--- re-building ‘spBFA-example.Rmd’ using rmarkdown
/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:1413:54: runtime error: reference binding to null pointer of type 'const double'
    #0 0x7b70c8d1972f in arma::subview<double>::colptr(unsigned int) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:1413
    #1 0x7b70c8d1972f in arma::subview_row<double>::subview_row(arma::Mat<double> const&, unsigned int) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:4271
    #2 0x7b70c8d28e7b in arma::Mat<double>::row(unsigned int) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:3350
    #3 0x7b70c8d28e7b in GetLogLik(Rcpp::Vector<19, Rcpp::PreserveStorage>, Rcpp::Vector<19, Rcpp::PreserveStorage>, int, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/spBFA/src/DIAG_GetLogLik.cpp:63
    #4 0x7b70c8f1414f in _spBFA_GetLogLik /data/gannet/ripley/R/packages/tests-gcc-SAN/spBFA/src/RcppExports.cpp:63
    #5 0x00000074f306 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763
    #6 0x000000753b8a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437
    #7 0x0000008ceba2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132
    #8 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #9 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #10 0x00000087238a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #11 0x00000087644a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #12 0x00000085cce3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #13 0x00000085cce3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #14 0x00000088abfe in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #15 0x00000085d106 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232
    #16 0x0000008921a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #17 0x0000008ceba2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132
    #18 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #19 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #20 0x000000923481 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #21 0x00000085dc9c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187
    #22 0x000000894c63 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998
    #23 0x000000a95c46 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411
    #24 0x0000008dbdb1 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152
    #25 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #26 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #27 0x000000923481 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #28 0x00000085dc9c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187
    #29 0x000000923481 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #30 0x0000008a6cc1 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956
    #31 0x0000008a6cc1 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849
    #32 0x0000008dea1c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862
    #33 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #34 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #35 0x00000087238a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #36 0x00000087644a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #37 0x00000085cce3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #38 0x00000085cce3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #39 0x0000008921a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #40 0x0000008ceba2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132
    #41 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #42 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #43 0x00000087238a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #44 0x00000087644a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #45 0x00000085cce3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #46 0x00000085cce3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #47 0x00000087238a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #48 0x00000087644a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #49 0x0000008e36a5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #50 0x0000008e36a5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103
    #51 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #52 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #53 0x00000087238a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #54 0x00000087644a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #55 0x00000085cce3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #56 0x00000085cce3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #57 0x000000a02488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #58 0x000000a02488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317
    #59 0x000000a1056a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235
    #60 0x000000a10602 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242
    #61 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #62 0x7f70e60115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03)
    #63 0x7f70e60116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03)
    #64 0x000000413ba4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413ba4) (BuildId: 09d1e93a0fe813e632cb484c467b0eaf790fc71f)

/data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/access.hpp:26:100: runtime error: reference binding to null pointer of type 'double'
    #0 0x7b70c8d195e8 in double& arma::access::rw<double>(double const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/access.hpp:26
    #1 0x7b70c8d195e8 in arma::subview<double>::colptr(unsigned int) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:1413
    #2 0x7b70c8d195e8 in arma::subview_row<double>::subview_row(arma::Mat<double> const&, unsigned int) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:4271
    #3 0x7b70c8d28e7b in arma::Mat<double>::row(unsigned int) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:3350
    #4 0x7b70c8d28e7b in GetLogLik(Rcpp::Vector<19, Rcpp::PreserveStorage>, Rcpp::Vector<19, Rcpp::PreserveStorage>, int, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/spBFA/src/DIAG_GetLogLik.cpp:63
    #5 0x7b70c8f1414f in _spBFA_GetLogLik /data/gannet/ripley/R/packages/tests-gcc-SAN/spBFA/src/RcppExports.cpp:63
    #6 0x00000074f306 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:763
    #7 0x000000753b8a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437
    #8 0x0000008ceba2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132
    #9 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #10 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #11 0x00000087238a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #12 0x00000087644a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #13 0x00000085cce3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #14 0x00000085cce3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #15 0x00000088abfe in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3581
    #16 0x00000085d106 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232
    #17 0x0000008921a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #18 0x0000008ceba2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132
    #19 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #20 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #21 0x000000923481 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #22 0x00000085dc9c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187
    #23 0x000000894c63 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3998
    #24 0x000000a95c46 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411
    #25 0x0000008dbdb1 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8152
    #26 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #27 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #28 0x000000923481 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #29 0x00000085dc9c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187
    #30 0x000000923481 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976
    #31 0x0000008a6cc1 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956
    #32 0x0000008a6cc1 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5849
    #33 0x0000008dea1c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7862
    #34 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #35 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #36 0x00000087238a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #37 0x00000087644a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #38 0x00000085cce3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #39 0x00000085cce3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #40 0x0000008921a1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3955
    #41 0x0000008ceba2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8132
    #42 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #43 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #44 0x00000087238a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #45 0x00000087644a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #46 0x00000085cce3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #47 0x00000085cce3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #48 0x00000087238a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #49 0x00000087644a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #50 0x0000008e36a5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #51 0x0000008e36a5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8103
    #52 0x0000008bbdeb in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7515
    #53 0x00000085c642 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167
    #54 0x00000087238a in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389
    #55 0x00000087644a in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302
    #56 0x00000085cce3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324
    #57 0x00000085cce3 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280
    #58 0x000000a02488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264
    #59 0x000000a02488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317
    #60 0x000000a1056a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235
    #61 0x000000a10602 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242
    #62 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29
    #63 0x7f70e60115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03)
    #64 0x7f70e60116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03)
    #65 0x000000413ba4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413ba4) (BuildId: 09d1e93a0fe813e632cb484c467b0eaf790fc71f)

[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘spBFA-example.Rmd’