--- re-building ‘features.Rmd’ using rmarkdown /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23: runtime error: nan is outside the range of representable values of type 'int' #0 0x7fbaff53ca56 in tmbutils::matrix asMatrix(SEXPREC*) /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23 #1 0x7fbaff6492e4 in objective_function::operator()() /data/gannet/ripley/R/packages/tests-clang-UBSAN/dsem/src/dsem.cpp:92:3 #2 0x7fbaff29721e in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7 #3 0x55a36da7f0c5 in R_doDotCall (/data/gannet/ripley/R/R-clang/bin/exec/R+0x8f0c5) #4 0x55a36da8127d in do_dotcall (/data/gannet/ripley/R/R-clang/bin/exec/R+0x9127d) #5 0x55a36dabfb73 in bcEval_loop eval.c #6 0x55a36dab913b in bcEval eval.c #7 0x55a36dab88f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #8 0x55a36dad0a58 in R_execClosure eval.c #9 0x55a36dacff4a in applyClosure_core eval.c #10 0x55a36dab9816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #11 0x55a36dab8d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #12 0x55a36dad5db7 in do_set (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe5db7) #13 0x55a36dab8b1f in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8b1f) #14 0x55a36dad7227 in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7227) #15 0x55a36dabfb73 in bcEval_loop eval.c #16 0x55a36dab913b in bcEval eval.c #17 0x55a36dab88f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #18 0x55a36dab9393 in forcePromise eval.c #19 0x55a36dab89bd in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc89bd) #20 0x55a36dad7706 in do_withVisible (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7706) #21 0x55a36db1afc7 in do_internal (/data/gannet/ripley/R/R-clang/bin/exec/R+0x12afc7) #22 0x55a36dabfdd5 in bcEval_loop eval.c #23 0x55a36dab913b in bcEval eval.c #24 0x55a36dab88f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #25 0x55a36dab9393 in forcePromise eval.c #26 0x55a36dab89bd in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc89bd) #27 0x55a36dab9393 in forcePromise eval.c #28 0x55a36daccebf in getvar eval.c #29 0x55a36dabd578 in bcEval_loop eval.c #30 0x55a36dab913b in bcEval eval.c #31 0x55a36dab88f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #32 0x55a36dad0a58 in R_execClosure eval.c #33 0x55a36dacff4a in applyClosure_core eval.c #34 0x55a36dab9816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #35 0x55a36dab8d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #36 0x55a36dad7227 in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7227) #37 0x55a36dabfb73 in bcEval_loop eval.c #38 0x55a36dab913b in bcEval eval.c #39 0x55a36dab88f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #40 0x55a36dad0a58 in R_execClosure eval.c #41 0x55a36dacff4a in applyClosure_core eval.c #42 0x55a36dab9816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #43 0x55a36dab8d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #44 0x55a36dad0a58 in R_execClosure eval.c #45 0x55a36dacff4a in applyClosure_core eval.c #46 0x55a36dabf405 in bcEval_loop eval.c #47 0x55a36dab913b in bcEval eval.c #48 0x55a36dab88f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #49 0x55a36dad0a58 in R_execClosure eval.c #50 0x55a36dacff4a in applyClosure_core eval.c #51 0x55a36dab9816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #52 0x55a36dab8d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #53 0x55a36db05f37 in Rf_ReplIteration (/data/gannet/ripley/R/R-clang/bin/exec/R+0x115f37) #54 0x55a36db07a3e in run_Rmainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x117a3e) #55 0x55a36db07aaa in Rf_mainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x117aaa) #56 0x55a36d9f1db7 in main (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1db7) #57 0x7fbb13e12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #58 0x7fbb13e12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #59 0x55a36d9f1cd4 in _start (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1cd4) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23 Read 3 items Read 4 records --- finished re-building ‘features.Rmd’ --- re-building ‘model-description.Rmd’ using rmarkdown /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23: runtime error: nan is outside the range of representable values of type 'int' #0 0x7ff898b3ca56 in tmbutils::matrix asMatrix(SEXPREC*) /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23 #1 0x7ff898c492e4 in objective_function::operator()() /data/gannet/ripley/R/packages/tests-clang-UBSAN/dsem/src/dsem.cpp:92:3 #2 0x7ff89889721e in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7 #3 0x55e96d9e70c5 in R_doDotCall (/data/gannet/ripley/R/R-clang/bin/exec/R+0x8f0c5) #4 0x55e96d9e927d in do_dotcall (/data/gannet/ripley/R/R-clang/bin/exec/R+0x9127d) #5 0x55e96da27b73 in bcEval_loop eval.c #6 0x55e96da2113b in bcEval eval.c #7 0x55e96da208f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #8 0x55e96da38a58 in R_execClosure eval.c #9 0x55e96da37f4a in applyClosure_core eval.c #10 0x55e96da21816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #11 0x55e96da20d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #12 0x55e96da3ddb7 in do_set (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe5db7) #13 0x55e96da20b1f in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8b1f) #14 0x55e96da3f227 in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7227) #15 0x55e96da27b73 in bcEval_loop eval.c #16 0x55e96da2113b in bcEval eval.c #17 0x55e96da208f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #18 0x55e96da21393 in forcePromise eval.c #19 0x55e96da209bd in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc89bd) #20 0x55e96da3f706 in do_withVisible (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7706) #21 0x55e96da82fc7 in do_internal (/data/gannet/ripley/R/R-clang/bin/exec/R+0x12afc7) #22 0x55e96da27dd5 in bcEval_loop eval.c #23 0x55e96da2113b in bcEval eval.c #24 0x55e96da208f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #25 0x55e96da21393 in forcePromise eval.c #26 0x55e96da209bd in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc89bd) #27 0x55e96da21393 in forcePromise eval.c #28 0x55e96da34ebf in getvar eval.c #29 0x55e96da25578 in bcEval_loop eval.c #30 0x55e96da2113b in bcEval eval.c #31 0x55e96da208f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #32 0x55e96da38a58 in R_execClosure eval.c #33 0x55e96da37f4a in applyClosure_core eval.c #34 0x55e96da21816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #35 0x55e96da20d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #36 0x55e96da3f227 in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7227) #37 0x55e96da27b73 in bcEval_loop eval.c #38 0x55e96da2113b in bcEval eval.c #39 0x55e96da208f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #40 0x55e96da38a58 in R_execClosure eval.c #41 0x55e96da37f4a in applyClosure_core eval.c #42 0x55e96da21816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #43 0x55e96da20d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #44 0x55e96da38a58 in R_execClosure eval.c #45 0x55e96da37f4a in applyClosure_core eval.c #46 0x55e96da27405 in bcEval_loop eval.c #47 0x55e96da2113b in bcEval eval.c #48 0x55e96da208f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #49 0x55e96da38a58 in R_execClosure eval.c #50 0x55e96da37f4a in applyClosure_core eval.c #51 0x55e96da21816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #52 0x55e96da20d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #53 0x55e96da6df37 in Rf_ReplIteration (/data/gannet/ripley/R/R-clang/bin/exec/R+0x115f37) #54 0x55e96da6fa3e in run_Rmainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x117a3e) #55 0x55e96da6faaa in Rf_mainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x117aaa) #56 0x55e96d959db7 in main (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1db7) #57 0x7ff8ad412574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #58 0x7ff8ad412627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #59 0x55e96d959cd4 in _start (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1cd4) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23 --- finished re-building ‘model-description.Rmd’ --- re-building ‘nonlinear.Rmd’ using rmarkdown /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23: runtime error: nan is outside the range of representable values of type 'int' #0 0x7f42c413ca56 in tmbutils::matrix asMatrix(SEXPREC*) /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23 #1 0x7f42c42492e4 in objective_function::operator()() /data/gannet/ripley/R/packages/tests-clang-UBSAN/dsem/src/dsem.cpp:92:3 #2 0x7f42c3e9721e in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7 #3 0x5620c783b0c5 in R_doDotCall (/data/gannet/ripley/R/R-clang/bin/exec/R+0x8f0c5) #4 0x5620c783d27d in do_dotcall (/data/gannet/ripley/R/R-clang/bin/exec/R+0x9127d) #5 0x5620c787bb73 in bcEval_loop eval.c #6 0x5620c787513b in bcEval eval.c #7 0x5620c78748f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #8 0x5620c788ca58 in R_execClosure eval.c #9 0x5620c788bf4a in applyClosure_core eval.c #10 0x5620c7875816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #11 0x5620c7874d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #12 0x5620c7891db7 in do_set (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe5db7) #13 0x5620c7874b1f in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8b1f) #14 0x5620c7893227 in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7227) #15 0x5620c787bb73 in bcEval_loop eval.c #16 0x5620c787513b in bcEval eval.c #17 0x5620c78748f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #18 0x5620c7875393 in forcePromise eval.c #19 0x5620c78749bd in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc89bd) #20 0x5620c7893706 in do_withVisible (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7706) #21 0x5620c78d6fc7 in do_internal (/data/gannet/ripley/R/R-clang/bin/exec/R+0x12afc7) #22 0x5620c787bdd5 in bcEval_loop eval.c #23 0x5620c787513b in bcEval eval.c #24 0x5620c78748f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #25 0x5620c7875393 in forcePromise eval.c #26 0x5620c78749bd in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc89bd) #27 0x5620c7875393 in forcePromise eval.c #28 0x5620c7888ebf in getvar eval.c #29 0x5620c7879578 in bcEval_loop eval.c #30 0x5620c787513b in bcEval eval.c #31 0x5620c78748f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #32 0x5620c788ca58 in R_execClosure eval.c #33 0x5620c788bf4a in applyClosure_core eval.c #34 0x5620c7875816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #35 0x5620c7874d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #36 0x5620c7893227 in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7227) #37 0x5620c787bb73 in bcEval_loop eval.c #38 0x5620c787513b in bcEval eval.c #39 0x5620c78748f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #40 0x5620c788ca58 in R_execClosure eval.c #41 0x5620c788bf4a in applyClosure_core eval.c #42 0x5620c7875816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #43 0x5620c7874d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #44 0x5620c788ca58 in R_execClosure eval.c #45 0x5620c788bf4a in applyClosure_core eval.c #46 0x5620c787b405 in bcEval_loop eval.c #47 0x5620c787513b in bcEval eval.c #48 0x5620c78748f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #49 0x5620c788ca58 in R_execClosure eval.c #50 0x5620c788bf4a in applyClosure_core eval.c #51 0x5620c7875816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #52 0x5620c7874d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #53 0x5620c78c1f37 in Rf_ReplIteration (/data/gannet/ripley/R/R-clang/bin/exec/R+0x115f37) #54 0x5620c78c3a3e in run_Rmainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x117a3e) #55 0x5620c78c3aaa in Rf_mainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x117aaa) #56 0x5620c77addb7 in main (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1db7) #57 0x7f42d8a12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #58 0x7f42d8a12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #59 0x5620c77adcd4 in _start (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1cd4) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23 --- finished re-building ‘nonlinear.Rmd’ --- re-building ‘random_slopes.Rmd’ using rmarkdown /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23: runtime error: nan is outside the range of representable values of type 'int' #0 0x7f3caa53ca56 in tmbutils::matrix asMatrix(SEXPREC*) /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23 #1 0x7f3caa6492e4 in objective_function::operator()() /data/gannet/ripley/R/packages/tests-clang-UBSAN/dsem/src/dsem.cpp:92:3 #2 0x7f3caa29721e in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7 #3 0x56102f2ce0c5 in R_doDotCall (/data/gannet/ripley/R/R-clang/bin/exec/R+0x8f0c5) #4 0x56102f2d027d in do_dotcall (/data/gannet/ripley/R/R-clang/bin/exec/R+0x9127d) #5 0x56102f30eb73 in bcEval_loop eval.c #6 0x56102f30813b in bcEval eval.c #7 0x56102f3078f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #8 0x56102f31fa58 in R_execClosure eval.c #9 0x56102f31ef4a in applyClosure_core eval.c #10 0x56102f308816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #11 0x56102f307d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #12 0x56102f324db7 in do_set (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe5db7) #13 0x56102f307b1f in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8b1f) #14 0x56102f326227 in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7227) #15 0x56102f30eb73 in bcEval_loop eval.c #16 0x56102f30813b in bcEval eval.c #17 0x56102f3078f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #18 0x56102f308393 in forcePromise eval.c #19 0x56102f3079bd in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc89bd) #20 0x56102f326706 in do_withVisible (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7706) #21 0x56102f369fc7 in do_internal (/data/gannet/ripley/R/R-clang/bin/exec/R+0x12afc7) #22 0x56102f30edd5 in bcEval_loop eval.c #23 0x56102f30813b in bcEval eval.c #24 0x56102f3078f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #25 0x56102f308393 in forcePromise eval.c #26 0x56102f3079bd in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc89bd) #27 0x56102f308393 in forcePromise eval.c #28 0x56102f31bebf in getvar eval.c #29 0x56102f30c578 in bcEval_loop eval.c #30 0x56102f30813b in bcEval eval.c #31 0x56102f3078f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #32 0x56102f31fa58 in R_execClosure eval.c #33 0x56102f31ef4a in applyClosure_core eval.c #34 0x56102f308816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #35 0x56102f307d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #36 0x56102f326227 in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7227) #37 0x56102f30eb73 in bcEval_loop eval.c #38 0x56102f30813b in bcEval eval.c #39 0x56102f3078f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #40 0x56102f31fa58 in R_execClosure eval.c #41 0x56102f31ef4a in applyClosure_core eval.c #42 0x56102f308816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #43 0x56102f307d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #44 0x56102f31fa58 in R_execClosure eval.c #45 0x56102f31ef4a in applyClosure_core eval.c #46 0x56102f30e405 in bcEval_loop eval.c #47 0x56102f30813b in bcEval eval.c #48 0x56102f3078f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #49 0x56102f31fa58 in R_execClosure eval.c #50 0x56102f31ef4a in applyClosure_core eval.c #51 0x56102f308816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #52 0x56102f307d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #53 0x56102f354f37 in Rf_ReplIteration (/data/gannet/ripley/R/R-clang/bin/exec/R+0x115f37) #54 0x56102f356a3e in run_Rmainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x117a3e) #55 0x56102f356aaa in Rf_mainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x117aaa) #56 0x56102f240db7 in main (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1db7) #57 0x7f3cbee12574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #58 0x7f3cbee12627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #59 0x56102f240cd4 in _start (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1cd4) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23 --- finished re-building ‘random_slopes.Rmd’ --- re-building ‘spatial_diffusion.Rmd’ using rmarkdown Read 21 records /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23: runtime error: nan is outside the range of representable values of type 'int' #0 0x7f5fcb33ca56 in tmbutils::matrix asMatrix(SEXPREC*) /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23 #1 0x7f5fcb4492e4 in objective_function::operator()() /data/gannet/ripley/R/packages/tests-clang-UBSAN/dsem/src/dsem.cpp:92:3 #2 0x7f5fcb09721e in getParameterOrder /data/gannet/ripley/R/test-clang/TMB/include/tmb_core.hpp:2065:7 #3 0x55726775a0c5 in R_doDotCall (/data/gannet/ripley/R/R-clang/bin/exec/R+0x8f0c5) #4 0x55726775c27d in do_dotcall (/data/gannet/ripley/R/R-clang/bin/exec/R+0x9127d) #5 0x55726779ab73 in bcEval_loop eval.c #6 0x55726779413b in bcEval eval.c #7 0x5572677938f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #8 0x5572677aba58 in R_execClosure eval.c #9 0x5572677aaf4a in applyClosure_core eval.c #10 0x557267794816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #11 0x557267793d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #12 0x5572677b0db7 in do_set (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe5db7) #13 0x557267793b1f in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8b1f) #14 0x5572677b2227 in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7227) #15 0x55726779ab73 in bcEval_loop eval.c #16 0x55726779413b in bcEval eval.c #17 0x5572677938f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #18 0x557267794393 in forcePromise eval.c #19 0x5572677939bd in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc89bd) #20 0x5572677b2706 in do_withVisible (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7706) #21 0x5572677f5fc7 in do_internal (/data/gannet/ripley/R/R-clang/bin/exec/R+0x12afc7) #22 0x55726779add5 in bcEval_loop eval.c #23 0x55726779413b in bcEval eval.c #24 0x5572677938f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #25 0x557267794393 in forcePromise eval.c #26 0x5572677939bd in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc89bd) #27 0x557267794393 in forcePromise eval.c #28 0x5572677a7ebf in getvar eval.c #29 0x557267798578 in bcEval_loop eval.c #30 0x55726779413b in bcEval eval.c #31 0x5572677938f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #32 0x5572677aba58 in R_execClosure eval.c #33 0x5572677aaf4a in applyClosure_core eval.c #34 0x557267794816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #35 0x557267793d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #36 0x5572677b2227 in do_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xe7227) #37 0x55726779ab73 in bcEval_loop eval.c #38 0x55726779413b in bcEval eval.c #39 0x5572677938f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #40 0x5572677aba58 in R_execClosure eval.c #41 0x5572677aaf4a in applyClosure_core eval.c #42 0x557267794816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #43 0x557267793d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #44 0x5572677aba58 in R_execClosure eval.c #45 0x5572677aaf4a in applyClosure_core eval.c #46 0x55726779a405 in bcEval_loop eval.c #47 0x55726779413b in bcEval eval.c #48 0x5572677938f4 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc88f4) #49 0x5572677aba58 in R_execClosure eval.c #50 0x5572677aaf4a in applyClosure_core eval.c #51 0x557267794816 in Rf_applyClosure (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc9816) #52 0x557267793d47 in Rf_eval (/data/gannet/ripley/R/R-clang/bin/exec/R+0xc8d47) #53 0x5572677e0f37 in Rf_ReplIteration (/data/gannet/ripley/R/R-clang/bin/exec/R+0x115f37) #54 0x5572677e2a3e in run_Rmainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x117a3e) #55 0x5572677e2aaa in Rf_mainloop (/data/gannet/ripley/R/R-clang/bin/exec/R+0x117aaa) #56 0x5572676ccdb7 in main (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1db7) #57 0x7f5fdfd11574 in __libc_start_call_main (/lib64/libc.so.6+0x3574) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #58 0x7f5fdfd11627 in __libc_start_main@GLIBC_2.2.5 (/lib64/libc.so.6+0x3627) (BuildId: 92b5376d35bb29c098175948cf3e7cbcae3aeae1) #59 0x5572676cccd4 in _start (/data/gannet/ripley/R/R-clang/bin/exec/R+0x1cd4) SUMMARY: UndefinedBehaviorSanitizer: undefined-behavior /data/gannet/ripley/R/test-clang/TMB/include/convert.hpp:139:23 --- finished re-building ‘spatial_diffusion.Rmd’