Gert,
On 16 December 2015 at 12:06, Gert van Valkenhoef wrote:
| 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
I wish I could tell you something more encouraging -- but this _sometimes_
happens with prebuilt R, or prebuilt packages. We try try chase this, and
when we do batch runs of R CMD check over all reverse depends we end up
rebuilding.
I was just bitten by this when upgrading to Ubuntu 15.10 as it brings in
g++-5.2 which has a _known_ ABI transition for C++11/14. About 15% of
packages got 'random' (but repeatable) seg.faults when there were none
before. And that went away with a proper R version also built with a gcc-5.2
toolchain.
So in short: check your toolchain. Things may then go away. If they don't
then there may be a real bug.
| 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
[ I am mildly opposed to ~/R. I unset R_LIBS_USER in /etc/R/Renviron and just
make sure I am part of the group owning /usr/local/lib/R/site-library. Then
an ordinary users can install there. ]
| 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'))"
[ I am very partial to using 'install.r devtools igraph meta truncnorm rcdd'
on the command-line where install.r is a part of r-cran-littler, or littler
now on CRAN, which I link into /usr/local/bin. ]
| 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
We have a dedicated list for running R on Debian/Ubuntu/... systems:
r-sig-debian. Consider lurking/posting there.
Cheers, Dirk
| 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
|
| [[alternative HTML version deleted]]
|
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--
http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
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