error
about a list not existing. Downgrading to 3.2.2 works, but *only* after
completely removing my local R packages and re-installing them. A
subsequent upgrade to 3.2.3 will again be broken, and even more
mysteriously it will also break a re-downgrade to 3.2.2 until I again purge
my local packages and re-install them.

To downgrade I am using (with the CRAN ubuntu mirror enabled):
sudo apt-get purge r-base-core
sudo rm -rf ~/R
sudo apt-get install r-base-core=3.2.2-1trusty0 r-base-dev=3.2.2-1trusty0
r-recommended=3.2.2-1trusty0
sudo apt-get install r-cran-rjags
R -e "install.packages(c('devtools','igraph','meta','truncnorm','rcdd'))"

The code that produces a SEGFAULT (usually after 5-15 iterations) under
3.2.3, but not 3.2.2:
library(devtools)
load_all('gemtc')
for (i in 1:100) { print(i); mtc.model(thrombolytic) }
(note that the SEGFAULT also happens without devtools)

The sessionInfo() in 3.2.2:

R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=nl_NL.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=nl_NL.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=nl_NL.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=nl_NL.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] gemtc_0.8       coda_0.16-1     lattice_0.20-33 devtools_1.9.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.2     roxygen2_5.0.1  rcdd_1.1-9      digest_0.6.8
 [5] truncnorm_1.0-7 grid_3.2.2      plyr_1.8.3      meta_4.3-2
 [9] magrittr_1.5    stringi_1.0-1   rjags_4-4       tools_3.2.2
[13] stringr_1.0.0   igraph_1.0.1    memoise_0.2.1

A core dump is here:
https://drive.google.com/a/rug.nl/file/d/0BxhVLNPmwLrycTYtOHNxNXZTMEk/view?usp=drive_web

I have tried debugging this but am stumped. Any help would be greatly
appreciated!

Kind regards,

Gert van Valkenhoef

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[Rd] Mystifying SEGFAULT on 3.2.3 but not 3.2.2
Gert van Valkenhoef