R Under development (unstable) (2025-01-31 r87670) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(ondisc) > > test_check("ondisc") Running test setup script. Generating dataset 1. Generating dataset 2. Generating dataset 3. Writing CSC data. Writing CSR data. Writing CSC data. Writing CSR data. Writing CSC data. Writing CSR data. Writing CSC data. Writing CSR data. Writing CSC data. Writing CSR data. Writing CSC data. 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Writing CSC data. Writing CSR data. Writing CSC data. Writing CSR data. A metadata_ondisc_matrix with the following components: An ondisc_matrix with 485 features and 808 cells. A cell covariate matrix with columns n_nonzero. A feature covariate matrix with columns n_nonzero. A metadata_ondisc_matrix with the following components: An ondisc_matrix with 471 features and 808 cells. A cell covariate matrix with columns n_nonzero, n_umis, p_mito. A feature covariate matrix with columns mean_expression, coef_of_variation, n_nonzero. A metadata_ondisc_matrix with the following components: An ondisc_matrix with 471 features and 808 cells. A cell covariate matrix with columns n_nonzero. A feature covariate matrix with columns n_nonzero. A multimodal_ondisc_matrix with the following modalities: 1. modality_1 A metadata_ondisc_matrix with the following components: An ondisc_matrix with 485 features and 808 cells. A cell covariate matrix with columns n_nonzero. A feature covariate matrix with columns n_nonzero. 2. modality_2 A metadata_ondisc_matrix with the following components: An ondisc_matrix with 830 features and 808 cells. A cell covariate matrix with columns n_nonzero, n_umis, p_mito. A feature covariate matrix with columns mean_expression, coef_of_variation, n_nonzero. Plus, a global cell-covariate matrix containing 4 covariates and 808 cells.An ondisc_matrix with 485 features and 808 cells. Showing 5 of 485 featuress and 6 of 808 cells: [,1] [,2] [,3] [,4] [,5] [,6] [1,] FALSE FALSE FALSE FALSE FALSE FALSE [2,] FALSE FALSE FALSE FALSE FALSE FALSE [3,] FALSE FALSE FALSE TRUE FALSE FALSE [4,] TRUE FALSE FALSE FALSE FALSE FALSE [5,] FALSE FALSE FALSE FALSE FALSE FALSE An ondisc_matrix with 471 features and 808 cells. Showing 5 of 471 featuress and 6 of 808 cells: [,1] [,2] [,3] [,4] [,5] [,6] [1,] 0 0 0 0 0 0 [2,] 0 0 0 0 0 0 [3,] 0 0 0 0 0 0 [4,] 0 0 0 0 0 0 [5,] 0 0 0 0 0 0 An ondisc_matrix with 471 features and 808 cells. Showing 5 of 471 featuress and 6 of 808 cells: [,1] [,2] [,3] [,4] [,5] [,6] [1,] FALSE FALSE FALSE FALSE FALSE FALSE [2,] FALSE FALSE FALSE FALSE FALSE FALSE [3,] FALSE FALSE FALSE FALSE FALSE FALSE [4,] FALSE FALSE FALSE FALSE FALSE FALSE [5,] FALSE TRUE FALSE FALSE FALSE FALSE /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49:62: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 4 byte alignment 0x000000000001: note: pointer points here #0 0x7f68d9122413 in Rcpp::traits::r_vector_cache<13, Rcpp::PreserveStorage>::ref(long) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/traits.h:49 #1 0x7f68d9136a5c in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:340 #2 0x7f68d9136a5c in index_h5_file(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, Rcpp::Vector<13, Rcpp::PreserveStorage>, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/ondisc/src/h5_functs_read.cpp:100 #3 0x7f68d911a3cc in _ondisc_index_h5_file /data/gannet/ripley/R/packages/tests-gcc-SAN/ondisc/src/RcppExports.cpp:83 #4 0x71e584 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #5 0x8bd404 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8672 #6 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #7 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #8 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #9 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #10 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #11 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #12 0x7f68ec871031 in eval_pipe_lazy /tmp/Rtmp25UvyD/R.INSTALL2d5f4f378b1e53/magrittr/src/pipe.c:186 #13 0x7f68ec871031 in magrittr_pipe /tmp/Rtmp25UvyD/R.INSTALL2d5f4f378b1e53/magrittr/src/pipe.c:105 #14 0x70e4c6 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #15 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #16 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #17 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #19 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #20 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #21 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #22 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #23 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #24 0x8bb815 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #25 0x8bb815 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8093 #26 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #27 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #28 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #29 0x853258 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #30 0x7f68ea62cb98 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1151 #31 0xa6942e in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #32 0x8bf46b in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8057 #33 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #34 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #35 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #36 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #37 0xa6c220 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #38 0xa6c220 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #39 0x87244d in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4161 #40 0xc9be96 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1559 #41 0xcd56fc in do_subset2 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:943 #42 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #43 0x8641c2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3669 #44 0x8406dc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1251 #45 0x8639d6 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3571 #46 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #47 0x84fa13 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3000 #48 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #49 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #50 0x84fa13 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3000 #51 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #52 0x8554e3 in do_for /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2882 #53 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #54 0x84fa13 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3000 #55 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #56 0x86bbe9 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945 #57 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #58 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #59 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #60 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #61 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #62 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #63 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #64 0x86cd53 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3963 #65 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #66 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #67 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #68 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #69 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #70 0x869447 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #71 0x869447 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2460 #72 0x4a8c79 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75 #73 0xa52e9a in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #74 0x8b49cd in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142 #75 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #76 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #77 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #78 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #79 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #80 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #81 0x9c9d99 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #82 0x9c9d99 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #83 0x9cb29b in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1219 #84 0x9d5812 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1226 #85 0x4293ff in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #86 0x7f68eca2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #87 0x7f68eca295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #88 0x429de4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x429de4) (BuildId: a84d18346db10b9f6a24beeffd63f6e34190cf95) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:340:62: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 4 byte alignment 0x000000000001: note: pointer points here #0 0x7f68d9137ba0 in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:340 #1 0x7f68d9137ba0 in index_h5_file(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, Rcpp::Vector<13, Rcpp::PreserveStorage>, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/ondisc/src/h5_functs_read.cpp:100 #2 0x7f68d911a3cc in _ondisc_index_h5_file /data/gannet/ripley/R/packages/tests-gcc-SAN/ondisc/src/RcppExports.cpp:83 #3 0x71e584 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #4 0x8bd404 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8672 #5 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #6 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #7 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #8 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #9 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #10 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #11 0x7f68ec871031 in eval_pipe_lazy /tmp/Rtmp25UvyD/R.INSTALL2d5f4f378b1e53/magrittr/src/pipe.c:186 #12 0x7f68ec871031 in magrittr_pipe /tmp/Rtmp25UvyD/R.INSTALL2d5f4f378b1e53/magrittr/src/pipe.c:105 #13 0x70e4c6 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #14 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #15 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #16 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #17 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #18 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #19 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #20 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #21 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #22 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #23 0x8bb815 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #24 0x8bb815 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8093 #25 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #26 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #28 0x853258 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #29 0x7f68ea62cb98 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1151 #30 0xa6942e in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #31 0x8bf46b in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8057 #32 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #33 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #35 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #36 0xa6c220 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #37 0xa6c220 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #38 0x87244d in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4161 #39 0xc9be96 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1559 #40 0xcd56fc in do_subset2 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:943 #41 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #42 0x8641c2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3669 #43 0x8406dc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1251 #44 0x8639d6 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3571 #45 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #46 0x84fa13 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3000 #47 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #48 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #49 0x84fa13 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3000 #50 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #51 0x8554e3 in do_for /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2882 #52 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #53 0x84fa13 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3000 #54 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #55 0x86bbe9 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945 #56 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #57 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #58 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #60 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #61 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #62 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #63 0x86cd53 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3963 #64 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #65 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #66 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #68 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #69 0x869447 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #70 0x869447 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2460 #71 0x4a8c79 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75 #72 0xa52e9a in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #73 0x8b49cd in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142 #74 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #75 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #76 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #77 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #78 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #79 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #80 0x9c9d99 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #81 0x9c9d99 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #82 0x9cb29b in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1219 #83 0x9d5812 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1226 #84 0x4293ff in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #85 0x7f68eca2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #86 0x7f68eca295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #87 0x429de4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x429de4) (BuildId: a84d18346db10b9f6a24beeffd63f6e34190cf95) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:340:62: runtime error: reference binding to misaligned address 0x000000000001 for type 'type', which requires 4 byte alignment 0x000000000001: note: pointer points here #0 0x7f68d9137c97 in Rcpp::Vector<13, Rcpp::PreserveStorage>::operator[](long) /data/gannet/ripley/R/test-dev/Rcpp/include/Rcpp/vector/Vector.h:340 #1 0x7f68d9137c97 in index_h5_file(std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, std::__cxx11::basic_string, std::allocator > const&, Rcpp::Vector<13, Rcpp::PreserveStorage>, bool) /data/gannet/ripley/R/packages/tests-gcc-SAN/ondisc/src/h5_functs_read.cpp:105 #2 0x7f68d911a3cc in _ondisc_index_h5_file /data/gannet/ripley/R/packages/tests-gcc-SAN/ondisc/src/RcppExports.cpp:83 #3 0x71e584 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:770 #4 0x8bd404 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8672 #5 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #6 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #7 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #8 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #9 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #10 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #11 0x7f68ec871031 in eval_pipe_lazy /tmp/Rtmp25UvyD/R.INSTALL2d5f4f378b1e53/magrittr/src/pipe.c:186 #12 0x7f68ec871031 in magrittr_pipe /tmp/Rtmp25UvyD/R.INSTALL2d5f4f378b1e53/magrittr/src/pipe.c:105 #13 0x70e4c6 in do_External /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:573 #14 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #15 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #16 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #17 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #18 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #19 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #20 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #21 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #22 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #23 0x8bb815 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #24 0x8bb815 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8093 #25 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #26 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #28 0x853258 in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #29 0x7f68ea62cb98 in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1151 #30 0xa6942e in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #31 0x8bf46b in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8057 #32 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #33 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #35 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #36 0xa6c220 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #37 0xa6c220 in R_possible_dispatch /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1687 #38 0x87244d in Rf_DispatchOrEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:4161 #39 0xc9be96 in R_DispatchOrEvalSP /data/gannet/ripley/R/svn/R-devel/src/main/subassign.c:1559 #40 0xcd56fc in do_subset2 /data/gannet/ripley/R/svn/R-devel/src/main/subset.c:943 #41 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #42 0x8641c2 in Rf_evalList /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3669 #43 0x8406dc in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1251 #44 0x8639d6 in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3571 #45 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #46 0x84fa13 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3000 #47 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #48 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #49 0x84fa13 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3000 #50 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #51 0x8554e3 in do_for /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2882 #52 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #53 0x84fa13 in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3000 #54 0x840316 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #55 0x86bbe9 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3945 #56 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #57 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #58 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #59 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #60 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #61 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #62 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #63 0x86cd53 in do_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3963 #64 0x8a7953 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8122 #65 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #66 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #68 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #69 0x869447 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #70 0x869447 in R_forceAndCall /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2460 #71 0x4a8c79 in do_lapply /data/gannet/ripley/R/svn/R-devel/src/main/apply.c:75 #72 0xa52e9a in do_internal /data/gannet/ripley/R/svn/R-devel/src/main/names.c:1411 #73 0x8b49cd in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8142 #74 0x878b1f in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7505 #75 0x83f862 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #76 0x84a832 in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #77 0x83e1da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #78 0x83fee6 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #79 0x83fee6 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #80 0x9c9d99 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #81 0x9c9d99 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #82 0x9cb29b in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1219 #83 0x9d5812 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1226 #84 0x4293ff in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #85 0x7f68eca2950f in __libc_start_call_main (/lib64/libc.so.6+0x2950f) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #86 0x7f68eca295c8 in __libc_start_main_alias_2 (/lib64/libc.so.6+0x295c8) (BuildId: 8257ee907646e9b057197533d1e4ac8ede7a9c5c) #87 0x429de4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x429de4) (BuildId: a84d18346db10b9f6a24beeffd63f6e34190cf95) [ FAIL 0 | WARN 2 | SKIP 0 | PASS 421 ] [ FAIL 0 | WARN 2 | SKIP 0 | PASS 421 ] > > proc.time() user system elapsed 84.403 5.692 111.804