Example script crashes R on macOS High Sierra

[jenniferthompson]

I'm on macOS 10.13.6 (High Sierra), running the code in the example vignette, and have consistently had R crash at the point in the vignette when predict_transitions() is first called. (Will include session info below.) I'm using the CRAN version of multistateutils - happy to try the development version if that would help, or stick to CRAN to help debug.

flexsurv::pmatrix.simfs() does work and gives the expected results per the vignette.

[run code in Example vignette up to this point]

> predict_transitions(models, newdata, tmat, times=365)

 *** caught illegal operation ***
address 0x10afd1a10, cause 'illegal opcode'

Traceback:
 1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states -     1, tcovs)
 2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat,     start_times, start_states - 1, tcovs))
 3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times,     start_states)
 4: state_occupancy(models, trans_mat, newdata_ext, tcovs, initial_times,     start_states, ci, M, agelimit, agecol, agescale)
 5: predict_transitions(models, newdata, tmat, times = 365)

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: 

Session info:

> devtools::session_info()
Session info ----------------------------------------------------------------------
 setting  value                       
 version  R version 3.5.0 (2018-04-23)
 system   x86_64, darwin15.6.0        
 ui       RStudio (1.1.453)           
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/Chicago             
 date     2018-08-29                  

Packages --------------------------------------------------------------------------
 package         * version date       source         
 base            * 3.5.0   2018-04-24 local          
 compiler          3.5.0   2018-04-24 local          
 data.table        1.11.4  2018-05-27 CRAN (R 3.5.0) 
 datasets        * 3.5.0   2018-04-24 local          
 deSolve           1.21    2018-05-09 CRAN (R 3.5.0) 
 devtools          1.13.6  2018-06-27 CRAN (R 3.5.0) 
 digest            0.6.15  2018-01-28 CRAN (R 3.5.0) 
 flexsurv        * 1.1     2017-03-27 CRAN (R 3.5.0) 
 graphics        * 3.5.0   2018-04-24 local          
 grDevices       * 3.5.0   2018-04-24 local          
 grid              3.5.0   2018-04-24 local          
 lattice           0.20-35 2017-03-25 CRAN (R 3.5.0) 
 magrittr          1.5     2014-11-22 CRAN (R 3.5.0) 
 Matrix            1.2-14  2018-04-13 CRAN (R 3.5.0) 
 memoise           1.1.0   2017-04-21 CRAN (R 3.5.0) 
 methods         * 3.5.0   2018-04-24 local          
 mstate          * 0.2.11  2018-04-09 CRAN (R 3.5.0) 
 muhaz             1.2.6   2014-08-09 CRAN (R 3.5.0) 
 multistateutils * 1.2.0   2018-07-21 CRAN (R 3.5.0) 
 mvtnorm           1.0-8   2018-05-31 CRAN (R 3.5.0) 
 quadprog          1.5-5   2013-04-17 CRAN (R 3.5.0) 
 RColorBrewer      1.1-2   2014-12-07 CRAN (R 3.5.0) 
 Rcpp              0.12.18 2018-07-23 cran (@0.12.18)
 splines           3.5.0   2018-04-24 local          
 stats           * 3.5.0   2018-04-24 local          
 survival        * 2.41-3  2017-04-04 CRAN (R 3.5.0) 
 tools             3.5.0   2018-04-24 local          
 utils           * 3.5.0   2018-04-24 local          
 withr             2.1.2   2018-03-15 CRAN (R 3.5.0) 
 yaml              2.1.19  2018-05-01 CRAN (R 3.5.0) 

[jenniferthompson]

Gist of exact code I've been using (copied from vignette)

This works fine for me on Ubuntu 16.04.5, matching another reviewer's experience.

[stulacy]

Hmm that's odd. I'll have a quick look at that as it worked fine on the Mac check on CRAN

[jenniferthompson]

Let me know if I can help with detective work! It seemed to install fine on my machine, though I just reinstalled and noticed this warning:

clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c simulation.cpp -o simulation.o
simulation.cpp:30:35: warning: moving a temporary object prevents copy elision [-Wpessimizing-move]
            nstate.add_transition(std::move(Transition::create_transition(trans_name, dest, as<List>(this_trans["coefs"]), tcovs)));
                                  ^
simulation.cpp:30:35: note: remove std::move call here
            nstate.add_transition(std::move(Transition::create_transition(trans_name, dest, as<List>(this_trans["coefs"]), tcovs)));
                                  ^~~~~~~~~~                                                                                     ~
1 warning generated.

[stulacy]

Can you try reinstalling from the CRAN development branch and see if that fixes it? If not, try reinstalling the data.table package as that could be partly causing it.

[jenniferthompson]

Installing the development branch seems to have done it! All the multistateutils functions in the Examples document run on my machine now. 🎉