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
[[alternative HTML version deleted]]
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]]
|
| ______________________________________________
| R-devel at r-project.org mailing list
| https://stat.ethz.ch/mailman/listinfo/r-devel
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org
Dear Dirk, Thank you for the analysis and the hints. I hadn't heard of install.r but it sounds like it might be helpful for us in automated deploy situations so thanks! For now my immediate problem has been solved by switching from rcdd to Rglpk. I was afraid it would be problematic because of the system dependency on libglpk, but it seems that it gets shipped (static linked) with the binary on Windows. Is that also true on OS X? How do I know what toolchain was used to build the R I got from CRAN so that I can check this hypothesis? Best, Gert On Wed, Dec 16, 2015 at 4:28 PM, Dirk Eddelbuettel <edd at debian.org> wrote:> > 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]] > | > | ______________________________________________ > | R-devel at r-project.org mailing list > | https://stat.ethz.ch/mailman/listinfo/r-devel > -- > http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org >[[alternative HTML version deleted]]