--- re-building ‘relationship.Rmd’ using rmarkdown ../../src/tbbmalloc/backref.cpp:150:21: runtime error: index 1 out of bounds for type 'BackRefBlock *[1]' #0 0x7b40bba455f1 in rml::internal::BackRefMaster::initEmptyBackRefBlock(rml::internal::BackRefBlock*) ../../src/tbbmalloc/backref.cpp:150 #1 0x7b40bba86979 in rml::internal::initBackRefMaster(rml::internal::Backend*) ../../src/tbbmalloc/backref.cpp:112 #2 0x7b40bba86979 in initMemoryManager ../../src/tbbmalloc/frontend.cpp:2029 #3 0x7b40bba86979 in doInitialization ../../src/tbbmalloc/frontend.cpp:2055 #4 0x7b40bba8b947 in internalMalloc ../../src/tbbmalloc/frontend.cpp:2637 #5 0x7b40bba8fe6c in scalable_malloc ../../src/tbbmalloc/frontend.cpp:2925 #6 0x7b40b987ddf1 in double* arma::memory::acquire(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/memory.hpp:58 #7 0x7b40b987ddf1 in arma::Mat::init_cold() /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:336 #8 0x7b40b98efcdb in arma::Mat::Mat(arma::Mat const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:897 #9 0x7b40b9959a2a in pnmfem_update_factors_rcpp(arma::Mat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/pnmfem.cpp:110 #10 0x7b40b985fba2 in _fastTopics_pnmfem_update_factors_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/RcppExports.cpp:152 #11 0x00000074c762 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766 #12 0x00000075106a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #13 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #14 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #15 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #16 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #17 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #18 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #19 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #20 0x000000888c4e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #21 0x00000085ac76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #22 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #23 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #24 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #25 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #26 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #27 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #28 0x000000892cb3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980 #29 0x000000a91eb6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #30 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #31 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #32 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #33 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #34 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #35 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #36 0x0000008a4d11 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #37 0x0000008a4d11 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831 #38 0x0000008dca6c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844 #39 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #40 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #41 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #42 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #43 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #44 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #45 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #46 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #47 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #48 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #49 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #50 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #51 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #52 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #53 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #54 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #55 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #56 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #57 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #58 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #60 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #61 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #62 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #63 0x000000a00488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #64 0x000000a00488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #65 0x000000a058ba in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #66 0x000000a0fad2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #67 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #68 0x7f40d6c115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #69 0x7f40d6c116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #70 0x000000413b84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b84) (BuildId: a52bda41d545dd16ece9203e22d5bb4aeecb611d) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/relationship_files/figure-html/plot-loglik-1.png 336x288 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4819 bytes Input file size = 5677 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 4126 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 4107 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 IDAT size = 3928 zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 3901 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 5 IDAT size = 3901 Output IDAT size = 3901 bytes (918 bytes decrease) Output file size = 3979 bytes (1698 bytes = 29.91% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/relationship_files/figure-html/loglik-poisson-vs-multinom-1.png 312x288 pixels, 8 bits/pixel, 248 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4423 bytes Input file size = 5257 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3772 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3772 Output IDAT size = 3772 bytes (651 bytes decrease) Output file size = 3850 bytes (1407 bytes = 26.76% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/relationship_files/figure-html/multinom2poisson-1-1.png 312x288 pixels, 8 bits/pixel, 248 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4487 bytes Input file size = 5321 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3845 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3805 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3805 Output IDAT size = 3805 bytes (682 bytes decrease) Output file size = 3883 bytes (1438 bytes = 27.02% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/relationship_files/figure-html/multinom2poisson-2-1.png 312x288 pixels, 8 bits/pixel, 248 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 4506 bytes Input file size = 5340 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 3857 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3819 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 3819 Output IDAT size = 3819 bytes (687 bytes decrease) Output file size = 3897 bytes (1443 bytes = 27.02% decrease) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘relationship.Rmd’ --- re-building ‘single_cell_rnaseq_basic.Rmd’ using rmarkdown ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/single_cell_rnaseq_basic_files/figure-html/structure-plot-with-celltype-labels-1.png 1800x420 pixels, 3x8 bits/pixel, RGB Input IDAT size = 38372 bytes Input file size = 38498 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32349 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 32349 Output IDAT size = 32349 bytes (6023 bytes decrease) Output file size = 32427 bytes (6071 bytes = 15.77% decrease) ../../src/tbbmalloc/backref.cpp:150:21: runtime error: index 1 out of bounds for type 'BackRefBlock *[1]' #0 0x7b069da455f1 in rml::internal::BackRefMaster::initEmptyBackRefBlock(rml::internal::BackRefBlock*) ../../src/tbbmalloc/backref.cpp:150 #1 0x7b069da86979 in rml::internal::initBackRefMaster(rml::internal::Backend*) ../../src/tbbmalloc/backref.cpp:112 #2 0x7b069da86979 in initMemoryManager ../../src/tbbmalloc/frontend.cpp:2029 #3 0x7b069da86979 in doInitialization ../../src/tbbmalloc/frontend.cpp:2055 #4 0x7b069da8b947 in internalMalloc ../../src/tbbmalloc/frontend.cpp:2637 #5 0x7b069da8fe6c in scalable_malloc ../../src/tbbmalloc/frontend.cpp:2925 #6 0x7b069b8181a8 in double* arma::memory::acquire(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/memory.hpp:58 #7 0x7b069b8184a9 in arma::SpMat::init_cold(unsigned long long, unsigned long long, unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/SpMat_meat.hpp:5065 #8 0x7b069b88a2da in arma::SpMat::SpMat(unsigned long long, unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/SpMat_meat.hpp:78 #9 0x7b069b88a2da in Rcpp::traits::Exporter >::get() /data/gannet/ripley/R/test-dev/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloAs.h:122 #10 0x7b069b85d2b3 in arma::SpMat Rcpp::internal::as >(SEXPREC*, Rcpp::traits::r_type_generic_tag) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/as.h:89 #11 0x7b069b85d2b3 in arma::SpMat Rcpp::as >(SEXPREC*) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/as.h:152 #12 0x7b069b85d2b3 in Rcpp::ConstReferenceInputParameter >::ConstReferenceInputParameter(SEXPREC*) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/InputParameter.h:72 #13 0x7b069b855950 in _fastTopics_cost_sparse_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/RcppExports.cpp:91 #14 0x00000074c762 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766 #15 0x00000075106a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #16 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #17 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #18 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #20 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #21 0x0000008505d1 in R_withCallingErrorHandler /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:2606 #22 0x7f06b679781f in R_evalHandleError /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:93 #23 0x7f06b679781f in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1109 #24 0x000000aa9596 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #25 0x00000085b198 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1264 #26 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #27 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #28 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #29 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #30 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #31 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #33 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #34 0x000000a930c3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #35 0x000000a930c3 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #36 0x000000a973f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #37 0x000000a99375 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #38 0x000000a99f96 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #39 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #40 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #41 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #42 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #43 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #44 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #45 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #46 0x000000888c4e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #47 0x00000085ac76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #48 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #49 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #50 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #51 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #53 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #54 0x000000892cb3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980 #55 0x000000a91eb6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #56 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #57 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #58 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #60 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #61 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #62 0x0000008a4d11 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #63 0x0000008a4d11 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831 #64 0x0000008dca6c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844 #65 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #66 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #68 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #69 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #70 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #71 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #72 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #73 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #74 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #75 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #76 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #77 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #78 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #79 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #80 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #81 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #82 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #83 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #84 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #85 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #86 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #87 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #88 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #89 0x000000a00488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #90 0x000000a00488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #91 0x000000a058ba in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #92 0x000000a0fad2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #93 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #94 0x7f06b98115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #95 0x7f06b98116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #96 0x000000413b84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b84) (BuildId: a52bda41d545dd16ece9203e22d5bb4aeecb611d) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7043:26: runtime error: reference binding to null pointer of type 'const double' #0 0x7b069b928afe in arma::Mat::colptr(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7043 #1 0x7b069b928afe in void arma::subview_each1, 1u>::operator%= >(arma::Base > const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_each_meat.hpp:282 #2 0x7b069b928afe in scalecols(arma::Mat&, arma::Col const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/misc.cpp:100 #3 0x7b069b950424 in mixem_update(arma::Mat const&, arma::Col const&, arma::Col&, arma::Mat&) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/mixem.cpp:91 #4 0x7b069b954475 in mixem(arma::Mat const&, arma::Col const&, arma::Col&, arma::Mat&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/mixem.cpp:71 #5 0x7b069b96c4e9 in poismixem(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Col&, arma::Mat&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/poismix.cpp:223 #6 0x7b069b96fd68 in poismixem(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Col const&, arma::Col&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/poismix.cpp:248 #7 0x7b069b955f5b in pnmfem_update_factor_sparse(arma::SpMat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, unsigned int, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/pnmfem.cpp:30 #8 0x7b069b960546 in pnmfem_update_factors_sparse_rcpp(arma::SpMat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/pnmfem.cpp:134 #9 0x7b069b8604f1 in _fastTopics_pnmfem_update_factors_sparse_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/RcppExports.cpp:167 #10 0x00000074c762 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766 #11 0x00000075106a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #12 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #13 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #14 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #15 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #16 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #17 0x0000008505d1 in R_withCallingErrorHandler /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:2606 #18 0x7f06b679781f in R_evalHandleError /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:93 #19 0x7f06b679781f in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1109 #20 0x000000aa9596 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #21 0x00000085b198 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1264 #22 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #23 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #24 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #25 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #26 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #27 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #28 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #29 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #30 0x000000a930c3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #31 0x000000a930c3 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #32 0x000000a973f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #33 0x000000a99375 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #34 0x000000a99f96 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #35 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #36 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #37 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #39 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #40 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #41 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #42 0x000000888c4e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #43 0x00000085ac76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #44 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #45 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #46 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #47 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #48 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #49 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #50 0x000000892cb3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980 #51 0x000000a91eb6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #52 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #53 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #54 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #55 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #56 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #57 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #58 0x0000008a4d11 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #59 0x0000008a4d11 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831 #60 0x0000008dca6c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844 #61 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #62 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #63 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #64 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #65 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #66 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #67 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #68 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #69 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #70 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #71 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #72 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #73 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #74 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #75 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #76 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #77 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #78 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #79 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #80 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #81 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #82 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #83 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #84 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #85 0x000000a00488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #86 0x000000a00488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #87 0x000000a058ba in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #88 0x000000a0fad2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #89 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #90 0x7f06b98115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #91 0x7f06b98116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #92 0x000000413b84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b84) (BuildId: a52bda41d545dd16ece9203e22d5bb4aeecb611d) /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 0x7b069b928ab0 in double& arma::access::rw(double const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/access.hpp:26 #1 0x7b069b928ab0 in arma::Mat::colptr(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7043 #2 0x7b069b928ab0 in void arma::subview_each1, 1u>::operator%= >(arma::Base > const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_each_meat.hpp:282 #3 0x7b069b928ab0 in scalecols(arma::Mat&, arma::Col const&) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/misc.cpp:100 #4 0x7b069b950424 in mixem_update(arma::Mat const&, arma::Col const&, arma::Col&, arma::Mat&) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/mixem.cpp:91 #5 0x7b069b954475 in mixem(arma::Mat const&, arma::Col const&, arma::Col&, arma::Mat&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/mixem.cpp:71 #6 0x7b069b96c4e9 in poismixem(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Col&, arma::Mat&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/poismix.cpp:223 #7 0x7b069b96fd68 in poismixem(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Col const&, arma::Col&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/poismix.cpp:248 #8 0x7b069b955f5b in pnmfem_update_factor_sparse(arma::SpMat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, unsigned int, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/pnmfem.cpp:30 #9 0x7b069b960546 in pnmfem_update_factors_sparse_rcpp(arma::SpMat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/pnmfem.cpp:134 #10 0x7b069b8604f1 in _fastTopics_pnmfem_update_factors_sparse_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/RcppExports.cpp:167 #11 0x00000074c762 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766 #12 0x00000075106a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #13 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #14 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #15 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #16 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #17 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #18 0x0000008505d1 in R_withCallingErrorHandler /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:2606 #19 0x7f06b679781f in R_evalHandleError /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:93 #20 0x7f06b679781f in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1109 #21 0x000000aa9596 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #22 0x00000085b198 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1264 #23 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #24 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #25 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #26 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #27 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #28 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #30 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #31 0x000000a930c3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #32 0x000000a930c3 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #33 0x000000a973f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #34 0x000000a99375 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #35 0x000000a99f96 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #36 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #37 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #38 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #39 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #40 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #41 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #42 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #43 0x000000888c4e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #44 0x00000085ac76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #45 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #46 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #47 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #48 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #49 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #50 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #51 0x000000892cb3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980 #52 0x000000a91eb6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #53 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #54 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #55 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #57 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #58 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #59 0x0000008a4d11 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #60 0x0000008a4d11 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831 #61 0x0000008dca6c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844 #62 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #63 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #64 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #65 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #66 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #67 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #68 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #69 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #70 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #71 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #72 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #73 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #74 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #75 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #76 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #77 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #78 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #79 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #80 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #81 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #82 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #83 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #84 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #85 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #86 0x000000a00488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #87 0x000000a00488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #88 0x000000a058ba in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #89 0x000000a0fad2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #90 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #91 0x7f06b98115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #92 0x7f06b98116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #93 0x000000413b84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b84) (BuildId: a52bda41d545dd16ece9203e22d5bb4aeecb611d) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7043:26: runtime error: reference binding to null pointer of type 'const double' #0 0x7b069b9482a7 in arma::Mat::colptr(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7043 #1 0x7b069b9482a7 in void arma::subview_each1, 0u>::operator/= >(arma::Base > const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_each_meat.hpp:312 #2 0x7b069b94ca67 in normalizerowsbymax(arma::Mat&) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/misc.cpp:118 #3 0x7b069b95042c in mixem_update(arma::Mat const&, arma::Col const&, arma::Col&, arma::Mat&) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/mixem.cpp:92 #4 0x7b069b954475 in mixem(arma::Mat const&, arma::Col const&, arma::Col&, arma::Mat&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/mixem.cpp:71 #5 0x7b069b96c4e9 in poismixem(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Col&, arma::Mat&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/poismix.cpp:223 #6 0x7b069b96fd68 in poismixem(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Col const&, arma::Col&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/poismix.cpp:248 #7 0x7b069b955f5b in pnmfem_update_factor_sparse(arma::SpMat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, unsigned int, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/pnmfem.cpp:30 #8 0x7b069b960546 in pnmfem_update_factors_sparse_rcpp(arma::SpMat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/pnmfem.cpp:134 #9 0x7b069b8604f1 in _fastTopics_pnmfem_update_factors_sparse_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/RcppExports.cpp:167 #10 0x00000074c762 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766 #11 0x00000075106a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #12 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #13 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #14 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #15 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #16 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #17 0x0000008505d1 in R_withCallingErrorHandler /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:2606 #18 0x7f06b679781f in R_evalHandleError /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:93 #19 0x7f06b679781f in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1109 #20 0x000000aa9596 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #21 0x00000085b198 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1264 #22 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #23 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #24 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #25 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #26 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #27 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #28 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #29 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #30 0x000000a930c3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #31 0x000000a930c3 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #32 0x000000a973f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #33 0x000000a99375 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #34 0x000000a99f96 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #35 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #36 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #37 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #39 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #40 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #41 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #42 0x000000888c4e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #43 0x00000085ac76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #44 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #45 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #46 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #47 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #48 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #49 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #50 0x000000892cb3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980 #51 0x000000a91eb6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #52 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #53 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #54 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #55 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #56 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #57 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #58 0x0000008a4d11 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #59 0x0000008a4d11 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831 #60 0x0000008dca6c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844 #61 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #62 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #63 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #64 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #65 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #66 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #67 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #68 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #69 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #70 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #71 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #72 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #73 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #74 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #75 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #76 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #77 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #78 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #79 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #80 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #81 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #82 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #83 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #84 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #85 0x000000a00488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #86 0x000000a00488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #87 0x000000a058ba in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #88 0x000000a0fad2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #89 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #90 0x7f06b98115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #91 0x7f06b98116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #92 0x000000413b84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b84) (BuildId: a52bda41d545dd16ece9203e22d5bb4aeecb611d) /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 0x7b069b94825b in double& arma::access::rw(double const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/access.hpp:26 #1 0x7b069b94825b in arma::Mat::colptr(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:7043 #2 0x7b069b94825b in void arma::subview_each1, 0u>::operator/= >(arma::Base > const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_each_meat.hpp:312 #3 0x7b069b94ca67 in normalizerowsbymax(arma::Mat&) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/misc.cpp:118 #4 0x7b069b95042c in mixem_update(arma::Mat const&, arma::Col const&, arma::Col&, arma::Mat&) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/mixem.cpp:92 #5 0x7b069b954475 in mixem(arma::Mat const&, arma::Col const&, arma::Col&, arma::Mat&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/mixem.cpp:71 #6 0x7b069b96c4e9 in poismixem(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Col&, arma::Mat&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/poismix.cpp:223 #7 0x7b069b96fd68 in poismixem(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Col const&, arma::Col&, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/poismix.cpp:248 #8 0x7b069b955f5b in pnmfem_update_factor_sparse(arma::SpMat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, unsigned int, unsigned int) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/pnmfem.cpp:30 #9 0x7b069b960546 in pnmfem_update_factors_sparse_rcpp(arma::SpMat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/pnmfem.cpp:134 #10 0x7b069b8604f1 in _fastTopics_pnmfem_update_factors_sparse_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/RcppExports.cpp:167 #11 0x00000074c762 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766 #12 0x00000075106a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #13 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #14 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #15 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #16 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #17 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #18 0x0000008505d1 in R_withCallingErrorHandler /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:2606 #19 0x7f06b679781f in R_evalHandleError /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:93 #20 0x7f06b679781f in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1109 #21 0x000000aa9596 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #22 0x00000085b198 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1264 #23 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #24 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #25 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #26 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #27 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #28 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #30 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #31 0x000000a930c3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #32 0x000000a930c3 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #33 0x000000a973f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #34 0x000000a99375 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #35 0x000000a99f96 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #36 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #37 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #38 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #39 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #40 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #41 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #42 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #43 0x000000888c4e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #44 0x00000085ac76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #45 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #46 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #47 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #48 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #49 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #50 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #51 0x000000892cb3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980 #52 0x000000a91eb6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #53 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #54 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #55 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #57 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #58 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #59 0x0000008a4d11 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #60 0x0000008a4d11 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831 #61 0x0000008dca6c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844 #62 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #63 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #64 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #65 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #66 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #67 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #68 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #69 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #70 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #71 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #72 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #73 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #74 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #75 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #76 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #77 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #78 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #79 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #80 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #81 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #82 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #83 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #84 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #85 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #86 0x000000a00488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #87 0x000000a00488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #88 0x000000a058ba in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #89 0x000000a0fad2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #90 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #91 0x7f06b98115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #92 0x7f06b98116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #93 0x000000413b84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b84) (BuildId: a52bda41d545dd16ece9203e22d5bb4aeecb611d) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:1420:54: runtime error: reference binding to null pointer of type 'const double' #0 0x7b069b8f0ee9 in arma::subview::colptr(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:1420 #1 0x7b069b8f0ee9 in arma::subview_col::subview_col(arma::Mat const&, unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:3274 #2 0x7b069b97e30b in arma::Mat::col(unsigned long long) const /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:3260 #3 0x7b069b97e30b in scd_kl_update(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Col const&, unsigned int, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/poismix.cpp:305 #4 0x7b069b9896b7 in scd_update_factor_sparse(arma::SpMat const&, arma::Mat const&, arma::Col const&, arma::Mat&, unsigned int, unsigned int, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/scd.cpp:37 #5 0x7b069b98dc48 in scd_update_factors_sparse(arma::SpMat const&, arma::Mat const&, arma::Mat&, arma::Col const&, unsigned int, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/scd.cpp:181 #6 0x7b069b98e01c in scd_update_factors_sparse_rcpp(arma::SpMat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, unsigned int, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/scd.cpp:126 #7 0x7b069b86915b in _fastTopics_scd_update_factors_sparse_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/RcppExports.cpp:373 #8 0x00000074c6be in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #9 0x00000075106a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #10 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #11 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #12 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #13 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #14 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #15 0x0000008505d1 in R_withCallingErrorHandler /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:2606 #16 0x7f06b679781f in R_evalHandleError /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:93 #17 0x7f06b679781f in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1109 #18 0x000000aa9596 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #19 0x00000085b198 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1264 #20 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #21 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #22 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #23 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #24 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #25 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #26 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #27 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #28 0x000000a930c3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #29 0x000000a930c3 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #30 0x000000a973f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #31 0x000000a99375 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #32 0x000000a99f96 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #33 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #34 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #35 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #36 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #37 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #38 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #39 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #40 0x000000888c4e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #41 0x00000085ac76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #42 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #43 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #44 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #45 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #47 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #48 0x000000892cb3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980 #49 0x000000a91eb6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #50 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #51 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #52 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #53 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #54 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #55 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #56 0x0000008a4d11 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #57 0x0000008a4d11 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831 #58 0x0000008dca6c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844 #59 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #60 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #61 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #62 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #63 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #64 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #65 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #66 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #67 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #68 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #69 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #70 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #71 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #72 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #73 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #74 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #75 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #76 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #77 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #78 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #79 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #80 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #81 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #82 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #83 0x000000a00488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #84 0x000000a00488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #85 0x000000a058ba in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #86 0x000000a0fad2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #87 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #88 0x7f06b98115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #89 0x7f06b98116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #90 0x000000413b84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b84) (BuildId: a52bda41d545dd16ece9203e22d5bb4aeecb611d) /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 0x7b069b8f0d91 in double& arma::access::rw(double const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/access.hpp:26 #1 0x7b069b8f0d91 in arma::subview::colptr(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:1420 #2 0x7b069b8f0d91 in arma::subview_col::subview_col(arma::Mat const&, unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/subview_meat.hpp:3274 #3 0x7b069b97e30b in arma::Mat::col(unsigned long long) const /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:3260 #4 0x7b069b97e30b in scd_kl_update(arma::Mat const&, arma::Col const&, arma::Col const&, arma::Col const&, unsigned int, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/poismix.cpp:305 #5 0x7b069b9896b7 in scd_update_factor_sparse(arma::SpMat const&, arma::Mat const&, arma::Col const&, arma::Mat&, unsigned int, unsigned int, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/scd.cpp:37 #6 0x7b069b98dc48 in scd_update_factors_sparse(arma::SpMat const&, arma::Mat const&, arma::Mat&, arma::Col const&, unsigned int, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/scd.cpp:181 #7 0x7b069b98e01c in scd_update_factors_sparse_rcpp(arma::SpMat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, unsigned int, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/scd.cpp:126 #8 0x7b069b86915b in _fastTopics_scd_update_factors_sparse_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/RcppExports.cpp:373 #9 0x00000074c6be in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #10 0x00000075106a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #11 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #12 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #13 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #14 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #15 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #16 0x0000008505d1 in R_withCallingErrorHandler /data/gannet/ripley/R/svn/R-devel/src/main/errors.c:2606 #17 0x7f06b679781f in R_evalHandleError /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:93 #18 0x7f06b679781f in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1109 #19 0x000000aa9596 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #20 0x00000085b198 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1264 #21 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #22 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #23 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #24 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #25 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #26 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #28 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #29 0x000000a930c3 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #30 0x000000a930c3 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #31 0x000000a973f0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #32 0x000000a99375 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:513 #33 0x000000a99f96 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #34 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #35 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #36 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #37 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #38 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #39 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #40 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #41 0x000000888c4e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #42 0x00000085ac76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #43 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #44 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #45 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #46 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #48 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #49 0x000000892cb3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980 #50 0x000000a91eb6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #51 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #52 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #53 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #54 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #55 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #56 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #57 0x0000008a4d11 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #58 0x0000008a4d11 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831 #59 0x0000008dca6c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844 #60 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #61 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #62 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #63 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #64 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #65 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #66 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #67 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #68 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #69 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #70 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #71 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #72 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #73 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #74 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #75 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #76 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #77 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #78 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #79 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #80 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #81 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #82 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #83 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #84 0x000000a00488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #85 0x000000a00488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #86 0x000000a058ba in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #87 0x000000a0fad2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #88 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #89 0x7f06b98115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #90 0x7f06b98116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #91 0x000000413b84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b84) (BuildId: a52bda41d545dd16ece9203e22d5bb4aeecb611d) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/single_cell_rnaseq_basic_files/figure-html/structure-plot-test-1.png 1800x420 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27766 bytes Input file size = 27880 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23783 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 23783 Output IDAT size = 23783 bytes (3983 bytes decrease) Output file size = 23861 bytes (4019 bytes = 14.42% decrease) trying URL 'https://stephenslab.github.io/fastTopics/pbmc_facs.RData' Content type 'application/octet-stream' length 8739244 bytes (8.3 MB) ================================================== downloaded 8.3 MB ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/single_cell_rnaseq_basic_files/figure-html/volcano-plot-bcells-1.png 1080x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 138355 bytes Input file size = 138625 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 99072 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 99072 Output IDAT size = 99072 bytes (39283 bytes decrease) Output file size = 99150 bytes (39475 bytes = 28.48% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/single_cell_rnaseq_basic_files/figure-html/volcano-plot-nk-1.png 1080x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 135141 bytes Input file size = 135411 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 97513 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 97513 Output IDAT size = 97513 bytes (37628 bytes decrease) Output file size = 97591 bytes (37820 bytes = 27.93% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/single_cell_rnaseq_basic_files/figure-html/volcano-plot-tcells-1.png 1080x960 pixels, 3x8 bits/pixel, RGB Input IDAT size = 126333 bytes Input file size = 126591 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 91103 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 91103 Output IDAT size = 91103 bytes (35230 bytes decrease) Output file size = 91181 bytes (35410 bytes = 27.97% decrease) --- finished re-building ‘single_cell_rnaseq_basic.Rmd’ --- re-building ‘topics_vs_clusters.Rmd’ using rmarkdown ../../src/tbbmalloc/backref.cpp:150:21: runtime error: index 1 out of bounds for type 'BackRefBlock *[1]' #0 0x7b19500455f1 in rml::internal::BackRefMaster::initEmptyBackRefBlock(rml::internal::BackRefBlock*) ../../src/tbbmalloc/backref.cpp:150 #1 0x7b1950086979 in rml::internal::initBackRefMaster(rml::internal::Backend*) ../../src/tbbmalloc/backref.cpp:112 #2 0x7b1950086979 in initMemoryManager ../../src/tbbmalloc/frontend.cpp:2029 #3 0x7b1950086979 in doInitialization ../../src/tbbmalloc/frontend.cpp:2055 #4 0x7b195008b947 in internalMalloc ../../src/tbbmalloc/frontend.cpp:2637 #5 0x7b195008fe6c in scalable_malloc ../../src/tbbmalloc/frontend.cpp:2925 #6 0x7b194f47ddf1 in double* arma::memory::acquire(unsigned long long) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/memory.hpp:58 #7 0x7b194f47ddf1 in arma::Mat::init_cold() /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:336 #8 0x7b194f4efcdb in arma::Mat::Mat(arma::Mat const&) /data/gannet/ripley/R/test-dev/RcppArmadillo/include/current/armadillo_bits/Mat_meat.hpp:897 #9 0x7b194f559a2a in pnmfem_update_factors_rcpp(arma::Mat const&, arma::Mat const&, arma::Mat const&, arma::Col const&, double) /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/pnmfem.cpp:110 #10 0x7b194f45fba2 in _fastTopics_pnmfem_update_factors_rcpp /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics/src/RcppExports.cpp:152 #11 0x00000074c762 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:766 #12 0x00000075106a in do_dotcall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:1437 #13 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #14 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #15 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #16 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #17 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #18 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #19 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #20 0x000000888c4e in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3563 #21 0x00000085ac76 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #22 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #23 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #24 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #25 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #26 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #27 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #28 0x000000892cb3 in do_withVisible /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3980 #29 0x000000a91eb6 in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #30 0x0000008d9e01 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8134 #31 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #32 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #33 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #34 0x00000085b80c in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1187 #35 0x0000009214d1 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #36 0x0000008a4d11 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #37 0x0000008a4d11 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5831 #38 0x0000008dca6c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7844 #39 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #40 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #41 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #42 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #43 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #44 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #45 0x0000008901f1 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3937 #46 0x0000008ccbf2 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8114 #47 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #48 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #49 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #50 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #51 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #52 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #53 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #54 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #55 0x0000008e16f5 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #56 0x0000008e16f5 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8085 #57 0x0000008b9e3b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7497 #58 0x00000085a1b2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x00000086fefa in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2389 #60 0x000000873fba in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2302 #61 0x00000085a853 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2324 #62 0x00000085a853 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #63 0x000000a00488 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:264 #64 0x000000a00488 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #65 0x000000a058ba in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1235 #66 0x000000a0fad2 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1242 #67 0x0000004131bf in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #68 0x7f196ce115f4 in __libc_start_call_main (/lib64/libc.so.6+0x35f4) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #69 0x7f196ce116a7 in __libc_start_main@@GLIBC_2.34 (/lib64/libc.so.6+0x36a7) (BuildId: a1dda014206b55b07f58fe8db80121b752dc3d03) #70 0x000000413b84 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x413b84) (BuildId: a52bda41d545dd16ece9203e22d5bb4aeecb611d) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/topics_vs_clusters_files/figure-html/plot-topic-proportions-1.png 360x360 pixels, 3x8 bits/pixel, RGB Input IDAT size = 53868 bytes Input file size = 54018 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38793 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 38793 Output IDAT size = 38793 bytes (15075 bytes decrease) Output file size = 38871 bytes (15147 bytes = 28.04% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/topics_vs_clusters_files/figure-html/tsne-from-counts-1-1.png 360x360 pixels, 8 bits/pixel, 256 colors in palette Reducing image to 8 bits/pixel, grayscale Input IDAT size = 11480 bytes Input file size = 12350 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 10757 zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 10492 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 1 f = 0 IDAT size = 10492 Output IDAT size = 10492 bytes (988 bytes decrease) Output file size = 10570 bytes (1780 bytes = 14.41% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/topics_vs_clusters_files/figure-html/tsne-from-counts-2-1.png 360x360 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27715 bytes Input file size = 27829 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20495 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20495 Output IDAT size = 20495 bytes (7220 bytes decrease) Output file size = 20573 bytes (7256 bytes = 26.07% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/topics_vs_clusters_files/figure-html/tsne-from-loadings-1.png 360x360 pixels, 3x8 bits/pixel, RGB Input IDAT size = 27297 bytes Input file size = 27411 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20556 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 20556 Output IDAT size = 20556 bytes (6741 bytes decrease) Output file size = 20634 bytes (6777 bytes = 24.72% decrease) ** Processing: /data/gannet/ripley/R/packages/tests-gcc-SAN/fastTopics.Rcheck/vign_test/fastTopics/vignettes/topics_vs_clusters_files/figure-html/pca-from-loadings-1.png 360x360 pixels, 3x8 bits/pixel, RGB Input IDAT size = 33477 bytes Input file size = 33603 bytes Trying: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24143 zc = 9 zm = 8 zs = 1 f = 0 zc = 1 zm = 8 zs = 2 f = 0 zc = 9 zm = 8 zs = 3 f = 0 zc = 9 zm = 8 zs = 0 f = 5 zc = 9 zm = 8 zs = 1 f = 5 zc = 1 zm = 8 zs = 2 f = 5 zc = 9 zm = 8 zs = 3 f = 5 Selecting parameters: zc = 9 zm = 8 zs = 0 f = 0 IDAT size = 24143 Output IDAT size = 24143 bytes (9334 bytes decrease) Output file size = 24221 bytes (9382 bytes = 27.92% decrease) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘topics_vs_clusters.Rmd’