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Type 'q()' to quit R. > pkgname <- "dnapath" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('dnapath') > > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("dnapath") > ### * dnapath > > flush(stderr()); flush(stdout()) > > ### Name: dnapath > ### Title: Differential Network Analysis Using Gene Pathways > ### Aliases: dnapath > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > results Differential network analysis results between stageii (group 1) and stageiv (group 2) over 13 out of 13 pathways analyzed. # A tibble: 13 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 Regulation of TP… 1.77 0.0909 37 7 10.1 10.2 2 Regulation of TP… 1.15 0.909 30 0 10.2 10.2 3 Regulation of TP… 0.880 0.273 14 1 7.70 7.60 4 TP53 Regulates T… 2.35 0.727 49 2 9.09 9.16 5 TP53 Regulates T… 1.30 1 14 0 7.76 7.94 6 TP53 Regulates T… 2.03 0.455 44 2 8.68 8.73 7 TP53 regulates t… 1.05 0.273 14 2 8.52 8.46 8 Regulation of TP… 1.28 0.273 19 1 10.8 10.8 9 TP53 Regulates T… 1.55 0.818 18 0 9.37 9.35 10 TP53 Regulates T… 1.32 0.727 20 0 8.59 8.61 11 TP53 regulates t… 0.954 0.818 21 0 9.88 9.92 12 TP53 Regulates T… 0.906 1 12 0 8.15 8.16 13 TP53 Regulates T… 0.998 0.182 12 2 7.91 7.91 > summary(results) # Summary over all pathways in the pathway list. # A tibble: 13 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 Regulation of TP… 1.77 0.0909 37 7 10.1 10.2 2 Regulation of TP… 1.15 0.909 30 0 10.2 10.2 3 Regulation of TP… 0.880 0.273 14 1 7.70 7.60 4 TP53 Regulates T… 2.35 0.727 49 2 9.09 9.16 5 TP53 Regulates T… 1.30 1 14 0 7.76 7.94 6 TP53 Regulates T… 2.03 0.455 44 2 8.68 8.73 7 TP53 regulates t… 1.05 0.273 14 2 8.52 8.46 8 Regulation of TP… 1.28 0.273 19 1 10.8 10.8 9 TP53 Regulates T… 1.55 0.818 18 0 9.37 9.35 10 TP53 Regulates T… 1.32 0.727 20 0 8.59 8.61 11 TP53 regulates t… 0.954 0.818 21 0 9.88 9.92 12 TP53 Regulates T… 0.906 1 12 0 8.15 8.16 13 TP53 Regulates T… 0.998 0.182 12 2 7.91 7.91 > # Remove results for pathways with p-values above 0.2. > top_results <- filter_pathways(results, 0.2) > # Sort the top results by the pathway DC score. > top_results <- sort(top_results, by = "dc_score") > top_results Differential network analysis results between stageii (group 1) and stageiv (group 2) over 2 out of 13 pathways analyzed. # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 Regulation of TP5… 1.77 0.0909 37 7 10.1 10.2 2 TP53 Regulates Tr… 0.998 0.182 12 2 7.91 7.91 > summary(top_results[[1]]) # Summary of pathway 1. # A tibble: 37 × 6 pathway genes dc_score p_value mean_expr1 mean_expr2 1 Regulation of TP53 Degradation … 1616 0.256 0.0909 10.9 10.7 2 Regulation of TP53 Degradation … 4193 0.228 0.0909 11.0 11.1 3 Regulation of TP53 Degradation … 5527 0.226 0.0909 10.4 10.6 4 Regulation of TP53 Degradation … 6446 0.218 0.0909 11.3 11.7 5 Regulation of TP53 Degradation … 51230 0.201 0.0909 10.1 9.96 6 Regulation of TP53 Degradation … 207 0.152 0.0909 11.4 11.6 7 Regulation of TP53 Degradation … 983 0.141 0.0909 8.49 8.56 8 Regulation of TP53 Degradation … 7157 0.221 0.182 11.1 10.8 9 Regulation of TP53 Degradation … 80196 0.214 0.182 9.37 9.36 10 Regulation of TP53 Degradation … 5519 0.177 0.182 9.14 9.20 # ℹ 27 more rows > plot(results[[1]]) # Plot of the differential network for pathway 1. > > # Use ... to adjust arguments in the network inference function. > # For example, using run_corr() with method = "spearman": > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10, + network_inference = run_corr, + method = "spearman") > results Differential network analysis results between stageii (group 1) and stageiv (group 2) over 13 out of 13 pathways analyzed. # A tibble: 13 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 Regulation of TP… 9.77 0.273 37 6 10.1 10.2 2 Regulation of TP… 7.07 0.727 30 2 10.2 10.2 3 Regulation of TP… 3.80 0.273 14 3 7.70 7.60 4 TP53 Regulates T… 10.1 1 49 1 9.09 9.16 5 TP53 Regulates T… 2.68 1 14 0 7.76 7.94 6 TP53 Regulates T… 10.6 0.182 44 6 8.68 8.73 7 TP53 regulates t… 3.51 0.455 14 3 8.52 8.46 8 Regulation of TP… 4.14 0.182 19 2 10.8 10.8 9 TP53 Regulates T… 3.79 0.727 18 0 9.37 9.35 10 TP53 Regulates T… 4.77 0.455 20 3 8.59 8.61 11 TP53 regulates t… 4.28 0.818 21 0 9.88 9.92 12 TP53 Regulates T… 2.54 0.909 12 1 8.15 8.16 13 TP53 Regulates T… 2.93 0.273 12 3 7.91 7.91 > > > > cleanEx() > nameEx("entrez_to_symbol") > ### * entrez_to_symbol > > flush(stderr()); flush(stdout()) > > ### Name: entrez_to_symbol > ### Title: Obtain gene symbols for entrezgene IDs > ### Aliases: entrez_to_symbol > > ### ** Examples > > > > > cleanEx() > nameEx("filter_pathways") > ### * filter_pathways > > flush(stderr()); flush(stdout()) > > ### Name: filter_pathways > ### Title: Remove pathways with non-significant DC scores. > ### Aliases: filter_pathways > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > results_sig <- filter_pathways(results) > > > > cleanEx() > nameEx("get_genes") > ### * get_genes > > flush(stderr()); flush(stdout()) > > ### Name: get_genes > ### Title: Get the gene names from a differential network analysis > ### Aliases: get_genes > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > genes <- get_genes(results) > > > > cleanEx() > nameEx("get_min_alpha") > ### * get_min_alpha > > flush(stderr()); flush(stdout()) > > ### Name: get_min_alpha > ### Title: Get the minimum alpha level for the permutation test > ### Aliases: get_min_alpha > > ### ** Examples > > data(meso) > data(p53_pathways) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 5) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > get_min_alpha(results) # 1 / (5 + 1) = 0.167 [1] 0.1666667 > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > get_min_alpha(results) # 1 / (10 + 1) = 0.091 [1] 0.09090909 > > > > cleanEx() > nameEx("get_networks") > ### * get_networks > > flush(stderr()); flush(stdout()) > > ### Name: get_networks > ### Title: Get the two association networks > ### Aliases: get_networks > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > # Extract the two estimated association networks for the first pathway > nw <- get_networks(results[[1]]) > # Plot the networks using the SeqNet::plot_network function. > # Note that the `compare_graph` argument is used so that the same node layout > # is used across all of the plots. > # Plot the two networks (in separate plots) > g <- SeqNet::plot_network(nw[[1]]) > SeqNet::plot_network(nw[[1]], compare_graph = g) > # Plot of the differential network for pathway 1. > # Again, the `compare_graph` argument is used to maintain the same layout. > plot(results[[1]], compare_graph = g) > # We see that genes 51230 and 7311 show strong differential connectivity. > # The plot_pair() function can be used to investigate these two genes further. > plot_pair(results[[1]], "51230", "7311") `geom_smooth()` using formula = 'y ~ x' > > > > cleanEx() > nameEx("get_reactome_pathways") > ### * get_reactome_pathways > > flush(stderr()); flush(stdout()) > > ### Name: get_reactome_pathways > ### Title: Obtain Reactome pathways > ### Aliases: get_reactome_pathways > > ### ** Examples > > # Obtaining a pathway list for human (Homo sapiens). > # In this example, overlapping pathways are not combined (this is > # specified by setting overlap_limit to NULL). > pathway_list <- get_reactome_pathways("Homo sapiens", overlap_limit = NULL, + min_size = 10, max_size = 20) vendor/sqlite3/sqlite3.c:111455:20: runtime error: index 2 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee2ab741 in sqlite3ExprListAppend vendor/sqlite3/sqlite3.c:111455 #1 0x7fd5ee4014c8 in selectExpander vendor/sqlite3/sqlite3.c:150034 #2 0x7fd5ee2760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #3 0x7fd5ee40946f in sqlite3SelectExpand vendor/sqlite3/sqlite3.c:150132 #4 0x7fd5ee40946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150214 #5 0x7fd5ee40946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #6 0x7fd5ee4181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #7 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #14 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #15 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #16 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #17 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #18 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #19 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #20 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #21 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #22 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #23 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #24 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #25 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #26 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #27 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) 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/data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #72 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #73 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #74 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #75 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #76 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #77 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #78 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #79 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #80 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #81 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #82 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #83 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #84 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #85 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #86 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #87 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #88 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #89 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #90 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #91 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #92 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #93 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #94 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #95 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #96 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #97 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #98 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #99 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #100 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #101 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #102 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #103 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #104 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #105 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #106 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #107 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #108 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #109 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #110 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #111 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #112 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #113 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #114 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #115 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #116 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #117 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #118 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #119 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #120 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #121 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #122 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #123 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #124 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #125 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #126 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #127 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #128 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #129 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #130 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #131 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #132 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:150038:26: runtime error: index 2 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee4034c7 in selectExpander vendor/sqlite3/sqlite3.c:150038 #1 0x7fd5ee2760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #2 0x7fd5ee40946f in sqlite3SelectExpand vendor/sqlite3/sqlite3.c:150132 #3 0x7fd5ee40946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150214 #4 0x7fd5ee40946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #5 0x7fd5ee4181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #6 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #7 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #8 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #9 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #10 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #11 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #12 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #13 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #14 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #15 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #16 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #17 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #18 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #19 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #20 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #21 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #22 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #23 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #24 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #25 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #26 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #27 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #28 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #29 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #30 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #31 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #32 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #33 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #34 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #35 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #36 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #37 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #38 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #39 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #40 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #41 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #42 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #43 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #44 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #45 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #46 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #47 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #48 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #49 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #50 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #51 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #52 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #53 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #54 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #55 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #56 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #57 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #58 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #59 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #60 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #61 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #62 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #63 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #64 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #65 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #66 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #67 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #68 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #69 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #70 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #71 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #72 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #73 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #74 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #75 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #76 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #77 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #78 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #79 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #80 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #81 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #82 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #83 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #84 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #85 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #86 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #87 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #88 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #89 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #90 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #91 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #92 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #93 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #94 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #95 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #96 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #97 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #98 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #99 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #100 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #101 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #102 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #103 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #104 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #105 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #106 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #107 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #108 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #109 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #110 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #111 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #112 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #113 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #114 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #115 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #116 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #117 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #118 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #119 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #120 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #121 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #122 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #123 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #124 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #125 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #126 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #127 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #128 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #129 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #130 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #131 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:111438:20: runtime error: index 4 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee2ab2e3 in sqlite3ExprListAppendGrow vendor/sqlite3/sqlite3.c:111438 #1 0x7fd5ee4014c8 in selectExpander vendor/sqlite3/sqlite3.c:150034 #2 0x7fd5ee2760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #3 0x7fd5ee40946f in sqlite3SelectExpand vendor/sqlite3/sqlite3.c:150132 #4 0x7fd5ee40946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150214 #5 0x7fd5ee40946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #6 0x7fd5ee4181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #7 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #14 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #15 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #16 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #17 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #18 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #19 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #20 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #21 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #22 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #23 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #24 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #25 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #26 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #27 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #28 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #29 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #30 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #31 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #32 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #33 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #35 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #36 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #37 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #38 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #39 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #40 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #41 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #42 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #43 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #44 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #45 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #46 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #47 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #48 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #49 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #50 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #51 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #53 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #54 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #55 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #56 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #57 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #58 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #59 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #60 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #61 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #62 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #63 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #64 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #65 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #66 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #67 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #68 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #69 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #70 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #71 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #72 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #73 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #74 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #75 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #76 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #77 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #78 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #79 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #80 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #81 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #82 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #83 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #84 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #85 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #86 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #87 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #88 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #89 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #90 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #91 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #92 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #93 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #94 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #95 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #96 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #97 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #98 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #99 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #100 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #101 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #102 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #103 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #104 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #105 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #106 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #107 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #108 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #109 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #110 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #111 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #112 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #113 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #114 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #115 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #116 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #117 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #118 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #119 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #120 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #121 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #122 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #123 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #124 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #125 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #126 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #127 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #128 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #129 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #130 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #131 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #132 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:109277:27: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee284a9c in sqlite3ResolveExprListNames vendor/sqlite3/sqlite3.c:109277 #1 0x7fd5ee2a53a1 in resolveSelectStep vendor/sqlite3/sqlite3.c:109027 #2 0x7fd5ee2760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #3 0x7fd5ee4095d3 in sqlite3ResolveSelectNames vendor/sqlite3/sqlite3.c:109330 #4 0x7fd5ee4095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150216 #5 0x7fd5ee4095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #6 0x7fd5ee4181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #7 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #14 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #15 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #16 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #17 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #18 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #19 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #20 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #21 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #22 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #23 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #24 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #25 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #26 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #27 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #28 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #29 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #30 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #31 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #32 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #33 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #35 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #36 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #37 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #38 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #39 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #40 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #41 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #42 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #43 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #44 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #45 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #46 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #47 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #48 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #49 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #50 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #51 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #53 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #54 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #55 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #56 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #57 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #58 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #59 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #60 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #61 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #62 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #63 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #64 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #65 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #66 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #67 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #68 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #69 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #70 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #71 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #72 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #73 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #74 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #75 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #76 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #77 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #78 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #79 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #80 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #81 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #82 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #83 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #84 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #85 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #86 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #87 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #88 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #89 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #90 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #91 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #92 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #93 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #94 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #95 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #96 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #97 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #98 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #99 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #100 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #101 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #102 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #103 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #104 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #105 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #106 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #107 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #108 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #109 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #110 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #111 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #112 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #113 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #114 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #115 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #116 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #117 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #118 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #119 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #120 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #121 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #122 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #123 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #124 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #125 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #126 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #127 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #128 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #129 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #130 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #131 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #132 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:108558:20: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee282bb7 in resolveAsName vendor/sqlite3/sqlite3.c:108558 #1 0x7fd5ee286e11 in resolveOrderGroupBy vendor/sqlite3/sqlite3.c:108872 #2 0x7fd5ee2a6408 in resolveSelectStep vendor/sqlite3/sqlite3.c:109120 #3 0x7fd5ee2760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #4 0x7fd5ee4095d3 in sqlite3ResolveSelectNames vendor/sqlite3/sqlite3.c:109330 #5 0x7fd5ee4095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150216 #6 0x7fd5ee4095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #7 0x7fd5ee4181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #8 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #9 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #10 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #11 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #12 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #13 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #14 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #15 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #16 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #17 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #18 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #19 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #20 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #21 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #22 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #23 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #24 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #25 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #26 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #27 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #28 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #29 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #30 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #31 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #32 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #33 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #34 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #35 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #36 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #37 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #38 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #39 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #40 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #41 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #42 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #43 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #44 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #45 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #47 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #48 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #49 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #50 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #51 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #52 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #53 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #54 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #55 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #56 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #57 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #58 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #59 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #60 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #61 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #62 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #63 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #64 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #65 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #66 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #68 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #69 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #70 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #71 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #72 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #73 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #74 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #75 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #76 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #77 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #78 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #79 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #80 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #81 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #82 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #83 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #84 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #85 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #86 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #87 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #88 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #89 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #90 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #91 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #92 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #93 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #94 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #95 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #96 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #97 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #98 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #99 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #100 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #101 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #102 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #103 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #104 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #105 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #106 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #107 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #108 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #109 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #110 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #111 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #112 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #113 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #114 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #115 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #116 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #117 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #118 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #119 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #120 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #121 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #122 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #123 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #124 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #125 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #126 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #127 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #128 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #129 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #130 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #131 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #132 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #133 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:108559:36: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee282bf3 in resolveAsName vendor/sqlite3/sqlite3.c:108559 #1 0x7fd5ee286e11 in resolveOrderGroupBy vendor/sqlite3/sqlite3.c:108872 #2 0x7fd5ee2a6408 in resolveSelectStep vendor/sqlite3/sqlite3.c:109120 #3 0x7fd5ee2760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #4 0x7fd5ee4095d3 in sqlite3ResolveSelectNames vendor/sqlite3/sqlite3.c:109330 #5 0x7fd5ee4095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150216 #6 0x7fd5ee4095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #7 0x7fd5ee4181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #8 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #9 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #10 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #11 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #12 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #13 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #14 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #15 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #16 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #17 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #18 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #19 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #20 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #21 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #22 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #23 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #24 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #25 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #26 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #27 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #28 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #29 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #30 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #31 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #32 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #33 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #34 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #35 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #36 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #37 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #38 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #39 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #40 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #41 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #42 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #43 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #44 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #45 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #47 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #48 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #49 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #50 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #51 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #52 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #53 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #54 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #55 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #56 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #57 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #58 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #59 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #60 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #61 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #62 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #63 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #64 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #65 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #66 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #67 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #68 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #69 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #70 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #71 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #72 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #73 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #74 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #75 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #76 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #77 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #78 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #79 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #80 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #81 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #82 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #83 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #84 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #85 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #86 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #87 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #88 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #89 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #90 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #91 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #92 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #93 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #94 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #95 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #96 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #97 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #98 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #99 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #100 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #101 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #102 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #103 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #104 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #105 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #106 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #107 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #108 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #109 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #110 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #111 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #112 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #113 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #114 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #115 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #116 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #117 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #118 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #119 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #120 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #121 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #122 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #123 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #124 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #125 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #126 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #127 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #128 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #129 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #130 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #131 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #132 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #133 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:108900:55: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee28755c in resolveOrderGroupBy vendor/sqlite3/sqlite3.c:108900 #1 0x7fd5ee2a6408 in resolveSelectStep vendor/sqlite3/sqlite3.c:109120 #2 0x7fd5ee2760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #3 0x7fd5ee4095d3 in sqlite3ResolveSelectNames vendor/sqlite3/sqlite3.c:109330 #4 0x7fd5ee4095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150216 #5 0x7fd5ee4095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #6 0x7fd5ee4181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #7 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #14 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #15 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #16 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #17 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #18 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #19 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #20 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #21 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #22 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #23 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #24 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #25 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #26 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #27 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #28 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #29 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #30 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #31 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #32 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #33 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #35 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #36 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #37 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #38 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #39 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #40 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #41 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #42 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #43 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #44 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #45 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #46 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #47 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #48 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #49 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #50 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #51 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #53 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #54 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #55 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #56 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #57 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #58 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #59 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #60 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #61 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #62 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #63 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #64 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #65 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #66 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #67 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #68 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #69 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #70 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #71 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #72 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #73 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #74 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #75 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #76 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #77 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #78 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #79 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #80 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #81 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #82 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #83 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #84 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #85 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #86 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #87 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #88 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #89 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #90 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #91 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #92 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #93 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #94 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #95 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #96 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #97 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #98 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #99 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #100 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #101 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #102 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #103 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #104 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #105 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #106 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #107 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #108 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #109 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #110 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #111 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #112 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #113 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #114 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #115 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #116 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #117 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #118 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #119 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #120 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #121 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #122 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #123 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #124 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #125 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #126 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #127 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #128 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #129 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #130 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #131 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #132 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:145839:24: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3d9fee in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145839 #1 0x7fd5ee4194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #2 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #3 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #4 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #5 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #6 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #7 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #8 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #9 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #10 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #11 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #12 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #13 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #14 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #15 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #16 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #17 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #18 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #19 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #20 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #21 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #22 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #23 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #24 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #25 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #26 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #27 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #28 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #30 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #31 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #32 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #33 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #34 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #35 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #36 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #37 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #38 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #39 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #40 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #41 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #42 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #43 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #44 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #45 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #46 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #48 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #49 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #50 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #51 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #52 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #53 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #54 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #55 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #56 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #57 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #58 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #59 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #60 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #61 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #62 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #63 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #64 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #65 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #66 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #67 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #68 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #69 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #70 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #71 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #72 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #73 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #74 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #75 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #76 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #77 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #78 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #79 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #80 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #81 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #82 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #83 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #84 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #85 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #86 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #87 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #88 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #89 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #90 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #91 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #92 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #93 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #94 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #95 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #96 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #97 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #98 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #99 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #100 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #101 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #102 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #103 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #104 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #105 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #106 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #107 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #108 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #109 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #110 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #111 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #112 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #113 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #114 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #115 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #116 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #117 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #118 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #119 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #120 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #121 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #122 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #123 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #124 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #125 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #126 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #127 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:145845:18: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3d9e7f in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145845 #1 0x7fd5ee4194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #2 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #3 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #4 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #5 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #6 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #7 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #8 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #9 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #10 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #11 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #12 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #13 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #14 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #15 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #16 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #17 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #18 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #19 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #20 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #21 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #22 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #23 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #24 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #25 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #26 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #27 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #28 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #30 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #31 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #32 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #33 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #34 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #35 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #36 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #37 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #38 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #39 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #40 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #41 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #42 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #43 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #44 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #45 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #46 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #48 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #49 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #50 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #51 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #52 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #53 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #54 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #55 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #56 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #57 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #58 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #59 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #60 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #61 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #62 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #63 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #64 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #65 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #66 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #67 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #68 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #69 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #70 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #71 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #72 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #73 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #74 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #75 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #76 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #77 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #78 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #79 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #80 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #81 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #82 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #83 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #84 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #85 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #86 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #87 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #88 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #89 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #90 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #91 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #92 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #93 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #94 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #95 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #96 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #97 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #98 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #99 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #100 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #101 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #102 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #103 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #104 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #105 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #106 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #107 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #108 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #109 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #110 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #111 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #112 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #113 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #114 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #115 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #116 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #117 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #118 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #119 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #120 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #121 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #122 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #123 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #124 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #125 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #126 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #127 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:145845:41: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3da06a in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145845 #1 0x7fd5ee4194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #2 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #3 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #4 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #5 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #6 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #7 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #8 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #9 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #10 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #11 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #12 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #13 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #14 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #15 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #16 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #17 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #18 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #19 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #20 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #21 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #22 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #23 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #24 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #25 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #26 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #27 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #28 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #30 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #31 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #32 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #33 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #34 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #35 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #36 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #37 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #38 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #39 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #40 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #41 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #42 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #43 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #44 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #45 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #46 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #48 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #49 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #50 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #51 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #52 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #53 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #54 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #55 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #56 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #57 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #58 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #59 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #60 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #61 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #62 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #63 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #64 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #65 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #66 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #67 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #68 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #69 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #70 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #71 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #72 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #73 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #74 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #75 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #76 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #77 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #78 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #79 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #80 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #81 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #82 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #83 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #84 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #85 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #86 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #87 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #88 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #89 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #90 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #91 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #92 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #93 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #94 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #95 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #96 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #97 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #98 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #99 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #100 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #101 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #102 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #103 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #104 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #105 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #106 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #107 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #108 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #109 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #110 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #111 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #112 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #113 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #114 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #115 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #116 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #117 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #118 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #119 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #120 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #121 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #122 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #123 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #124 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #125 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #126 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #127 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:145847:30: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3da718 in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145847 #1 0x7fd5ee4194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #2 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #3 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #4 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #5 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #6 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #7 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #8 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #9 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #10 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #11 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #12 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #13 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #14 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #15 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #16 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #17 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #18 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #19 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #20 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #21 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #22 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #23 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #24 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #25 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #26 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #27 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #28 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #30 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #31 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #32 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #33 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #34 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #35 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #36 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #37 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #38 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #39 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #40 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #41 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #42 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #43 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #44 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #45 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #46 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #48 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #49 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #50 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #51 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #52 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #53 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #54 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #55 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #56 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #57 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #58 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #59 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #60 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #61 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #62 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #63 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #64 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #65 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #66 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #67 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #68 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #69 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #70 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #71 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #72 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #73 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #74 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #75 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #76 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #77 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #78 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #79 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #80 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #81 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #82 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #83 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #84 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #85 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #86 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #87 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #88 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #89 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #90 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #91 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #92 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #93 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #94 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #95 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #96 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #97 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #98 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #99 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #100 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #101 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #102 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #103 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #104 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #105 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #106 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #107 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #108 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #109 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #110 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #111 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #112 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #113 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #114 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #115 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #116 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #117 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #118 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #119 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #120 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #121 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #122 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #123 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #124 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #125 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #126 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #127 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:145759:24: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3d9f95 in generateColumnTypes vendor/sqlite3/sqlite3.c:145759 #1 0x7fd5ee3d9f95 in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145874 #2 0x7fd5ee4194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #3 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #4 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #5 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #6 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #7 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #8 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #9 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #10 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #11 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #12 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #13 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #14 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #15 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #16 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #17 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #18 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #19 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #20 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #21 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #22 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #23 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #24 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #25 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #26 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #27 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #28 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #29 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #31 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #32 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #33 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #34 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #35 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #36 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #37 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #38 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #39 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #40 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #41 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #42 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #43 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #44 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #45 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #46 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #47 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #48 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #49 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #50 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #51 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #52 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #53 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #54 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #55 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #56 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #57 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #58 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #59 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #60 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #61 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #62 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #63 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #64 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #65 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #66 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #67 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #68 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #69 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #70 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #71 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #72 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #73 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #74 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #75 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #76 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #77 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #78 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #79 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #80 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #81 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #82 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #83 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #84 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #85 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #86 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #87 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #88 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #89 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #90 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #91 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #92 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #93 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #94 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #95 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #96 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #97 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #98 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #99 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #100 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #101 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #102 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #103 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #104 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #105 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #106 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #107 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #108 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #109 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #110 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #111 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #112 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #113 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #114 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #115 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #116 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #117 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #118 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #119 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #120 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #121 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #122 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #123 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #124 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #125 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #126 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #127 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #128 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:145214:35: runtime error: index 7 out of bounds for type 'CollSeq *[1]' #0 0x7fd5ee3d0ef8 in sqlite3KeyInfoAlloc vendor/sqlite3/sqlite3.c:145214 #1 0x7fd5ee3d1e09 in sqlite3KeyInfoFromExprList vendor/sqlite3/sqlite3.c:145287 #2 0x7fd5ee41a7c1 in sqlite3Select vendor/sqlite3/sqlite3.c:151707 #3 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #4 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #5 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #6 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #7 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #8 0x7fd5ee38a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #9 0x7fd5ee38a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #10 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #11 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #12 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #13 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #14 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #15 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #16 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #17 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #18 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #19 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #20 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #21 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #22 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #23 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #24 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #25 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #26 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #27 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #28 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #29 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #31 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #32 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #33 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #34 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #35 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #36 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #37 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #38 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #39 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #40 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #41 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #42 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #43 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #44 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #45 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #46 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #47 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #48 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #49 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #50 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #51 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #52 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #53 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #54 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #55 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #56 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #57 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #58 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #59 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #60 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #61 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #62 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #63 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #64 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #65 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #66 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #67 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #68 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #69 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #70 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #71 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #72 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #73 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #74 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #75 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #76 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #77 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #78 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #79 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #80 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #81 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #82 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #83 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #84 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #85 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #86 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #87 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #88 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #89 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #90 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #91 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #92 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #93 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #94 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #95 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #96 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #97 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #98 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #99 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #100 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #101 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #102 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #103 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #104 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #105 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #106 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #107 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #108 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #109 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #110 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #111 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #112 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #113 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #114 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #115 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #116 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #117 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #118 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #119 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #120 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #121 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #122 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #123 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #124 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #125 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #126 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #127 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #128 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:93710:29: runtime error: index 5 out of bounds for type 'u32 [1]' #0 0x7fd5ee1fb70d in allocateCursor vendor/sqlite3/sqlite3.c:93710 #1 0x7fd5ee21231a in sqlite3VdbeExec vendor/sqlite3/sqlite3.c:97773 #2 0x7fd5ee250e4d in sqlite3Step vendor/sqlite3/sqlite3.c:91376 #3 0x7fd5ee250e4d in sqlite3_step vendor/sqlite3/sqlite3.c:91437 #4 0x7fd5ee38aa34 in sqlite3_exec vendor/sqlite3/sqlite3.c:137126 #5 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #6 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #7 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #8 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #9 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #10 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #11 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #12 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #13 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #14 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #15 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #16 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #17 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #18 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #19 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #20 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #21 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #22 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #23 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #24 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #25 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #26 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #27 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #28 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #29 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #30 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #31 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #32 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #33 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #34 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #35 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #36 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #37 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #38 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #39 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #40 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #41 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #42 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #43 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #44 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #45 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #46 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #47 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #48 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #49 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #50 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #51 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #52 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #53 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #54 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #55 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #56 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #57 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #58 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #59 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #60 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #61 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #62 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #63 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #64 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #65 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #66 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #67 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #68 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #69 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #70 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #71 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #72 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #73 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #74 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #75 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #76 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #77 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #78 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #79 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #80 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #81 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #82 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #83 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #84 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #85 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #86 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #87 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #88 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #89 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #90 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #91 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #92 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #93 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #94 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #95 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #96 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #97 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #98 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #99 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #100 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #101 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #102 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #103 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #104 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #105 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #106 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #107 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #108 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #109 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #110 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #111 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #112 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #113 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #114 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #115 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #116 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #117 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #118 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #119 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #120 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #121 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #122 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #123 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:96477:23: runtime error: index 1 out of bounds for type 'u32 [1]' #0 0x7fd5ee248405 in sqlite3VdbeExec vendor/sqlite3/sqlite3.c:96477 #1 0x7fd5ee250e4d in sqlite3Step vendor/sqlite3/sqlite3.c:91376 #2 0x7fd5ee250e4d in sqlite3_step vendor/sqlite3/sqlite3.c:91437 #3 0x7fd5ee38aa34 in sqlite3_exec vendor/sqlite3/sqlite3.c:137126 #4 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #5 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #6 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #7 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #8 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #9 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #10 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #11 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #12 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #13 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #14 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #15 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #16 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #17 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #18 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #19 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #20 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #21 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #22 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #23 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #24 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #25 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #26 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #27 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #28 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #29 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #30 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #32 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #33 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #34 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #35 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #36 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #37 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #38 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #39 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #40 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #41 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #42 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #43 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #44 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #45 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #46 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #47 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #48 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #49 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #50 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #51 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #52 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #53 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #54 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #55 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #57 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #58 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #59 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #60 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #61 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #62 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #63 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #64 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #65 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #66 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #67 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #68 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #69 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #70 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #71 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #72 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #73 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #74 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #75 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #76 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #77 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #78 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #79 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #80 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #81 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #82 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #83 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #84 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #85 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #86 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #87 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #88 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #89 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #90 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #91 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #92 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #93 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #94 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #95 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #96 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #97 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #98 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #99 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #100 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #101 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #102 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #103 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #104 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #105 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #106 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #107 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #108 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #109 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #110 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #111 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #112 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #113 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #114 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #115 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #116 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #117 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #118 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #119 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #120 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #121 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #122 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:96482:20: runtime error: index 4 out of bounds for type 'u32 [1]' #0 0x7fd5ee23fb07 in sqlite3VdbeExec vendor/sqlite3/sqlite3.c:96482 #1 0x7fd5ee250e4d in sqlite3Step vendor/sqlite3/sqlite3.c:91376 #2 0x7fd5ee250e4d in sqlite3_step vendor/sqlite3/sqlite3.c:91437 #3 0x7fd5ee38aa34 in sqlite3_exec vendor/sqlite3/sqlite3.c:137126 #4 0x7fd5ee3aec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #5 0x7fd5ee3b1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #6 0x7fd5ee3b1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #7 0x7fd5ee3b9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #8 0x7fd5ee50e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #9 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #10 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #11 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #12 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #13 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #14 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #15 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #16 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #17 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #18 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #19 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #20 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #21 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #22 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #23 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #24 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #25 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #26 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #27 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #28 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #29 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #30 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #31 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #32 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #33 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #34 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #35 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #36 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #37 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #38 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #39 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #40 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #41 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #42 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #43 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #44 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #45 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #46 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #47 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #48 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #49 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #50 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #51 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #52 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #53 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #54 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #55 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #57 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #58 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #59 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #60 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #61 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #62 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #63 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #64 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #65 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #66 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #67 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #68 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #69 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #70 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #71 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #72 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #73 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #74 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #75 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #76 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #77 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #78 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #79 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #80 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #81 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #82 0x8b4f71 in forcePromise /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:956 #83 0x8b4f71 in getvar /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:5835 #84 0x8e909c in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7848 #85 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #86 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #87 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #88 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #89 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #90 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #91 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #92 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #93 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #94 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #95 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #96 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #97 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #98 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #99 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #100 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #101 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #102 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #103 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #104 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #105 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #106 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #107 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #108 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #109 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #110 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #111 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #112 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #113 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #114 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #115 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #116 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #117 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #118 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #119 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #120 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #121 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #122 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:145930:42: runtime error: index 2 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3dc6f6 in sqlite3ColumnsFromExprList.isra.0 vendor/sqlite3/sqlite3.c:145930 #1 0x7fd5ee3fc0b6 in sqlite3ExpandSubquery vendor/sqlite3/sqlite3.c:149644 #2 0x7fd5ee3fc0b6 in selectExpander vendor/sqlite3/sqlite3.c:149767 #3 0x7fd5ee2760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #4 0x7fd5ee40946f in sqlite3SelectExpand vendor/sqlite3/sqlite3.c:150132 #5 0x7fd5ee40946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150214 #6 0x7fd5ee40946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #7 0x7fd5ee4181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #8 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #9 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #10 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #11 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #12 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #13 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #14 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #15 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #16 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #17 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #18 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #19 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #20 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #21 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #22 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #23 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #24 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #25 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #26 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #27 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #28 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #29 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #30 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #31 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #32 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #33 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #34 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #35 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #36 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #37 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #39 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #40 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #41 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #42 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #43 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #44 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #45 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #46 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #47 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #48 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #49 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #50 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #51 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #53 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #54 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #55 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #56 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #57 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #58 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #59 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #60 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #61 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #62 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #63 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #64 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #65 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #66 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #67 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #68 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #69 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #70 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:146060:48: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3dde7c in sqlite3SubqueryColumnTypes vendor/sqlite3/sqlite3.c:146060 #1 0x7fd5ee3f0fee in selectAddSubqueryTypeInfo vendor/sqlite3/sqlite3.c:150167 #2 0x7fd5ee276583 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107021 #3 0x7fd5ee4096e3 in sqlite3SelectAddTypeInfo vendor/sqlite3/sqlite3.c:150188 #4 0x7fd5ee4096e3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150218 #5 0x7fd5ee4096e3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #6 0x7fd5ee4181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #7 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #14 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #15 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #16 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #17 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #18 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #19 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #20 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #21 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #22 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #25 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #26 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #27 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #28 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #29 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #31 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #32 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #33 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #34 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #35 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #36 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #37 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #38 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #39 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #40 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #41 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #42 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #43 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #44 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #45 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #46 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #47 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #48 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #49 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #50 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #51 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #52 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #53 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #54 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #55 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #57 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #58 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #59 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #60 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #61 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #62 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #63 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #64 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #65 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #66 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #67 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #68 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #69 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:145675:34: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3cbcf5 in columnTypeImpl vendor/sqlite3/sqlite3.c:145675 #1 0x7fd5ee3d9c69 in generateColumnTypes vendor/sqlite3/sqlite3.c:145775 #2 0x7fd5ee3d9c69 in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145874 #3 0x7fd5ee4194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #4 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #5 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #6 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #7 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #8 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #9 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #10 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #11 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #12 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #13 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #14 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #15 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #16 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #17 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #18 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #19 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #20 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #21 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #22 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #23 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #24 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #25 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #26 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #28 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #29 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #30 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #31 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #32 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #33 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #35 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #36 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #37 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #38 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #39 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #40 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #41 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #42 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #43 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #44 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #45 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #46 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #47 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #48 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #49 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #50 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #51 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #52 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #53 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #54 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #55 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #56 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #57 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #58 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #59 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #60 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #61 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #62 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #63 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #64 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #65 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #66 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:147855:39: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3f52fb in compoundHasDifferentAffinities vendor/sqlite3/sqlite3.c:147855 #1 0x7fd5ee3f52fb in flattenSubquery vendor/sqlite3/sqlite3.c:148192 #2 0x7fd5ee418c2e in sqlite3Select vendor/sqlite3/sqlite3.c:151374 #3 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #4 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #5 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #6 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #7 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #8 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #9 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #10 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #11 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #12 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #13 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #14 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #15 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #16 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #17 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #18 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #20 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #21 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #22 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #23 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #24 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #25 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #26 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #27 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #28 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #29 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #30 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #31 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #32 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #33 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #34 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #35 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #36 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #37 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #38 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #39 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #40 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #41 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #42 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #43 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #44 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #45 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #46 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #48 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #49 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #50 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #51 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #53 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #54 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #55 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #56 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #57 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #58 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #59 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #60 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #61 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #62 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #63 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #64 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #65 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:147860:47: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3f5239 in compoundHasDifferentAffinities vendor/sqlite3/sqlite3.c:147860 #1 0x7fd5ee3f5239 in flattenSubquery vendor/sqlite3/sqlite3.c:148192 #2 0x7fd5ee418c2e in sqlite3Select vendor/sqlite3/sqlite3.c:151374 #3 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #4 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #5 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #6 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #7 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #8 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #9 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #10 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #11 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #12 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #13 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #14 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #15 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #16 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #17 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #18 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #19 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #20 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #21 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #22 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #23 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #24 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #25 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #26 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #27 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #28 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #29 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #30 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #31 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #32 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #33 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #34 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #35 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #36 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #37 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #38 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #39 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #40 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #41 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #42 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #43 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #44 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #45 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #46 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #47 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #48 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #49 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #50 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #51 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #52 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #53 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #54 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #55 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #56 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #57 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #58 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #59 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #60 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #61 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #62 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #63 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #64 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #65 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:147583:32: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3eb18d in substExpr vendor/sqlite3/sqlite3.c:147583 #1 0x7fd5ee75f515 in substExprList.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:147665 #2 0x7fd5ee75f741 in substExprList vendor/sqlite3/sqlite3.c:147663 #3 0x7fd5ee75f741 in substSelect.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:147678 #4 0x7fd5ee3f47ab in substSelect vendor/sqlite3/sqlite3.c:147676 #5 0x7fd5ee3f47ab in flattenSubquery vendor/sqlite3/sqlite3.c:148436 #6 0x7fd5ee418c2e in sqlite3Select vendor/sqlite3/sqlite3.c:151374 #7 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #14 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #15 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #16 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #17 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #18 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #19 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #20 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #21 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #22 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #25 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #26 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #27 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #28 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #29 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #31 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #32 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #33 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #34 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #35 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #36 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #37 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #38 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #39 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #40 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #41 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #42 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #43 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #44 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #45 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #46 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #47 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #48 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #49 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #50 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #51 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #52 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #53 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #54 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #55 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #57 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #58 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #59 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #60 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #61 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #62 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #63 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #64 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #65 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #66 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #67 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #68 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #69 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:147625:34: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3eb40e in substExpr vendor/sqlite3/sqlite3.c:147625 #1 0x7fd5ee75f515 in substExprList.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:147665 #2 0x7fd5ee75f741 in substExprList vendor/sqlite3/sqlite3.c:147663 #3 0x7fd5ee75f741 in substSelect.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:147678 #4 0x7fd5ee3f47ab in substSelect vendor/sqlite3/sqlite3.c:147676 #5 0x7fd5ee3f47ab in flattenSubquery vendor/sqlite3/sqlite3.c:148436 #6 0x7fd5ee418c2e in sqlite3Select vendor/sqlite3/sqlite3.c:151374 #7 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #14 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #15 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #16 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #17 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #18 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #19 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #20 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #21 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #22 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #23 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #25 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #26 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #27 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #28 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #29 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #30 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #31 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #32 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #33 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #34 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #35 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #36 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #37 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #38 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #39 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #40 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #41 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #42 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #43 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #44 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #45 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #46 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #47 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #48 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #49 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #50 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #51 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #52 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #53 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #54 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #55 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #57 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #58 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #59 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #60 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #61 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #62 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #63 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #64 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #65 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #66 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #67 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #68 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #69 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:163112:55: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee75bf44 in sqlite3WhereExprListUsage.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:163112 #1 0x7fd5ee486c1d in sqlite3WhereExprListUsage vendor/sqlite3/sqlite3.c:163110 #2 0x7fd5ee486c1d in exprAnalyze vendor/sqlite3/sqlite3.c:162413 #3 0x7fd5ee48a6ff in exprAnalyzeOrTerm vendor/sqlite3/sqlite3.c:162201 #4 0x7fd5ee48a6ff in exprAnalyze vendor/sqlite3/sqlite3.c:162584 #5 0x7fd5ee4d9d64 in sqlite3WhereExprAnalyze vendor/sqlite3/sqlite3.c:163133 #6 0x7fd5ee4d9d64 in sqlite3WhereBegin vendor/sqlite3/sqlite3.c:169832 #7 0x7fd5ee41ae1b in sqlite3Select vendor/sqlite3/sqlite3.c:151779 #8 0x7fd5ee3e1e5c in multiSelectOrderBy vendor/sqlite3/sqlite3.c:147359 #9 0x7fd5ee3e1e5c in multiSelect vendor/sqlite3/sqlite3.c:146636 #10 0x7fd5ee41c467 in sqlite3Select vendor/sqlite3/sqlite3.c:151392 #11 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #12 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #13 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #14 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #15 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #16 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #17 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #18 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #19 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #20 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #21 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #22 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #23 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #24 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #25 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #26 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #28 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #29 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #30 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #31 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #32 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #33 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #35 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #36 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #37 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #38 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #39 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #40 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #41 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #42 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #43 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #44 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #45 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #46 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #47 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #48 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #49 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #50 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #51 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #52 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #53 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #54 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #55 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #56 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #57 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #58 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #59 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #60 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #61 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #62 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #63 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #64 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #65 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #66 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #67 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #68 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #69 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #70 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #71 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #72 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #73 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:114966:43: runtime error: index 2 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee2c987d in sqlite3ExprCodeRunJustOnce vendor/sqlite3/sqlite3.c:114966 #1 0x7fd5ee2c9c56 in sqlite3ExprCodeTemp vendor/sqlite3/sqlite3.c:114998 #2 0x7fd5ee2d0a31 in sqlite3ExprIfFalse vendor/sqlite3/sqlite3.c:115480 #3 0x7fd5ee466e39 in sqlite3WhereCodeOneLoopStart vendor/sqlite3/sqlite3.c:161029 #4 0x7fd5ee4dc650 in sqlite3WhereBegin vendor/sqlite3/sqlite3.c:170294 #5 0x7fd5ee41ae1b in sqlite3Select vendor/sqlite3/sqlite3.c:151779 #6 0x7fd5ee3e1e5c in multiSelectOrderBy vendor/sqlite3/sqlite3.c:147359 #7 0x7fd5ee3e1e5c in multiSelect vendor/sqlite3/sqlite3.c:146636 #8 0x7fd5ee41c467 in sqlite3Select vendor/sqlite3/sqlite3.c:151392 #9 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #10 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #11 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #12 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #13 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #14 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #15 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #16 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #17 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #18 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #19 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #20 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #21 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #22 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #23 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #24 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #25 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #26 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #27 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #28 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #29 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #30 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #31 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #33 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #34 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #35 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #36 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #37 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #38 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #39 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #40 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #41 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #42 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #43 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #44 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #45 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #46 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #47 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #48 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #49 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #50 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #51 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #52 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #53 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #54 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #55 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #56 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #57 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #58 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #59 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #60 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #61 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #62 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #63 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #64 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #65 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #66 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #67 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #68 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #69 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #70 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #71 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:122207:56: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3041c2 in sqlite3FinishCoding vendor/sqlite3/sqlite3.c:122207 #1 0x7fd5ee509834 in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177464 #2 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #3 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #4 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #5 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #6 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #7 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #8 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #9 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #10 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #11 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #12 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #13 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #14 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #15 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #16 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #17 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #18 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #19 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #20 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #21 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #22 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #23 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #24 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #25 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #26 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #27 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #28 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #29 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #30 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #31 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #32 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #33 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #34 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #35 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #36 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #37 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #39 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #40 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #41 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #42 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #43 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #44 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #45 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #46 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #47 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #48 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #49 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #50 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #51 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #52 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #53 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #54 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #55 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #56 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #57 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #58 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #59 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #60 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #61 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #62 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #63 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:122207:39: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee304155 in sqlite3FinishCoding vendor/sqlite3/sqlite3.c:122207 #1 0x7fd5ee509834 in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177464 #2 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #3 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #4 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #5 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #6 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #7 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #8 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #9 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #10 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #11 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #12 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #13 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #14 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #15 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #16 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #17 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #18 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #19 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #20 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #21 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #22 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #23 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #24 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #25 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #26 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #27 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #28 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #29 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #30 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #31 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #32 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #33 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #34 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #35 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #36 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #37 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #39 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #40 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #41 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #42 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #43 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #44 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #45 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #46 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #47 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #48 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #49 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #50 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #51 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #52 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #53 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #54 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #55 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #56 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #57 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #58 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #59 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #60 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #61 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #62 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #63 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:96527:18: runtime error: index 1 out of bounds for type 'u32 [1]' #0 0x7fd5ee24c7a9 in sqlite3VdbeExec vendor/sqlite3/sqlite3.c:96527 #1 0x7fd5ee250e4d in sqlite3Step vendor/sqlite3/sqlite3.c:91376 #2 0x7fd5ee250e4d in sqlite3_step vendor/sqlite3/sqlite3.c:91437 #3 0x7fd5ee053af9 in SqliteResultImpl::step_run() /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:341 #4 0x7fd5ee06d532 in SqliteResultImpl::step() /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:334 #5 0x7fd5ee06d532 in SqliteResultImpl::after_bind(bool) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:306 #6 0x7fd5ee06d532 in SqliteResultImpl::after_bind(bool) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:303 #7 0x7fd5ee06d532 in SqliteResultImpl::bind(cpp11::r_vector const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:147 #8 0x7fd5ee06d532 in DbResult::bind(cpp11::r_vector const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/DbResult.cpp:49 #9 0x7fd5ee06d532 in result_bind(DbResult*, cpp11::r_vector) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:32 #10 0x7fd5ee06d532 in _RSQLite_result_bind /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:101 #11 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #12 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #13 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #14 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #15 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #16 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #17 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #18 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #19 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #20 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #21 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #22 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #23 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #24 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #25 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #26 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #27 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #28 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #30 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #31 0x8d9222 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8118 #32 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #33 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #35 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #36 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #37 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #38 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #39 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #40 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #41 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #42 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #43 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #44 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #45 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #46 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #47 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:144911:22: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee3d65e4 in selectInnerLoop vendor/sqlite3/sqlite3.c:144911 #1 0x7fd5ee41f733 in sqlite3Select vendor/sqlite3/sqlite3.c:151828 #2 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #3 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #4 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #5 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #6 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #7 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #8 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #9 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #10 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #11 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #12 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #13 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #14 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #15 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #16 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #17 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #18 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #19 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #20 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #21 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #22 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #23 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #24 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #25 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #26 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #27 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #28 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #29 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #30 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #31 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #32 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #33 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #34 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #35 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #36 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #37 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #38 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #39 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #40 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #41 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #42 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #43 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #44 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #45 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #46 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #47 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #48 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #49 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #50 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #51 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #52 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #53 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #54 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #55 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #56 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #57 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #58 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #59 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #60 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #61 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #62 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #63 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #64 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #65 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #66 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #67 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #68 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #69 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #70 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #71 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #72 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #73 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) Obtaining reactome pathway information for species: Homo sapiens vendor/sqlite3/sqlite3.c:79337:14: runtime error: load of address 0x7fd608321640 with insufficient space for an object of type 'struct MemPage *' 0x7fd608321640: note: pointer points here d6 7f 00 00 90 71 68 00 10 52 00 00 90 35 68 00 10 52 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ^ #0 0x7fd5ee1a2177 in balance_nonroot vendor/sqlite3/sqlite3.c:79337 #1 0x7fd5ee1a74f9 in balance vendor/sqlite3/sqlite3.c:79798 #2 0x7fd5ee1b472d in sqlite3BtreeInsert vendor/sqlite3/sqlite3.c:80253 #3 0x7fd5ee220a56 in sqlite3VdbeExec vendor/sqlite3/sqlite3.c:99891 #4 0x7fd5ee250e4d in sqlite3Step vendor/sqlite3/sqlite3.c:91376 #5 0x7fd5ee250e4d in sqlite3_step vendor/sqlite3/sqlite3.c:91437 #6 0x7fd5ee053af9 in SqliteResultImpl::step_run() /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:341 #7 0x7fd5ee0570aa in SqliteResultImpl::step() /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:334 #8 0x7fd5ee0570aa in SqliteResultImpl::fetch_rows(int, int&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:322 #9 0x7fd5ee0570aa in SqliteResultImpl::fetch(int) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:158 #10 0x7fd5ee0570aa in DbResult::fetch(int) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/DbResult.cpp:56 #11 0x7fd5ee0570aa in result_fetch(DbResult*, int) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:27 #12 0x7fd5ee0570aa in _RSQLite_result_fetch /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:94 #13 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #14 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #15 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #16 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #17 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #18 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #19 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #20 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #21 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #22 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #23 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #24 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #25 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #26 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #27 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #28 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #29 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #30 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #31 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #32 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #33 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #34 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #35 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #36 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #37 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #38 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #39 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #40 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #41 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #42 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #43 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #44 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #45 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #46 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #47 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #48 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #49 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #50 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #51 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #52 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #53 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #54 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #55 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #56 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #57 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #58 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #59 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #60 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #61 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #62 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #63 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #64 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #65 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #66 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #67 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #68 0x5d2714 in do_switch /data/gannet/ripley/R/svn/R-devel/src/main/builtin.c:1078 #69 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #70 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #71 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #72 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #73 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #74 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #75 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #76 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #77 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #78 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #79 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #80 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #81 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #82 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #83 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #84 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #85 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #86 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #87 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #88 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #89 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #90 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #91 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #92 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #93 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #94 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #95 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #96 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:110207:24: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee759460 in heightOfExprList.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:110207 #1 0x7fd5ee28a42a in heightOfExprList vendor/sqlite3/sqlite3.c:110204 #2 0x7fd5ee28a42a in exprSetHeight vendor/sqlite3/sqlite3.c:110241 #3 0x7fd5ee28ae2f in sqlite3ExprSetHeightAndFlags vendor/sqlite3/sqlite3.c:110257 #4 0x7fd5ee28ae2f in sqlite3ExprSetHeightAndFlags vendor/sqlite3/sqlite3.c:110255 #5 0x7fd5ee50b84a in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178460 #6 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #7 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #8 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #9 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #10 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #11 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #12 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #13 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #14 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #15 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #16 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #17 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #18 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #19 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #20 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #21 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #22 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #23 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #24 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #25 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #26 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #27 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #28 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #29 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #30 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #31 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #32 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #33 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #34 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #35 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #36 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #37 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #38 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #39 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #40 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #41 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #42 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #43 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #44 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #45 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #46 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #47 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #48 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #49 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #50 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #51 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #52 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #53 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #54 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #55 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #56 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #57 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #58 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #59 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #60 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #61 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #62 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #63 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #64 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #65 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #66 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #67 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #68 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #69 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #70 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #71 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #72 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #73 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #74 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #75 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #76 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #77 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #78 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #79 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #80 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #81 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #82 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #83 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #84 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #85 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #86 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #87 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #88 0x867d98 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1264 #89 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #90 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #91 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #92 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #93 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #94 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #95 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #96 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #97 0xa9e773 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #98 0xa9e773 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #99 0xaa2aa0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #100 0xaa48f3 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:509 #101 0xaa5646 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #102 0x8e6431 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8138 #103 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #104 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #105 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #106 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #107 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #108 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #109 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #110 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #111 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #112 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #113 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #114 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #115 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #116 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #117 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #118 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:111673:28: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee28a7e0 in sqlite3ExprListFlags vendor/sqlite3/sqlite3.c:111673 #1 0x7fd5ee28a7e0 in exprSetHeight vendor/sqlite3/sqlite3.c:110242 #2 0x7fd5ee28ae2f in sqlite3ExprSetHeightAndFlags vendor/sqlite3/sqlite3.c:110257 #3 0x7fd5ee28ae2f in sqlite3ExprSetHeightAndFlags vendor/sqlite3/sqlite3.c:110255 #4 0x7fd5ee50b84a in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178460 #5 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #6 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #7 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #8 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #9 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #10 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #11 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #12 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #13 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #14 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #15 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #16 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #17 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #18 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #19 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #20 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #21 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #22 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #23 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #24 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #25 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #26 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #27 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #28 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #29 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #30 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #31 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #32 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #33 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #34 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #35 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #36 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #37 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #38 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #39 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #40 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #41 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #42 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #43 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #44 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #45 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #46 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #47 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #48 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #49 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #50 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #51 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #52 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #53 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #54 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #55 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #56 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #57 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #58 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #59 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #60 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #61 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #62 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #63 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #64 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #65 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #66 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #67 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #68 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #69 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #70 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #71 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #72 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #73 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #74 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #75 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #76 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #77 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #78 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #79 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #80 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #81 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #82 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #83 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #84 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #85 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #86 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #87 0x867d98 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1264 #88 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #89 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #90 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #91 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #92 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #93 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #94 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #95 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #96 0xa9e773 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #97 0xa9e773 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #98 0xaa2aa0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #99 0xaa48f3 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:509 #100 0xaa5646 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #101 0x8e6431 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8138 #102 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #103 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #104 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #105 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #106 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #107 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #108 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #109 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #110 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #111 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #112 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #113 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #114 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #115 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #116 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #117 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) vendor/sqlite3/sqlite3.c:149853:19: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7fd5ee405b5f in selectExpander vendor/sqlite3/sqlite3.c:149853 #1 0x7fd5ee2760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #2 0x7fd5ee40946f in sqlite3SelectExpand vendor/sqlite3/sqlite3.c:150132 #3 0x7fd5ee40946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150214 #4 0x7fd5ee40946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #5 0x7fd5ee4181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #6 0x7fd5ee507ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #7 0x7fd5ee540521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #8 0x7fd5ee540521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #9 0x7fd5ee3aa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #10 0x7fd5ee3b256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #11 0x7fd5ee061595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #12 0x7fd5ee061595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #13 0x7fd5ee061595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #14 0x7fd5ee061595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #15 0x7fd5ee061595 in SqliteResult::create_and_send_query(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:17 #16 0x7fd5ee061595 in result_create(cpp11::external_pointer, &(void cpp11::default_deleter >(boost::shared_ptr*))>, std::__cxx11::basic_string, std::allocator >) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:10 #17 0x7fd5ee061595 in _RSQLite_result_create /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/cpp11.cpp:72 #18 0x75b256 in R_doDotCall /data/gannet/ripley/R/svn/R-devel/src/main/dotcode.c:757 #19 0x8efc2a in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8668 #20 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #21 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #22 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #23 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #24 0x92db01 in forcePromise.part.0.lto_priv.0 /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:976 #25 0x8682e7 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1193 #26 0x8fdac7 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8012 #27 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #28 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #29 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #30 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #31 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #32 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #33 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #34 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #35 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #36 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #37 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #38 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #39 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #40 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #41 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #42 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #43 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #44 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #45 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #46 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #47 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #48 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #49 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #50 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #51 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #52 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #53 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #54 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #55 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #56 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #57 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #58 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #59 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #60 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #61 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #62 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #63 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #64 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #65 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #66 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #67 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #68 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #69 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #70 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #71 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #72 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #73 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #74 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #75 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #76 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #77 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #78 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #79 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #80 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #81 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #82 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #83 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #84 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #85 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #86 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #87 0x7fd6097e0c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #88 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #89 0x867d98 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1264 #90 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #91 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #92 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #93 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #94 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #95 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #96 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #97 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #98 0xa9e773 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #99 0xa9e773 in applyMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:120 #100 0xaa2aa0 in dispatchMethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:473 #101 0xaa48f3 in Rf_usemethod.isra.0 /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:509 #102 0xaa5646 in do_usemethod /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:579 #103 0x8e6431 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8138 #104 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #105 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #106 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #107 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #108 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #109 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #110 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #111 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #112 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #113 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #114 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #115 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #116 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #117 0x7fd60c638087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #118 0x7fd60c63814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #119 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) > > > > cleanEx() > nameEx("head.dnapath_list") > ### * head.dnapath_list > > flush(stderr()); flush(stdout()) > > ### Name: head.dnapath_list > ### Title: Return the first part of the dnapath results. > ### Aliases: head.dnapath_list > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > head(results) # A tibble: 5 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 Regulation of TP5… 1.77 0.0909 37 7 10.1 10.2 2 Regulation of TP5… 1.15 0.909 30 0 10.2 10.2 3 Regulation of TP5… 0.880 0.273 14 1 7.70 7.60 4 TP53 Regulates Tr… 2.35 0.727 49 2 9.09 9.16 5 TP53 Regulates Tr… 1.30 1 14 0 7.76 7.94 > > > > cleanEx() > nameEx("length.dnapath_list") > ### * length.dnapath_list > > flush(stderr()); flush(stdout()) > > ### Name: length.dnapath_list > ### Title: The number of pathways in a 'dnapath_list' object. > ### Aliases: length.dnapath_list > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > length(results) [1] 13 > > > > cleanEx() > nameEx("names.dnapath") > ### * names.dnapath > > flush(stderr()); flush(stdout()) > > ### Name: names.dnapath > ### Title: The pathway names in a 'dnapath' object. > ### Aliases: names.dnapath > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > names(results[[1]]) [1] "Regulation of TP53 Degradation (See also: Regulation of TP53 Expression and Degradation)" > > > > cleanEx() > nameEx("names.dnapath_list") > ### * names.dnapath_list > > flush(stderr()); flush(stdout()) > > ### Name: names.dnapath_list > ### Title: The pathway names in a 'dnapath_list' object. > ### Aliases: names.dnapath_list > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > names(results) [1] "Regulation of TP53 Degradation (See also: Regulation of TP53 Expression and Degradation)" [2] "Regulation of TP53 Activity through Acetylation" [3] "Regulation of TP53 Activity through Association with Co-factors" [4] "TP53 Regulates Transcription of Cell Cycle Genes" [5] "TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest" [6] "TP53 Regulates Transcription of Cell Death Genes" [7] "TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain" [8] "Regulation of TP53 Activity through Methylation" [9] "TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest" [10] "TP53 Regulates Transcription of Genes Involved in Cytochrome C Release" [11] "TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain" [12] "TP53 Regulates Transcription of Death Receptors and Ligands" [13] "TP53 Regulates Transcription of Caspase Activators and Caspases" > > > > cleanEx() > nameEx("plot.dnapath") > ### * plot.dnapath > > flush(stderr()); flush(stdout()) > > ### Name: plot.dnapath > ### Title: Plot function for 'dnapath' object. > ### Aliases: plot.dnapath > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > # Plot of the differential network for pathway 1. > plot(results[[1]]) > # Plot of the differential network for pathway 1; remove any edges from > # the plot that have p-values above 0.1. > plot(results[[1]], alpha = 0.1) > > > > cleanEx() > nameEx("plot_pair") > ### * plot_pair > > flush(stderr()); flush(stdout()) > > ### Name: plot_pair > ### Title: Plot the expression values of two genes > ### Aliases: plot_pair > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > # Plot of the marginal association between the first two genes. > genes <- get_genes(results)[1:2] > g <- plot_pair(results, genes[1], genes[2]) > # The ggplot object, g, can be further modified. > # Here we move the legend and use a log scale for the expression values > # (the log scale doesn't help with these data but is shown for demonstration). > g <- g + + ggplot2::theme(legend.position = "bottom") + + ggplot2::scale_x_log10() + + ggplot2::scale_y_log10() > g `geom_smooth()` using formula = 'y ~ x' > > > > cleanEx() > nameEx("rename_genes") > ### * rename_genes > > flush(stderr()); flush(stdout()) > > ### Name: rename_genes > ### Title: Rename genes in the differential network analysis > ### Aliases: rename_genes > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > summary(results[[1]]) # Summary of pathway 1; note that it uses entrezgene IDs. # A tibble: 37 × 6 pathway genes dc_score p_value mean_expr1 mean_expr2 1 Regulation of TP53 Degradation … 1616 0.256 0.0909 10.9 10.7 2 Regulation of TP53 Degradation … 4193 0.228 0.0909 11.0 11.1 3 Regulation of TP53 Degradation … 5527 0.226 0.0909 10.4 10.6 4 Regulation of TP53 Degradation … 6446 0.218 0.0909 11.3 11.7 5 Regulation of TP53 Degradation … 51230 0.201 0.0909 10.1 9.96 6 Regulation of TP53 Degradation … 207 0.152 0.0909 11.4 11.6 7 Regulation of TP53 Degradation … 983 0.141 0.0909 8.49 8.56 8 Regulation of TP53 Degradation … 7157 0.221 0.182 11.1 10.8 9 Regulation of TP53 Degradation … 80196 0.214 0.182 9.37 9.36 10 Regulation of TP53 Degradation … 5519 0.177 0.182 9.14 9.20 # ℹ 27 more rows > > > > > cleanEx() > nameEx("rev.dnapath_list") > ### * rev.dnapath_list > > flush(stderr()); flush(stdout()) > > ### Name: rev.dnapath_list > ### Title: Reverse the order of pathways in a 'dnapath_list' object. > ### Aliases: rev.dnapath_list > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > # Filter out pathways that have p-values above 0.2. > results <- filter_pathways(results, 0.2) > results <- sort(results, by = "dc_score") # Sort by the pathway DC score. > results <- rev(results) # Reverse the ordering. > > > > cleanEx() > nameEx("run_aracne") > ### * run_aracne > > flush(stderr()); flush(stdout()) > > ### Name: run_aracne > ### Title: Wrapper for ARACNE method > ### Aliases: run_aracne > > ### ** Examples > > data(meso) > data(p53_pathways) > > # To create a short example, we subset on two pathways from the p53 pathway list, > # and will only run 5 permutations for significance testing. > pathway_list <- p53_pathways[c(8, 13)] > n_perm <- 5 > > # Use this method to perform differential network analysis. > # The parameters in run_aracne() can be adjusted using the ... argument. > # For example, the 'estimator' parameter can be specified as shown here. > results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_aracne, + estimator = "spearman") > summary(results) Warning in summary.dnapath_list(results) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.166666666666667 # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.167)` mean_expr1 mean_expr2 1 Regulation of T… 1.22 0.833 19 1 10.8 10.8 2 TP53 Regulates … 0.918 0.333 12 2 7.91 7.91 > > # The group-specific association matrices can be extracted using get_networks(). > nw_list <- get_networks(results[[1]]) # Get networks for pathway 1. > > > > > cleanEx() > nameEx("run_bc3net") > ### * run_bc3net > > flush(stderr()); flush(stdout()) > > ### Name: run_bc3net > ### Title: Wrapper for BC3Net method > ### Aliases: run_bc3net > > ### ** Examples > > data(meso) > data(p53_pathways) > > # To create a short example, we subset on one pathway from the p53 pathway list, > # and will only run 1 permutation for significance testing. > pathway_list <- p53_pathways[13] > n_perm <- 1 > > # Use this method to perform differential network analysis. > # The parameters in run_bc3net() can be adjusted using the ... argument. > # For example, the 'estimator' and 'boot' parameter can be specified as shown here. > results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_bc3net, + boot = 10, + estimator = "pearson", + mtc1 = FALSE, + mtc2 = FALSE) > summary(results) # A tibble: 11 × 6 pathway genes dc_score p_value mean_expr1 mean_expr2 1 TP53 Regulates Transcription of… 317 1.36 0.5 8.64 8.79 2 TP53 Regulates Transcription of… 839 1.06 0.5 8.88 8.83 3 TP53 Regulates Transcription of… 8738 0.73 0.5 7.23 7.17 4 TP53 Regulates Transcription of… 835 0.7 0.5 9.73 9.70 5 TP53 Regulates Transcription of… 472 0.5 0.5 10.2 10.4 6 TP53 Regulates Transcription of… 834 1.05 1 9.14 9.39 7 TP53 Regulates Transcription of… 58484 0.87 1 5.77 6.05 8 TP53 Regulates Transcription of… 7161 0.69 1 3.88 3.47 9 TP53 Regulates Transcription of… 7157 0.59 1 11.1 10.8 10 TP53 Regulates Transcription of… 8626 0.47 1 3.49 3.14 11 TP53 Regulates Transcription of… 843 0.26 1 8.94 9.23 > > # The group-specific association matrices can be extracted using get_networks(). > nw_list <- get_networks(results) # Get networks for pathway 1. > > > > > cleanEx() > nameEx("run_c3net") > ### * run_c3net > > flush(stderr()); flush(stdout()) > > ### Name: run_c3net > ### Title: Wrapper for C3Net method > ### Aliases: run_c3net > > ### ** Examples > > data(meso) > data(p53_pathways) > > # To create a short example, we subset on one pathway from the p53 pathway list, > # and will only run 1 permutation for significance testing. > pathway_list <- p53_pathways[13] > n_perm <- 1 > > # Use this method to perform differential network analysis. > # The parameters in run_c3net() can be adjusted using the ... argument. > # For example, the 'estimator' parameter can be specified as shown here. > results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_c3net, + estimator = "pearson", + mtc = FALSE) > summary(results) # A tibble: 11 × 6 pathway genes dc_score p_value mean_expr1 mean_expr2 1 TP53 Regulates Transcription of… 317 0.421 0.5 8.64 8.79 2 TP53 Regulates Transcription of… 8626 0.202 0.5 3.49 3.14 3 TP53 Regulates Transcription of… 835 0.137 0.5 9.73 9.70 4 TP53 Regulates Transcription of… 8738 0.109 0.5 7.23 7.17 5 TP53 Regulates Transcription of… 472 0.0919 0.5 10.2 10.4 6 TP53 Regulates Transcription of… 7157 0.0830 0.5 11.1 10.8 7 TP53 Regulates Transcription of… 834 0.182 1 9.14 9.39 8 TP53 Regulates Transcription of… 7161 0.0623 1 3.88 3.47 9 TP53 Regulates Transcription of… 58484 0.0616 1 5.77 6.05 10 TP53 Regulates Transcription of… 843 0.0572 1 8.94 9.23 11 TP53 Regulates Transcription of… 839 0.0560 1 8.88 8.83 > > # The group-specific association matrices can be extracted using get_networks(). > nw_list <- get_networks(results) # Get networks for the pathway. > > > > > cleanEx() > nameEx("run_clr") > ### * run_clr > > flush(stderr()); flush(stdout()) > > ### Name: run_clr > ### Title: Wrapper for CLR method > ### Aliases: run_clr > > ### ** Examples > > data(meso) > data(p53_pathways) > > # To create a short example, we subset on two pathways from the p53 pathway list, > # and will only run 5 permutations for significance testing. > pathway_list <- p53_pathways[c(8, 13)] > n_perm <- 5 > > # Use this method to perform differential network analysis. > # The parameters in run_clr() can be adjusted using the ... argument. > # For example, the 'estimator' paramter can be specified as shown here. > results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_clr, + estimator = "spearman") > summary(results) Warning in summary.dnapath_list(results) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.166666666666667 # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.167)` mean_expr1 mean_expr2 1 Regulation of T… 14.1 0.667 19 4 10.8 10.8 2 TP53 Regulates … 9.20 0.333 12 1 7.91 7.91 > > # The group-specific association matrices can be extracted using get_networks(). > nw_list <- get_networks(results[[1]]) # Get networks for pathway 1. > > > > > cleanEx() > nameEx("run_corr") > ### * run_corr > > flush(stderr()); flush(stdout()) > > ### Name: run_corr > ### Title: Wrapper for correlation co-expression > ### Aliases: run_corr > > ### ** Examples > > data(meso) > data(p53_pathways) > > # To create a short example, we subset on two pathways from the p53 pathway list, > # and will only run 5 permutations for significance testing. > pathway_list <- p53_pathways[c(8, 13)] > n_perm <- 5 > > # Use this method to perform differential network analysis. > # The parameters in run_corr() can be adjusted using the ... argument. > # For example, the 'method' parameter can be specified as shown here. > results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_corr, + method = "spearman") > summary(results) Warning in summary.dnapath_list(results) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.166666666666667 # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.167)` mean_expr1 mean_expr2 1 Regulation of T… 4.14 0.333 19 3 10.8 10.8 2 TP53 Regulates … 2.93 0.167 12 6 7.91 7.91 > > # The group-specific association matrices can be extracted using get_networks(). > nw_list <- get_networks(results[[1]]) # Get networks for pathway 1. > > > > > cleanEx() > nameEx("run_genie3") > ### * run_genie3 > > flush(stderr()); flush(stdout()) > > ### Name: run_genie3 > ### Title: Wrapper for GENIE3 method > ### Aliases: run_genie3 > > ### ** Examples > > if(!requireNamespace("GENIE3", quietly = TRUE)) { + data(meso) + data(p53_pathways) + + # To create a short example, we subset on two pathways from the p53 pathway list, + # and will only run 5 permutations for significance testing. + pathway_list <- p53_pathways[c(8, 13)] + n_perm <- 5 + + # Use this method to perform differential network analysis. + # The parameters in run_genie3() can be adjusted using the ... argument. + # For example, the 'nTrees' parameter can be specified as shown here. + results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_genie3, + nTrees = 100) + summary(results) + + # The group-specific association matrices can be extracted using get_networks(). + nw_list <- get_networks(results[[1]]) # Get networks for pathway 1. + + # nw_list has length 2 and contains the inferred networks for the two groups. + # The gene names are the Entrezgene IDs from the original expression dataset. + # Renaming the genes in the dnapath results to rename those in the networks. + # NOTE: The temporary directory, tempdir(), is used in this example. In practice, + # this argument can be removed or changed to an existing directory + results <- rename_genes(results, to = "symbol", species = "human", + dir_save = tempdir()) + nw_list <- get_networks(results[[1]]) # The genes (columns) will have new names. + + # (Optional) Plot the network using SeqNet package (based on igraph plotting). + # First rename entrezgene IDs into gene symbols. + SeqNet::plot_network(nw_list[[1]]) + } > > > > cleanEx() > nameEx("run_glasso") > ### * run_glasso > > flush(stderr()); flush(stdout()) > > ### Name: run_glasso > ### Title: Wrapper for glasso method > ### Aliases: run_glasso > > ### ** Examples > > data(meso) > data(p53_pathways) > > # To create a short example, we subset on one pathway from the p53 pathway list, > # and will only run 1 permutation for significance testing. > pathway_list <- p53_pathways[13] > n_perm <- 1 > > # Use this method to perform differential network analysis. > # The parameters in run_glasso() can be adjusted using the ... argument. > # For example, the 'criterion' parameter can be specified as shown here. > results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_glasso, + criterion = "ric") > summary(results) # A tibble: 0 × 6 # ℹ 6 variables: pathway , genes , dc_score , p_value , # mean_expr1 , mean_expr2 > > # The group-specific association matrices can be extracted using get_networks(). > nw_list <- get_networks(results) # Get networks for pathway 1. > > > > > cleanEx() > nameEx("run_mrnet") > ### * run_mrnet > > flush(stderr()); flush(stdout()) > > ### Name: run_mrnet > ### Title: Wrapper for MRNET method > ### Aliases: run_mrnet > > ### ** Examples > > data(meso) > data(p53_pathways) > > # To create a short example, we subset on two pathways from the p53 pathway list, > # and will only run 3 permutations for significance testing. > pathway_list <- p53_pathways[c(8, 13)] > n_perm <- 3 > > # Use this method to perform differential network analysis. > # The parameters in run_mrnet() can be adjusted using the ... argument. > # For example, the 'estimator' parameter can be specified as shown here. > results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_mrnet, + estimator = "spearman") > summary(results) Warning in summary.dnapath_list(results) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.25 # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.25)` mean_expr1 mean_expr2 1 Regulation of TP… 1.21 0.5 19 3 10.8 10.8 2 TP53 Regulates T… 0.859 0.25 12 4 7.91 7.91 > > # The group-specific association matrices can be extracted using get_networks(). > nw_list <- get_networks(results[[1]]) # Get networks for pathway 1. > > > > > cleanEx() > nameEx("run_pcor") > ### * run_pcor > > flush(stderr()); flush(stdout()) > > ### Name: run_pcor > ### Title: Wrapper for partial correlations from corpcor > ### Aliases: run_pcor > > ### ** Examples > > data(meso) > data(p53_pathways) > > # To create a short example, we subset on two pathways from the p53 pathway list, > # and will only run 3 permutations for significance testing. > pathway_list <- p53_pathways[c(8, 13)] > n_perm <- 3 > > # Use this method to perform differential network analysis. > results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_pcor) > summary(results) Warning in summary.dnapath_list(results) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.25 # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.25)` mean_expr1 mean_expr2 1 Regulation of TP… 1.28 0.25 19 13 10.8 10.8 2 TP53 Regulates T… 0.998 0.25 12 7 7.91 7.91 > > # The group-specific association matrices can be extracted using get_networks(). > nw_list <- get_networks(results[[1]]) # Get networks for pathway 1. > > > > > cleanEx() > nameEx("run_pcor_fdr") > ### * run_pcor_fdr > > flush(stderr()); flush(stdout()) > > ### Name: run_pcor_fdr > ### Title: Wrapper for partial correlations with Empirical Bayes FDR > ### correction > ### Aliases: run_pcor_fdr > > ### ** Examples > > data(meso) > data(p53_pathways) > > # To create a short example, we subset on two pathways from the p53 pathway list, > # and will only run 3 permutations for significance testing. > pathway_list <- p53_pathways[c(8, 13)] > n_perm <- 3 > > # Use this method to perform differential network analysis. > results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_pcor) > summary(results) Warning in summary.dnapath_list(results) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.25 # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.25)` mean_expr1 mean_expr2 1 Regulation of TP… 1.28 0.25 19 13 10.8 10.8 2 TP53 Regulates T… 0.998 0.25 12 7 7.91 7.91 > > # The group-specific association matrices can be extracted using get_networks(). > nw_list <- get_networks(results[[1]]) # Get networks for pathway 1. > > > > > cleanEx() > nameEx("run_silencer") > ### * run_silencer > > flush(stderr()); flush(stdout()) > > ### Name: run_silencer > ### Title: Wrapper for silencer method > ### Aliases: run_silencer > > ### ** Examples > > data(meso) > data(p53_pathways) > > # To create a short example, we subset on two pathways from the p53 pathway list, > # and will only run 1 permutation for significance testing. > pathway_list <- p53_pathways[13] > n_perm <- 1 > > # Use this method to perform differential network analysis. > # The parameters in run_silencer() can be adjusted using the ... argument. > # For example, the 'method' parameter can be specified as shown here. > results <- dnapath(x = meso$gene_expression, + pathway_list = pathway_list, + group_labels = meso$groups, + n_perm = n_perm, + network_inference = run_silencer, + method = "spearman") > summary(results) # A tibble: 11 × 6 pathway genes dc_score p_value mean_expr1 mean_expr2 1 TP53 Regulates Transcription of… 7157 6.73 0.5 11.1 10.8 2 TP53 Regulates Transcription of… 8626 5.17 0.5 3.49 3.14 3 TP53 Regulates Transcription of… 839 3.83 0.5 8.88 8.83 4 TP53 Regulates Transcription of… 843 3.71 0.5 8.94 9.23 5 TP53 Regulates Transcription of… 8738 3.60 0.5 7.23 7.17 6 TP53 Regulates Transcription of… 317 2.66 0.5 8.64 8.79 7 TP53 Regulates Transcription of… 472 1.98 0.5 10.2 10.4 8 TP53 Regulates Transcription of… 58484 4.26 1 5.77 6.05 9 TP53 Regulates Transcription of… 7161 3.81 1 3.88 3.47 10 TP53 Regulates Transcription of… 835 2.09 1 9.73 9.70 11 TP53 Regulates Transcription of… 834 1.86 1 9.14 9.39 > > # The group-specific association matrices can be extracted using get_networks(). > nw_list <- get_networks(results) # Get networks for the pathway > > > > > cleanEx() > nameEx("sort.dnapath_list") > ### * sort.dnapath_list > > flush(stderr()); flush(stdout()) > > ### Name: sort.dnapath_list > ### Title: Sort function for 'dnapath_list' object. > ### Aliases: sort.dnapath_list > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > # Filter out pathways that have p-values above 0.2. > results_sig <- filter_pathways(results, 0.2) > sort(results_sig, by = "dc_score") # Sort by the pathway DC score. Differential network analysis results between stageii (group 1) and stageiv (group 2) over 2 out of 13 pathways analyzed. # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 Regulation of TP5… 1.77 0.0909 37 7 10.1 10.2 2 TP53 Regulates Tr… 0.998 0.182 12 2 7.91 7.91 > sort(results_sig, by = "n_genes") # Sort by the pathway size. Differential network analysis results between stageii (group 1) and stageiv (group 2) over 2 out of 13 pathways analyzed. # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 Regulation of TP5… 1.77 0.0909 37 7 10.1 10.2 2 TP53 Regulates Tr… 0.998 0.182 12 2 7.91 7.91 > sort(results_sig, by = "mean_expr") # Sort by the mean expression. Differential network analysis results between stageii (group 1) and stageiv (group 2) over 2 out of 13 pathways analyzed. # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 Regulation of TP5… 1.77 0.0909 37 7 10.1 10.2 2 TP53 Regulates Tr… 0.998 0.182 12 2 7.91 7.91 > > > > cleanEx() > nameEx("sub-.dnapath") > ### * sub-.dnapath > > flush(stderr()); flush(stdout()) > > ### Name: [.dnapath > ### Title: Extract results of a single pathway from a 'dnapath' object. > ### Aliases: [.dnapath > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways[[1]], + group_labels = meso$groups, n_perm = 10) > results[1] Differential network analysis between stageii (group 1) and stageiv (group 2). Results for an unnamed pathway (out of 1 pathways analyzed) containing 37 genes. Pathway p-value = 0.091. The mean expression of genes in the pathway is 10.1 in group 1 and 10.2 in group 2. # A tibble: 37 × 6 pathway genes dc_score p_value mean_expr1 mean_expr2 1 unnamed 1616 0.256 0.0909 10.9 10.7 2 unnamed 4193 0.228 0.0909 11.0 11.1 3 unnamed 5527 0.226 0.0909 10.4 10.6 4 unnamed 6446 0.218 0.0909 11.3 11.7 5 unnamed 51230 0.201 0.0909 10.1 9.96 6 unnamed 207 0.152 0.0909 11.4 11.6 7 unnamed 983 0.141 0.0909 8.49 8.56 8 unnamed 7157 0.221 0.182 11.1 10.8 9 unnamed 80196 0.214 0.182 9.37 9.36 10 unnamed 5519 0.177 0.182 9.14 9.20 # ℹ 27 more rows > > > > cleanEx() > nameEx("sub-sub-.dnapath") > ### * sub-sub-.dnapath > > flush(stderr()); flush(stdout()) > > ### Name: [[.dnapath > ### Title: Extract results of a single pathway from a 'dnapath' object. > ### Aliases: [[.dnapath > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways[[1]], + group_labels = meso$groups, n_perm = 10) > results[[1]] Differential network analysis between stageii (group 1) and stageiv (group 2). Results for an unnamed pathway (out of 1 pathways analyzed) containing 37 genes. Pathway p-value = 0.091. The mean expression of genes in the pathway is 10.1 in group 1 and 10.2 in group 2. # A tibble: 37 × 6 pathway genes dc_score p_value mean_expr1 mean_expr2 1 unnamed 1616 0.256 0.0909 10.9 10.7 2 unnamed 4193 0.228 0.0909 11.0 11.1 3 unnamed 5527 0.226 0.0909 10.4 10.6 4 unnamed 6446 0.218 0.0909 11.3 11.7 5 unnamed 51230 0.201 0.0909 10.1 9.96 6 unnamed 207 0.152 0.0909 11.4 11.6 7 unnamed 983 0.141 0.0909 8.49 8.56 8 unnamed 7157 0.221 0.182 11.1 10.8 9 unnamed 80196 0.214 0.182 9.37 9.36 10 unnamed 5519 0.177 0.182 9.14 9.20 # ℹ 27 more rows > > > > cleanEx() > nameEx("sub-sub-.dnapath_list") > ### * sub-sub-.dnapath_list > > flush(stderr()); flush(stdout()) > > ### Name: [[.dnapath_list > ### Title: Extract results of a single pathway from a 'dnapath_list' > ### object. > ### Aliases: [[.dnapath_list > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > results[[1]] Differential network analysis between stageii (group 1) and stageiv (group 2). Results for the pathway "Regulation of TP53 Degradation (See also: Regulation of TP53 Expression and Degradation)" (out of 13 pathways analyzed) containing 37 genes. Pathway p-value = 0.091. The mean expression of genes in the pathway is 10.1 in group 1 and 10.2 in group 2. # A tibble: 37 × 6 pathway genes dc_score p_value mean_expr1 mean_expr2 1 Regulation of TP53 Degradation … 1616 0.256 0.0909 10.9 10.7 2 Regulation of TP53 Degradation … 4193 0.228 0.0909 11.0 11.1 3 Regulation of TP53 Degradation … 5527 0.226 0.0909 10.4 10.6 4 Regulation of TP53 Degradation … 6446 0.218 0.0909 11.3 11.7 5 Regulation of TP53 Degradation … 51230 0.201 0.0909 10.1 9.96 6 Regulation of TP53 Degradation … 207 0.152 0.0909 11.4 11.6 7 Regulation of TP53 Degradation … 983 0.141 0.0909 8.49 8.56 8 Regulation of TP53 Degradation … 7157 0.221 0.182 11.1 10.8 9 Regulation of TP53 Degradation … 80196 0.214 0.182 9.37 9.36 10 Regulation of TP53 Degradation … 5519 0.177 0.182 9.14 9.20 # ℹ 27 more rows > > > > cleanEx() > nameEx("subset.dnapath_list") > ### * subset.dnapath_list > > flush(stderr()); flush(stdout()) > > ### Name: subset.dnapath_list > ### Title: Subset function for 'dnapath_list' object. > ### Aliases: subset.dnapath_list > > ### ** Examples > > data(meso) > # Obtain a pathway list for this short example: > pathway_list <- get_reactome_pathways("human", overlap_limit = NULL, + min_size = 13, max_size = 19) Obtaining reactome pathway information for species: Homo sapiens > # Run the differential network analysis. > results <- dnapath(x = meso$gene_expression, pathway_list = pathway_list, + group_labels = meso$groups, n_perm = 5, seed = 0) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > summary(results) # Summary over all pathways in the pathway list. Warning in summary.dnapath_list(results) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.166666666666667 # A tibble: 79 × 7 pathway dc_score p_value n_genes `n_dc (0.167)` mean_expr1 mean_expr2 1 Activation of … 0.332 1 15 0 10.2 9.85 2 Downregulation… 0.345 1 13 0 12.7 12.6 3 AKT phosphoryl… 0.162 1 14 0 10.8 10.8 4 Regulation of … 0.880 0.333 14 2 7.70 7.60 5 TICAM1-depende… 0.352 0.667 13 0 14.2 14.0 6 Activation of … 0.352 0.667 19 0 14.2 14.0 7 Regulation of … 0.352 0.667 15 0 14.2 14.0 8 FOXO-mediated … 0.435 0.333 16 0 9.87 9.87 9 Negative regul… 0.352 0.667 15 0 14.2 14.0 10 Beta-catenin p… 0.129 0.833 17 0 10.8 11.0 # ℹ 69 more rows > > # Subset on pathways that contain "cell cycle" in its name. > cell_cycle_pathways <- subset(results, pathways = "cell cycle") > summary(cell_cycle_pathways) Warning in summary.dnapath_list(cell_cycle_pathways) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.166666666666667 # A tibble: 4 × 7 pathway dc_score p_value n_genes `n_dc (0.167)` mean_expr1 mean_expr2 1 TP53 Regulates … 1.30 1 14 0 7.76 7.94 2 Regulation of M… 0.327 0.833 18 0 9.34 9.55 3 FOXO-mediated t… 0.385 0.167 17 3 10.1 10.2 4 TP53 Regulates … 1.55 0.833 18 0 9.37 9.35 > # Subset on pathways that contain the gene 1026 (Entrezgene ID). > pathways_with_1026 <- subset(results, genes = "1026") > summary(pathways_with_1026) Warning in summary.dnapath_list(pathways_with_1026) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.166666666666667 # A tibble: 6 × 7 pathway dc_score p_value n_genes `n_dc (0.167)` mean_expr1 mean_expr2 1 AKT phosphoryla… 0.162 1 14 0 10.8 10.8 2 TP53 Regulates … 1.30 1 14 0 7.76 7.94 3 Aberrant regula… 0.790 1 17 1 8.77 8.87 4 Defective bindi… 0.790 1 17 1 8.77 8.87 5 Regulation of M… 0.327 0.833 18 0 9.34 9.55 6 FOXO-mediated t… 0.385 0.167 17 3 10.1 10.2 > > # Multiple pathways and/or genes can also be specified. > # Specifying both acts as an "OR" operation. For example, the following subset > # will contain pathways containing the words "acetylation" or "methylation" > # OR pathways that contain the genes "1108" or "11200". > results_OR <- subset(results, + pathways = c("acetylation", "methylation"), + genes = c("1108", "11200")) > summary(results_OR) Warning in summary.dnapath_list(results_OR) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.166666666666667 # A tibble: 2 × 7 pathway dc_score p_value n_genes `n_dc (0.167)` mean_expr1 mean_expr2 1 Regulation of T… 1.28 0.167 19 8 10.8 10.8 2 Chk1/Chk2(Cds1)… 0.720 0.667 15 3 7.33 7.23 > # To subset on pathways that have both a specific pathway name AND > # certain genes, call the subset function twice: once specifying the > # `pathways` argument, then pass those results back into subset() with the > # `genes` argument specified. For example: > results_AND <- subset(results, + pathways = c("acetylation", "methylation")) > results_AND <- subset(results_AND, + genes = c("1108", "11200")) > summary(results_AND) Warning in summary.dnapath_list(results_AND) : alpha_gene = 0.1 is too low given the number of permutations. Setting to 0.166666666666667 # A tibble: 1 × 7 pathway dc_score p_value n_genes `n_dc (0.167)` mean_expr1 mean_expr2 1 Regulation of T… 1.28 0.167 19 8 10.8 10.8 > > > > cleanEx() > nameEx("summarize_edges") > ### * summarize_edges > > flush(stderr()); flush(stdout()) > > ### Name: summarize_edges > ### Title: Summarize differential connections for a pathway > ### Aliases: summarize_edges > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > summarize_edges(results[[1]]) # A tibble: 64 × 6 pathway edges dc_score p_value nw1 nw2 1 Regulation of TP53 Degradation (See … 207 … 0.0134 0.0909 -2.81e-2 0.0877 2 Regulation of TP53 Degradation (See … 207 … 0.00297 0.0909 -3.80e-2 -0.0925 3 Regulation of TP53 Degradation (See … 208 … 0.0176 0.0909 -8.57e-2 0.0471 4 Regulation of TP53 Degradation (See … 208 … 0.0146 0.0909 4.81e-2 -0.0729 5 Regulation of TP53 Degradation (See … 208 … 0.0240 0.0909 -1.11e-1 0.0440 6 Regulation of TP53 Degradation (See … 1000… 0.0253 0.0909 -1.24e-1 0.0355 7 Regulation of TP53 Degradation (See … 1000… 0.00711 0.0909 -5.15e-4 -0.0848 8 Regulation of TP53 Degradation (See … 1000… 0.0183 0.0909 2.91e-2 -0.106 9 Regulation of TP53 Degradation (See … 472 … 0.00486 0.0909 3.88e-2 0.109 10 Regulation of TP53 Degradation (See … 472 … 0.00519 0.0909 2.82e-2 0.100 # ℹ 54 more rows > > > > cleanEx() > nameEx("summarize_genes") > ### * summarize_genes > > flush(stderr()); flush(stdout()) > > ### Name: summarize_genes > ### Title: Summarize the differential connectivity of genes over all > ### pathways. > ### Aliases: summarize_genes > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > summarize_genes(results) # Summary of genes across all pathways. # A tibble: 150 × 5 gene n_pathways `n_dc (0.1)` mean_expr1 mean_expr2 1 6446 1 1 11.3 11.7 2 207 3 1 11.4 11.6 3 124446 2 1 11.5 11.4 4 7157 13 1 11.1 10.8 5 4193 2 1 11.0 11.1 6 1616 1 1 10.9 10.7 7 5111 2 1 10.5 10.8 8 5527 1 1 10.4 10.6 9 9540 2 1 10.2 10.0 10 94241 2 1 10.1 10.1 # ℹ 140 more rows > summarize_genes(results[[1]]) # Summary of genes within the first pathway. # A tibble: 7 × 6 pathway genes dc_score p_value mean_expr1 mean_expr2 1 Regulation of TP53 Degradation (… 6446 0.218 0.0909 11.3 11.7 2 Regulation of TP53 Degradation (… 207 0.152 0.0909 11.4 11.6 3 Regulation of TP53 Degradation (… 4193 0.228 0.0909 11.0 11.1 4 Regulation of TP53 Degradation (… 1616 0.256 0.0909 10.9 10.7 5 Regulation of TP53 Degradation (… 5527 0.226 0.0909 10.4 10.6 6 Regulation of TP53 Degradation (… 51230 0.201 0.0909 10.1 9.96 7 Regulation of TP53 Degradation (… 983 0.141 0.0909 8.49 8.56 > > > > cleanEx() > nameEx("summarize_pathways") > ### * summarize_pathways > > flush(stderr()); flush(stdout()) > > ### Name: summarize_pathways > ### Title: Summarize the differential connectivity of pathways. > ### Aliases: summarize_pathways > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > summarize_pathways(results) # A tibble: 13 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 Regulation of TP… 1.77 0.0909 37 7 10.1 10.2 2 Regulation of TP… 1.15 0.909 30 0 10.2 10.2 3 Regulation of TP… 0.880 0.273 14 1 7.70 7.60 4 TP53 Regulates T… 2.35 0.727 49 2 9.09 9.16 5 TP53 Regulates T… 1.30 1 14 0 7.76 7.94 6 TP53 Regulates T… 2.03 0.455 44 2 8.68 8.73 7 TP53 regulates t… 1.05 0.273 14 2 8.52 8.46 8 Regulation of TP… 1.28 0.273 19 1 10.8 10.8 9 TP53 Regulates T… 1.55 0.818 18 0 9.37 9.35 10 TP53 Regulates T… 1.32 0.727 20 0 8.59 8.61 11 TP53 regulates t… 0.954 0.818 21 0 9.88 9.92 12 TP53 Regulates T… 0.906 1 12 0 8.15 8.16 13 TP53 Regulates T… 0.998 0.182 12 2 7.91 7.91 > > > > cleanEx() > nameEx("summary.dnapath") > ### * summary.dnapath > > flush(stderr()); flush(stdout()) > > ### Name: summary.dnapath > ### Title: Summary function for 'dnapath' object. > ### Aliases: summary.dnapath > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > summary(results[[1]]) # Summary of the first pathway in the results. # A tibble: 37 × 6 pathway genes dc_score p_value mean_expr1 mean_expr2 1 Regulation of TP53 Degradation … 1616 0.256 0.0909 10.9 10.7 2 Regulation of TP53 Degradation … 4193 0.228 0.0909 11.0 11.1 3 Regulation of TP53 Degradation … 5527 0.226 0.0909 10.4 10.6 4 Regulation of TP53 Degradation … 6446 0.218 0.0909 11.3 11.7 5 Regulation of TP53 Degradation … 51230 0.201 0.0909 10.1 9.96 6 Regulation of TP53 Degradation … 207 0.152 0.0909 11.4 11.6 7 Regulation of TP53 Degradation … 983 0.141 0.0909 8.49 8.56 8 Regulation of TP53 Degradation … 7157 0.221 0.182 11.1 10.8 9 Regulation of TP53 Degradation … 80196 0.214 0.182 9.37 9.36 10 Regulation of TP53 Degradation … 5519 0.177 0.182 9.14 9.20 # ℹ 27 more rows > > > > cleanEx() > nameEx("summary.dnapath_list") > ### * summary.dnapath_list > > flush(stderr()); flush(stdout()) > > ### Name: summary.dnapath_list > ### Title: Summary function for 'dnapath_list' object. > ### Aliases: summary.dnapath_list > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > summary(results) # Summary across all pathways in the analysis. # A tibble: 13 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 Regulation of TP… 1.77 0.0909 37 7 10.1 10.2 2 Regulation of TP… 1.15 0.909 30 0 10.2 10.2 3 Regulation of TP… 0.880 0.273 14 1 7.70 7.60 4 TP53 Regulates T… 2.35 0.727 49 2 9.09 9.16 5 TP53 Regulates T… 1.30 1 14 0 7.76 7.94 6 TP53 Regulates T… 2.03 0.455 44 2 8.68 8.73 7 TP53 regulates t… 1.05 0.273 14 2 8.52 8.46 8 Regulation of TP… 1.28 0.273 19 1 10.8 10.8 9 TP53 Regulates T… 1.55 0.818 18 0 9.37 9.35 10 TP53 Regulates T… 1.32 0.727 20 0 8.59 8.61 11 TP53 regulates t… 0.954 0.818 21 0 9.88 9.92 12 TP53 Regulates T… 0.906 1 12 0 8.15 8.16 13 TP53 Regulates T… 0.998 0.182 12 2 7.91 7.91 > > > > cleanEx() > nameEx("symbol_to_entrez") > ### * symbol_to_entrez > > flush(stderr()); flush(stdout()) > > ### Name: symbol_to_entrez > ### Title: Obtain entrezgene IDs for gene symbols > ### Aliases: symbol_to_entrez > > ### ** Examples > > > > > cleanEx() > nameEx("tail.dnapath_list") > ### * tail.dnapath_list > > flush(stderr()); flush(stdout()) > > ### Name: tail.dnapath_list > ### Title: Return the last part of the dnapath results. > ### Aliases: tail.dnapath_list > > ### ** Examples > > data(meso) > data(p53_pathways) > set.seed(0) > results <- dnapath(x = meso$gene_expression, pathway_list = p53_pathways, + group_labels = meso$groups, n_perm = 10) Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! Warning: 1 instances of variables with zero scale detected! > tail(results) # A tibble: 5 × 7 pathway dc_score p_value n_genes `n_dc (0.1)` mean_expr1 mean_expr2 1 TP53 Regulates Tr… 1.55 0.818 18 0 9.37 9.35 2 TP53 Regulates Tr… 1.32 0.727 20 0 8.59 8.61 3 TP53 regulates tr… 0.954 0.818 21 0 9.88 9.92 4 TP53 Regulates Tr… 0.906 1 12 0 8.15 8.16 5 TP53 Regulates Tr… 0.998 0.182 12 2 7.91 7.91 > > > > ### *