MarcLavielle
commented
5 years ago I don't know... this may happen if you have several versions of R installed on your computer (/Library/Frameworks/R.framework/Versions/) If that's the case, just keep one best, Marc
Le mer. 6 févr. 2019 à 21:22, Bryan Mayer notifications@github.com a écrit :
I was trying to run the tutorial code for using simulx http://monolix.lixoft.com/case-studies/tobramycin-case-study-part-5-dosing-regimen-simulations-with-simulx/ (downloaded the project scripts from this link http://dataset.lixoft.com/filesToWebsite/caseStudies/01_Tobramycin/simulx_forWebsite.zip) and it crashed my R session.
Code and error as follows:
setwd("~/simulx_forWebsite/simulx/")
library(mlxR)
Loading required package: ggplot2
project.file <- '../monolixProjects/project_07.mlxtran'
res1 <- simulx(project = project.file)
caught segfault
address 0x18, cause 'memory not mapped'
Traceback:
1: simulxunit(model = model, lv = lv, settings = settings, out.trt = out.trt, riov = riov)
2: simulx(project = project.file)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
(RStudio crashed without providing an error.)
I dug a little deeper using lldb
(lldb) process attach --name rsession --waitfor
libR.dylib was compiled with optimization - stepping may behave oddly; variables may not be available.
Process 24593 stopped
thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGSTOP
frame #0: 0x0000000101262f9b libR.dylib`R_Parse1File at gram.c:3534 [opt]
Target 0: (rsession) stopped.
Executable module set to "/Applications/RStudio.app/Contents/MacOS/rsession".
Architecture set to: x86_64h-apple-macosx.
(lldb) c
Process 24593 resuming
libR.dylib was compiled with optimization - stepping may behave oddly; variables may not be available.
Process 24593 stopped
thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x18)
frame #0: 0x000000010da37022 libR.dylib`GetNewPage(node_class=
) at memory.c:895 [opt] Target 0: (rsession) stopped.
(lldb) bt
thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x18)
- frame #0: 0x000000010da37022 libR.dylib`GetNewPage(node_class=
) at memory.c:895 [opt] frame #1: 0x000000010da3bad2 libR.dylib`Rf_allocVector3(type=13, length=
, allocator= ) at memory.c:2486 [opt] frame #2: 0x000000010d907d4f libR.dylib`get_package_CEntry_table [inlined] Rf_allocVector(type=13, length=1) at Rinlinedfuns.h:196 [opt]
frame #3: 0x000000010d907d4a libR.dylib`get_package_CEntry_table [inlined] Rf_ScalarInteger(x=0) at Rinlinedfuns.h:594 [opt]
frame #4: 0x000000010d907d4a libR.dylib`get_package_CEntry_table(package="Rcpp") at Rdynload.c:1415 [opt]
frame #5: 0x000000010d907e06 libR.dylib`R_GetCCallable(package="Rcpp", name="enterRNGScope") at Rdynload.c:1440 [opt]
frame #6: 0x000000010bee609e mlxComputeR.so`mlxComputeR + 78
frame #7: 0x000000010120d48d libR.dylib`R_doDotCall(ofun=
, nargs= , cargs= , call=0x000000010726c288) at dotcode.c:570 [opt] frame #8: 0x000000010120f333 libR.dylib`do_dotcall(call=0x000000010726c288, op=
, args= , env= ) at dotcode.c:1252 [opt] frame #9: 0x00000001012428de libR.dylib`bcEval(body=
, rho=0x00000001072705d0, useCache= ) at eval.c:6738 [opt] frame #10: 0x000000010123d7db libR.dylib`Rf_eval(e=
, rho= ) at eval.c:624 [opt] frame #11: 0x000000010125014c libR.dylib`R_execClosure(call=0x0000000108fab0b8, newrho=0x00000001072705d0, sysparent=
, rho= , arglist= , op= ) at eval.c:0 [opt] frame #12: 0x00000001012427f3 libR.dylib`bcEval(body=
, rho=0x000000010ca5dd58, useCache= ) at eval.c:6749 [opt] frame #13: 0x000000010123d7db libR.dylib`Rf_eval(e=
, rho= ) at eval.c:624 [opt] frame #14: 0x000000010125014c libR.dylib`R_execClosure(call=0x000000010ca140e8, newrho=0x000000010ca5dd58, sysparent=
, rho= , arglist= , op= ) at eval.c:0 [opt] frame #15: 0x000000010123dd0c libR.dylib`Rf_eval(e=0x000000010ca143c0, rho=0x0000000102046198) at eval.c:747 [opt]
frame #16: 0x0000000101253169 libR.dylib`do_set(call=
, op=0x0000000102802ee8, args=0x000000010ca14350, rho=0x0000000102046198) at eval.c:2787 [opt] frame #17: 0x000000010123d9ce libR.dylib`Rf_eval(e=
, rho=0x0000000102046198) at eval.c:699 [opt] frame #18: 0x0000000101280bda libR.dylib`Rf_ReplIteration(rho=0x0000000102046198, savestack=
, browselevel=0, state=0x00007ffeefbfc8b0) at main.c:258 [opt] frame #19: 0x00000001012821bf libR.dylib`run_Rmainloop [inlined] R_ReplConsole(rho=
, savestack=0, browselevel=0) at main.c:308 [opt] frame #20: 0x0000000101282156 libR.dylib`run_Rmainloop at main.c:1082 [opt]
frame #21: 0x00000001008522f9 rsession`rstudio::r::session::runEmbeddedR(rstudio::core::FilePath const&, rstudio::core::FilePath const&, bool, bool, SA_TYPE, rstudio::r::session::Callbacks const&, rstudio::r::session::InternalCallbacks*) + 425
frame #22: 0x00000001008312fc rsession`rstudio::r::session::run(rstudio::r::session::ROptions const&, rstudio::r::session::RCallbacks const&) + 3164
frame #23: 0x0000000100109063 rsession`main + 28963
frame #24: 0x0000000100003cb4 rsession`start + 52
My session info prior to running the code:
library(mlxR)
Loading required package: ggplot2
devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
setting value
version R version 3.5.1 (2018-07-02)
os macOS 10.14.3
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Los_Angeles
date 2019-02-06
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.0 2017-04-11 [1] CRAN (R 3.5.0)
backports 1.1.3 2018-12-14 [1] CRAN (R 3.5.0)
bindr 0.1.1 2018-03-13 [1] CRAN (R 3.5.0)
bindrcpp 0.2.2 2018-03-29 [1] CRAN (R 3.5.0)
callr 3.1.1 2018-12-21 [1] CRAN (R 3.5.0)
cli 1.0.1 2018-09-25 [1] CRAN (R 3.5.0)
colorspace 1.4-0 2019-01-13 [1] CRAN (R 3.5.2)
crayon 1.3.4 2017-09-16 [1] CRAN (R 3.5.0)
desc 1.2.0 2018-05-01 [1] CRAN (R 3.5.0)
devtools 2.0.1 2018-10-26 [1] CRAN (R 3.5.1)
digest 0.6.18 2018-10-10 [1] CRAN (R 3.5.0)
dplyr 0.7.8 2018-11-10 [1] CRAN (R 3.5.1)
fs 1.2.6 2018-08-23 [1] CRAN (R 3.5.0)
ggplot2 * 3.1.0 2018-10-25 [1] CRAN (R 3.5.1)
glue 1.3.0 2018-07-17 [1] CRAN (R 3.5.0)
gtable 0.2.0 2016-02-26 [1] CRAN (R 3.5.0)
lazyeval 0.2.1 2017-10-29 [1] CRAN (R 3.5.0)
magrittr 1.5 2014-11-22 [1] CRAN (R 3.5.0)
memoise 1.1.0 2017-04-21 [1] CRAN (R 3.5.0)
mlxR * 3.3.0 2018-02-20 [1] CRAN (R 3.5.1)
munsell 0.5.0 2018-06-12 [1] CRAN (R 3.5.0)
pillar 1.3.1 2018-12-15 [1] CRAN (R 3.5.0)
pkgbuild 1.0.2 2018-10-16 [1] CRAN (R 3.5.0)
pkgconfig 2.0.2 2018-08-16 [1] CRAN (R 3.5.0)
pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.5.0)
plyr 1.8.4 2016-06-08 [1] CRAN (R 3.5.0)
prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.5.0)
processx 3.2.1 2018-12-05 [1] CRAN (R 3.5.0)
ps 1.3.0 2018-12-21 [1] CRAN (R 3.5.0)
purrr 0.3.0 2019-01-27 [1] CRAN (R 3.5.2)
R6 2.3.0 2018-10-04 [1] CRAN (R 3.5.0)
Rcpp 1.0.0 2018-11-07 [1] CRAN (R 3.5.1)
remotes 2.0.2 2018-10-30 [1] CRAN (R 3.5.0)
rlang 0.3.1 2019-01-08 [1] CRAN (R 3.5.2)
rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.5.0)
scales 1.0.0 2018-08-09 [1] CRAN (R 3.5.0)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.5.0)
testthat 2.0.1 2018-10-13 [1] CRAN (R 3.5.0)
tibble 2.0.1 2019-01-12 [1] CRAN (R 3.5.2)
tidyselect 0.2.5 2018-10-11 [1] CRAN (R 3.5.0)
usethis 1.4.0 2018-08-14 [1] CRAN (R 3.5.0)
withr 2.1.2 2018-03-15 [1] CRAN (R 3.5.0)
XML 3.98-1.16 2018-08-19 [1] CRAN (R 3.5.1)
[1] /Library/Frameworks/R.framework/Versions/3.5/Resources/library
It is possible that this is a mac-related compiler issue on my end but I also want to make sure this isn't a memory bug resulting from the Mojave release of macOS.
Thanks, Bryan
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-- Marc Lavielle
CMAP, Ecole Polytechnique91128 Palaiseau Cedex
Francehttps://soutienvenezuela.org/en/ Tel: (33) 1 69 33 46 00 (33) 6 37 31 93 05
Marc.Lavielle@inria.fr http://www.cmap.polytechnique.fr/~lavielle
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mayerbry
I was trying to run the tutorial code for using simulx (downloaded the project scripts from this link) and it crashed my R session.
Code and error as follows:
(RStudio crashed without providing an error.)
I dug a little deeper using
lldbMy session info prior to running the code:
It is possible that this is a mac-related compiler issue on my end but I also want to make sure this isn't a memory bug resulting from the Mojave release of macOS.
Thanks, Bryan