R Under development (unstable) (2025-04-21 r88165) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > pkgname <- "Mega2R" > source(file.path(R.home("share"), "R", "examples-header.R")) > options(warn = 1) > library('Mega2R') Loading required package: SKAT Loading required package: Matrix Loading required package: SPAtest Loading required package: RSpectra Loading required package: pedgene Loading required package: CompQuadForm Loading required package: survey Loading required package: grid Loading required package: survival Attaching package: ‘survey’ The following object is masked from ‘package:graphics’: dotchart Loading required package: kinship2 Loading required package: quadprog Loading required package: gdsfmt > > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv') > base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv') > cleanEx() > nameEx("DOSKAT") > ### * DOSKAT > > flush(stderr()); flush(stdout()) > > ### Name: DOSKAT > ### Title: SKAT call back function > ### Aliases: DOSKAT > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = init_SKAT(db, verbose = TRUE, allMarkers = FALSE) vendor/sqlite3/sqlite3.c:111455:20: runtime error: index 2 out of bounds for type 'ExprList_item [1]' #0 0x7f70a1aab741 in sqlite3ExprListAppend vendor/sqlite3/sqlite3.c:111455 #1 0x7f70a1c014c8 in selectExpander vendor/sqlite3/sqlite3.c:150034 #2 0x7f70a1a760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #3 0x7f70a1c0946f in sqlite3SelectExpand vendor/sqlite3/sqlite3.c:150132 #4 0x7f70a1c0946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150214 #5 0x7f70a1c0946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #6 0x7f70a1c181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #7 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #14 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #15 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #16 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #17 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #18 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #19 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #20 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #21 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #22 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #23 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #24 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #25 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #26 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #27 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #131 0x7f70bca3814a 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 0x7f70a1c034c7 in selectExpander vendor/sqlite3/sqlite3.c:150038 #1 0x7f70a1a760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #2 0x7f70a1c0946f in sqlite3SelectExpand vendor/sqlite3/sqlite3.c:150132 #3 0x7f70a1c0946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150214 #4 0x7f70a1c0946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #5 0x7f70a1c181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #6 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #7 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #8 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #9 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #10 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #11 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #12 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #13 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #14 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #15 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #16 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #17 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #18 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #19 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #20 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #21 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #22 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #23 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #24 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #25 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #26 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #130 0x7f70bca3814a 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 0x7f70a1aab2e3 in sqlite3ExprListAppendGrow vendor/sqlite3/sqlite3.c:111438 #1 0x7f70a1c014c8 in selectExpander vendor/sqlite3/sqlite3.c:150034 #2 0x7f70a1a760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #3 0x7f70a1c0946f in sqlite3SelectExpand vendor/sqlite3/sqlite3.c:150132 #4 0x7f70a1c0946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150214 #5 0x7f70a1c0946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #6 0x7f70a1c181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #7 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #14 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #15 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #16 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #17 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #18 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #19 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #20 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #21 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #22 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #23 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #24 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #25 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #26 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #27 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #131 0x7f70bca3814a 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 0x7f70a1a84a9c in sqlite3ResolveExprListNames vendor/sqlite3/sqlite3.c:109277 #1 0x7f70a1aa53a1 in resolveSelectStep vendor/sqlite3/sqlite3.c:109027 #2 0x7f70a1a760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #3 0x7f70a1c095d3 in sqlite3ResolveSelectNames vendor/sqlite3/sqlite3.c:109330 #4 0x7f70a1c095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150216 #5 0x7f70a1c095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #6 0x7f70a1c181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #7 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #14 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #15 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #16 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #17 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #18 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #19 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #20 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #21 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #22 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #23 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #24 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #25 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #26 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #27 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #131 0x7f70bca3814a 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 0x7f70a1a82bb7 in resolveAsName vendor/sqlite3/sqlite3.c:108558 #1 0x7f70a1a86e11 in resolveOrderGroupBy vendor/sqlite3/sqlite3.c:108872 #2 0x7f70a1aa6408 in resolveSelectStep vendor/sqlite3/sqlite3.c:109120 #3 0x7f70a1a760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #4 0x7f70a1c095d3 in sqlite3ResolveSelectNames vendor/sqlite3/sqlite3.c:109330 #5 0x7f70a1c095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150216 #6 0x7f70a1c095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #7 0x7f70a1c181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #8 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #9 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #10 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #11 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #12 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #13 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #14 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #15 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #16 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #17 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #18 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #19 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #20 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #21 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #22 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #23 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #24 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #25 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #26 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #27 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #28 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #132 0x7f70bca3814a 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 0x7f70a1a82bf3 in resolveAsName vendor/sqlite3/sqlite3.c:108559 #1 0x7f70a1a86e11 in resolveOrderGroupBy vendor/sqlite3/sqlite3.c:108872 #2 0x7f70a1aa6408 in resolveSelectStep vendor/sqlite3/sqlite3.c:109120 #3 0x7f70a1a760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #4 0x7f70a1c095d3 in sqlite3ResolveSelectNames vendor/sqlite3/sqlite3.c:109330 #5 0x7f70a1c095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150216 #6 0x7f70a1c095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #7 0x7f70a1c181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #8 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #9 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #10 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #11 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #12 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #13 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #14 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #15 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #16 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #17 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #18 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #19 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #20 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #21 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #22 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #23 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #24 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #25 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #26 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #27 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #28 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #132 0x7f70bca3814a 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 0x7f70a1a8755c in resolveOrderGroupBy vendor/sqlite3/sqlite3.c:108900 #1 0x7f70a1aa6408 in resolveSelectStep vendor/sqlite3/sqlite3.c:109120 #2 0x7f70a1a760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #3 0x7f70a1c095d3 in sqlite3ResolveSelectNames vendor/sqlite3/sqlite3.c:109330 #4 0x7f70a1c095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150216 #5 0x7f70a1c095d3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #6 0x7f70a1c181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #7 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #14 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #15 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #16 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #17 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #18 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #19 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #20 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #21 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #22 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #23 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #24 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #25 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #26 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #27 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #131 0x7f70bca3814a 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 0x7f70a1bd9fee in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145839 #1 0x7f70a1c194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #2 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #3 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #4 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #5 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #6 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #7 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #8 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #9 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #10 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #11 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #12 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #13 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #14 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #15 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #16 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #17 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #18 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #19 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #20 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #21 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #22 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #126 0x7f70bca3814a 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 0x7f70a1bd9e7f in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145845 #1 0x7f70a1c194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #2 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #3 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #4 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #5 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #6 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #7 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #8 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #9 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #10 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #11 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #12 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #13 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #14 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #15 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #16 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #17 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #18 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #19 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #20 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #21 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #22 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #126 0x7f70bca3814a 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 0x7f70a1bda06a in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145845 #1 0x7f70a1c194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #2 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #3 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #4 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #5 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #6 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #7 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #8 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #9 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #10 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #11 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #12 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #13 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #14 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #15 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #16 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #17 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #18 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #19 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #20 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #21 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #22 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #126 0x7f70bca3814a 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 0x7f70a1bda718 in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145847 #1 0x7f70a1c194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #2 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #3 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #4 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #5 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #6 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #7 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #8 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #9 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #10 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #11 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #12 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #13 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #14 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #15 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #16 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #17 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #18 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #19 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #20 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #21 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #22 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #126 0x7f70bca3814a 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 0x7f70a1bd9f95 in generateColumnTypes vendor/sqlite3/sqlite3.c:145759 #1 0x7f70a1bd9f95 in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145874 #2 0x7f70a1c194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #3 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #4 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #5 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #6 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #7 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #8 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #9 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #10 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #11 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #12 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #13 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #14 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #15 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #16 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #17 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #18 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #19 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #20 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #21 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #22 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #23 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #127 0x7f70bca3814a 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 0x7f70a1bd0ef8 in sqlite3KeyInfoAlloc vendor/sqlite3/sqlite3.c:145214 #1 0x7f70a1bd1e09 in sqlite3KeyInfoFromExprList vendor/sqlite3/sqlite3.c:145287 #2 0x7f70a1c1a7c1 in sqlite3Select vendor/sqlite3/sqlite3.c:151707 #3 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #4 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #5 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #6 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #7 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #8 0x7f70a1b8a9e8 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #9 0x7f70a1b8a9e8 in sqlite3_exec vendor/sqlite3/sqlite3.c:137112 #10 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #11 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #12 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #13 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #14 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #15 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #16 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #17 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #18 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #19 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #20 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #21 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #22 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #23 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #127 0x7f70bca3814a 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 0x7f70a19fb70d in allocateCursor vendor/sqlite3/sqlite3.c:93710 #1 0x7f70a1a1231a in sqlite3VdbeExec vendor/sqlite3/sqlite3.c:97773 #2 0x7f70a1a50e4d in sqlite3Step vendor/sqlite3/sqlite3.c:91376 #3 0x7f70a1a50e4d in sqlite3_step vendor/sqlite3/sqlite3.c:91437 #4 0x7f70a1b8aa34 in sqlite3_exec vendor/sqlite3/sqlite3.c:137126 #5 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #6 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #7 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #8 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #9 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #10 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #11 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #12 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #13 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #14 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #15 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #16 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #17 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #18 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #122 0x7f70bca3814a 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 0x7f70a1a48405 in sqlite3VdbeExec vendor/sqlite3/sqlite3.c:96477 #1 0x7f70a1a50e4d in sqlite3Step vendor/sqlite3/sqlite3.c:91376 #2 0x7f70a1a50e4d in sqlite3_step vendor/sqlite3/sqlite3.c:91437 #3 0x7f70a1b8aa34 in sqlite3_exec vendor/sqlite3/sqlite3.c:137126 #4 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #5 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #6 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #7 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #8 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #9 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #10 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #11 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #12 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #13 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #14 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #15 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #16 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #17 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #121 0x7f70bca3814a 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 0x7f70a1a3fb07 in sqlite3VdbeExec vendor/sqlite3/sqlite3.c:96482 #1 0x7f70a1a50e4d in sqlite3Step vendor/sqlite3/sqlite3.c:91376 #2 0x7f70a1a50e4d in sqlite3_step vendor/sqlite3/sqlite3.c:91437 #3 0x7f70a1b8aa34 in sqlite3_exec vendor/sqlite3/sqlite3.c:137126 #4 0x7f70a1baec71 in sqlite3InitOne vendor/sqlite3/sqlite3.c:142974 #5 0x7f70a1bb1776 in sqlite3Init vendor/sqlite3/sqlite3.c:143049 #6 0x7f70a1bb1ad2 in sqlite3ReadSchema vendor/sqlite3/sqlite3.c:143075 #7 0x7f70a1bb9c20 in sqlite3Pragma vendor/sqlite3/sqlite3.c:140021 #8 0x7f70a1d0e4ce in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:178571 #9 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #10 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #11 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #12 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #13 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #14 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #15 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #16 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #17 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #121 0x7f70bca3814a 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 0x7f70a1bdc6f6 in sqlite3ColumnsFromExprList.isra.0 vendor/sqlite3/sqlite3.c:145930 #1 0x7f70a1bfc0b6 in sqlite3ExpandSubquery vendor/sqlite3/sqlite3.c:149644 #2 0x7f70a1bfc0b6 in selectExpander vendor/sqlite3/sqlite3.c:149767 #3 0x7f70a1a760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #4 0x7f70a1c0946f in sqlite3SelectExpand vendor/sqlite3/sqlite3.c:150132 #5 0x7f70a1c0946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150214 #6 0x7f70a1c0946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #7 0x7f70a1c181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #8 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #9 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #10 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #11 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #12 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #13 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #14 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #15 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #16 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #17 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #41 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x7f70b9b76c7a 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 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #53 0x7f70b9b76c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #54 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #55 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #70 0x7f70bca3814a 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:146060:48: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7f70a1bdde7c in sqlite3SubqueryColumnTypes vendor/sqlite3/sqlite3.c:146060 #1 0x7f70a1bf0fee in selectAddSubqueryTypeInfo vendor/sqlite3/sqlite3.c:150167 #2 0x7f70a1a76583 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107021 #3 0x7f70a1c096e3 in sqlite3SelectAddTypeInfo vendor/sqlite3/sqlite3.c:150188 #4 0x7f70a1c096e3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150218 #5 0x7f70a1c096e3 in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #6 0x7f70a1c181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #7 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #14 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #15 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #16 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #39 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #40 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #45 0x7f70b9b76c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #46 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #47 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #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 0x7f70b9b76c7a 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 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #69 0x7f70bca3814a 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:145675:34: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7f70a1bcbcf5 in columnTypeImpl vendor/sqlite3/sqlite3.c:145675 #1 0x7f70a1bd9c69 in generateColumnTypes vendor/sqlite3/sqlite3.c:145775 #2 0x7f70a1bd9c69 in sqlite3GenerateColumnNames vendor/sqlite3/sqlite3.c:145874 #3 0x7f70a1c194f6 in sqlite3Select vendor/sqlite3/sqlite3.c:151190 #4 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #5 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #6 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #7 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #8 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #9 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #10 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #11 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #12 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #13 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #36 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #37 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x7f70b9b76c7a 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 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #49 0x7f70b9b76c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #50 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #51 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #52 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #53 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #54 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #55 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #56 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #57 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #58 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #59 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #60 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #61 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #62 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #63 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #64 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #65 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #66 0x7f70bca3814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #67 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 0x7f70a1bf52fb in compoundHasDifferentAffinities vendor/sqlite3/sqlite3.c:147855 #1 0x7f70a1bf52fb in flattenSubquery vendor/sqlite3/sqlite3.c:148192 #2 0x7f70a1c18c2e in sqlite3Select vendor/sqlite3/sqlite3.c:151374 #3 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #4 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #5 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #6 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #7 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #8 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #9 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #10 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #11 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #12 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #35 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #36 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #65 0x7f70bca3814a 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:147860:47: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7f70a1bf5239 in compoundHasDifferentAffinities vendor/sqlite3/sqlite3.c:147860 #1 0x7f70a1bf5239 in flattenSubquery vendor/sqlite3/sqlite3.c:148192 #2 0x7f70a1c18c2e in sqlite3Select vendor/sqlite3/sqlite3.c:151374 #3 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #4 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #5 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #6 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #7 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #8 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #9 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #10 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #11 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #12 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #35 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #36 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #65 0x7f70bca3814a 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:147583:32: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7f70a1beb18d in substExpr vendor/sqlite3/sqlite3.c:147583 #1 0x7f70a1f5f515 in substExprList.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:147665 #2 0x7f70a1f5f741 in substExprList vendor/sqlite3/sqlite3.c:147663 #3 0x7f70a1f5f741 in substSelect.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:147678 #4 0x7f70a1bf47ab in substSelect vendor/sqlite3/sqlite3.c:147676 #5 0x7f70a1bf47ab in flattenSubquery vendor/sqlite3/sqlite3.c:148436 #6 0x7f70a1c18c2e in sqlite3Select vendor/sqlite3/sqlite3.c:151374 #7 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #14 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #15 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #16 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #39 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #40 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #45 0x7f70b9b76c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #46 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #47 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #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 0x7f70b9b76c7a 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 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #69 0x7f70bca3814a 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:147625:34: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7f70a1beb40e in substExpr vendor/sqlite3/sqlite3.c:147625 #1 0x7f70a1f5f515 in substExprList.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:147665 #2 0x7f70a1f5f741 in substExprList vendor/sqlite3/sqlite3.c:147663 #3 0x7f70a1f5f741 in substSelect.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:147678 #4 0x7f70a1bf47ab in substSelect vendor/sqlite3/sqlite3.c:147676 #5 0x7f70a1bf47ab in flattenSubquery vendor/sqlite3/sqlite3.c:148436 #6 0x7f70a1c18c2e in sqlite3Select vendor/sqlite3/sqlite3.c:151374 #7 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #8 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #9 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #10 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #11 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #12 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #13 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #14 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #15 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #16 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #39 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #40 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #45 0x7f70b9b76c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #46 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #47 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #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 0x7f70b9b76c7a 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 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 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #69 0x7f70bca3814a 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:163112:55: runtime error: index 1 out of bounds for type 'ExprList_item [1]' #0 0x7f70a1f5bf44 in sqlite3WhereExprListUsage.part.0.lto_priv.0 vendor/sqlite3/sqlite3.c:163112 #1 0x7f70a1c86c1d in sqlite3WhereExprListUsage vendor/sqlite3/sqlite3.c:163110 #2 0x7f70a1c86c1d in exprAnalyze vendor/sqlite3/sqlite3.c:162413 #3 0x7f70a1c8a6ff in exprAnalyzeOrTerm vendor/sqlite3/sqlite3.c:162201 #4 0x7f70a1c8a6ff in exprAnalyze vendor/sqlite3/sqlite3.c:162584 #5 0x7f70a1cd9d64 in sqlite3WhereExprAnalyze vendor/sqlite3/sqlite3.c:163133 #6 0x7f70a1cd9d64 in sqlite3WhereBegin vendor/sqlite3/sqlite3.c:169832 #7 0x7f70a1c1ae1b in sqlite3Select vendor/sqlite3/sqlite3.c:151779 #8 0x7f70a1be1e5c in multiSelectOrderBy vendor/sqlite3/sqlite3.c:147359 #9 0x7f70a1be1e5c in multiSelect vendor/sqlite3/sqlite3.c:146636 #10 0x7f70a1c1c467 in sqlite3Select vendor/sqlite3/sqlite3.c:151392 #11 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #12 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #13 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #14 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #15 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #16 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #17 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #18 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #19 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #20 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #44 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #49 0x7f70b9b76c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #50 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #51 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #52 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #53 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #54 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #55 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #56 0x7f70b9b76c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #57 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #58 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #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 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #63 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #64 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #65 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #66 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #67 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #68 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #69 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #70 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #71 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #72 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #73 0x7f70bca3814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #74 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 0x7f70a1ac987d in sqlite3ExprCodeRunJustOnce vendor/sqlite3/sqlite3.c:114966 #1 0x7f70a1ac9c56 in sqlite3ExprCodeTemp vendor/sqlite3/sqlite3.c:114998 #2 0x7f70a1ad0a31 in sqlite3ExprIfFalse vendor/sqlite3/sqlite3.c:115480 #3 0x7f70a1c66e39 in sqlite3WhereCodeOneLoopStart vendor/sqlite3/sqlite3.c:161029 #4 0x7f70a1cdc650 in sqlite3WhereBegin vendor/sqlite3/sqlite3.c:170294 #5 0x7f70a1c1ae1b in sqlite3Select vendor/sqlite3/sqlite3.c:151779 #6 0x7f70a1be1e5c in multiSelectOrderBy vendor/sqlite3/sqlite3.c:147359 #7 0x7f70a1be1e5c in multiSelect vendor/sqlite3/sqlite3.c:146636 #8 0x7f70a1c1c467 in sqlite3Select vendor/sqlite3/sqlite3.c:151392 #9 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #10 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #11 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #12 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #13 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #14 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #15 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #16 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #17 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #18 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #42 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x7f70b9b76c7a 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 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #54 0x7f70b9b76c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #55 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #56 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #57 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #58 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #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 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #62 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #63 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #64 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #65 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #66 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #67 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #68 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #69 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #70 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #71 0x7f70bca3814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #72 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 0x7f70a1b041c2 in sqlite3FinishCoding vendor/sqlite3/sqlite3.c:122207 #1 0x7f70a1d09834 in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177464 #2 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #3 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #4 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #5 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #6 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #7 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #8 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #9 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #10 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #33 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #34 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #58 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #59 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #60 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #61 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #62 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #63 0x7f70bca3814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #64 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 0x7f70a1b04155 in sqlite3FinishCoding vendor/sqlite3/sqlite3.c:122207 #1 0x7f70a1d09834 in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177464 #2 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #3 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #4 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #5 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #6 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #7 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #8 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #9 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #10 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #33 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #34 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #58 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #59 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #60 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #61 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #62 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #63 0x7f70bca3814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #64 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 0x7f70a1a4c7a9 in sqlite3VdbeExec vendor/sqlite3/sqlite3.c:96527 #1 0x7f70a1a50e4d in sqlite3Step vendor/sqlite3/sqlite3.c:91376 #2 0x7f70a1a50e4d in sqlite3_step vendor/sqlite3/sqlite3.c:91437 #3 0x7f70a1853af9 in SqliteResultImpl::step_run() /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:341 #4 0x7f70a186d532 in SqliteResultImpl::step() /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:334 #5 0x7f70a186d532 in SqliteResultImpl::after_bind(bool) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:306 #6 0x7f70a186d532 in SqliteResultImpl::after_bind(bool) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:303 #7 0x7f70a186d532 in SqliteResultImpl::bind(cpp11::r_vector const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:147 #8 0x7f70a186d532 in DbResult::bind(cpp11::r_vector const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/DbResult.cpp:49 #9 0x7f70a186d532 in result_bind(DbResult*, cpp11::r_vector) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/result.cpp:32 #10 0x7f70a186d532 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 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 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #34 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #35 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #36 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #37 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #38 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #39 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #40 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #41 0x7f70bca3814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #42 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) int_table 35 3 int_table pId key value charstar_table 9 3 charstar_table pId key value vendor/sqlite3/sqlite3.c:111616:44: runtime error: index 2 out of bounds for type 'ExprList_item [1]' #0 0x7f70a1d17538 in sqlite3ExprListSetSpan vendor/sqlite3/sqlite3.c:111616 #1 0x7f70a1d17538 in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177853 #2 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #3 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #4 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #5 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #6 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #7 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #8 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #9 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #10 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #43 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #44 0x87cf2b in do_begin /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2996 #45 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #46 0x87e7ca in R_execClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2393 #47 0x8829da in applyClosure_core /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2306 #48 0x8edd25 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #49 0x8edd25 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8089 #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 0x886dfd in R_execMethod /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2562 #54 0x7f70b9b76c7a in R_dispatchGeneric /data/gannet/ripley/R/svn/R-devel/src/library/methods/src/methods_list_dispatch.c:1154 #55 0xab4c46 in do_standardGeneric /data/gannet/ripley/R/svn/R-devel/src/main/objects.c:1348 #56 0x8f2831 in bcEval_loop /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:8053 #57 0x8c646b in bcEval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:7501 #58 0x866db2 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1167 #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 0x867453 in Rf_applyClosure /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:2328 #62 0x867453 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1280 #63 0x8976ee in do_set /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:3567 #64 0x867876 in Rf_eval /data/gannet/ripley/R/svn/R-devel/src/main/eval.c:1232 #65 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #66 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #67 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #68 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #69 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #70 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #71 0x7f70bca3814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #72 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 0x7f70a1c05b5f in selectExpander vendor/sqlite3/sqlite3.c:149853 #1 0x7f70a1a760a2 in sqlite3WalkSelect vendor/sqlite3/sqlite3.c:107013 #2 0x7f70a1c0946f in sqlite3SelectExpand vendor/sqlite3/sqlite3.c:150132 #3 0x7f70a1c0946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150214 #4 0x7f70a1c0946f in sqlite3SelectPrep vendor/sqlite3/sqlite3.c:150205 #5 0x7f70a1c181de in sqlite3Select vendor/sqlite3/sqlite3.c:151150 #6 0x7f70a1d07ecc in yy_reduce.isra.0 vendor/sqlite3/sqlite3.c:177755 #7 0x7f70a1d40521 in sqlite3Parser vendor/sqlite3/sqlite3.c:179205 #8 0x7f70a1d40521 in sqlite3RunParser vendor/sqlite3/sqlite3.c:180539 #9 0x7f70a1baa9e9 in sqlite3Prepare vendor/sqlite3/sqlite3.c:143386 #10 0x7f70a1bb256f in sqlite3LockAndPrepare vendor/sqlite3/sqlite3.c:143461 #11 0x7f70a1861595 in sqlite3_prepare_v2 vendor/sqlite3/sqlite3.c:143548 #12 0x7f70a1861595 in SqliteResultImpl::prepare(sqlite3*, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:85 #13 0x7f70a1861595 in SqliteResultImpl::SqliteResultImpl(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResultImpl.cpp:15 #14 0x7f70a1861595 in SqliteResult::SqliteResult(boost::shared_ptr const&, std::__cxx11::basic_string, std::allocator > const&) /tmp/RtmpPuoXuy/R.INSTALL2037453b86db88/RSQLite/src/SqliteResult.cpp:12 #15 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70a1861595 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0x7f70b9b76c7a 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 0xa0bc63 in Rf_ReplIteration /data/gannet/ripley/R/svn/R-devel/src/main/main.c:265 #71 0xa0bc63 in R_ReplConsole /data/gannet/ripley/R/svn/R-devel/src/main/main.c:317 #72 0xa10f7a in run_Rmainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1234 #73 0xa1b192 in Rf_mainloop /data/gannet/ripley/R/svn/R-devel/src/main/main.c:1241 #74 0x42bd5f in main /data/gannet/ripley/R/svn/R-devel/src/main/Rmain.c:29 #75 0x7f70bca38087 in __libc_start_call_main (/lib64/libc.so.6+0x2a087) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #76 0x7f70bca3814a in __libc_start_main_impl (/lib64/libc.so.6+0x2a14a) (BuildId: c8c3fa52aaee3f5d73b6fd862e39e9d4c010b6ba) #77 0x42c6e4 in _start (/data/gannet/ripley/R/gcc-SAN3/bin/exec/R+0x42c6e4) (BuildId: 81ac5d208640ad2c0ea4b82c75c2cb3222da06bb) pedigree_table 1 8 pedigree_table pId Num EntryCnt Name PedPre OriginalID origped pedigree_link person_table 69 11 person_table pId UniqueID OrigID FamName PerPre ID Father Mother Sex pedigree_link person_link pedigree_brkloop_table 1 8 pedigree_brkloop_table pId Num EntryCnt Name PedPre OriginalID origped pedigree_link person_brkloop_table 69 11 person_brkloop_table pId UniqueID OrigID FamName PerPre ID Father Mother Sex pedigree_link person_link locus_table 17 5 locus_table pId LocusName Type AlleleCnt locus_link allele_table 34 5 allele_table pId AlleleName Frequency indexX locus_link marker_table 16 7 marker_table pId MarkerName pos_avg pos_female pos_male chromosome locus_link map_table 32 6 map_table pId marker map position pos_female pos_male mapnames_table 2 6 mapnames_table pId map sex_averaged_map male_sex_map female_sex_map name traitaff_table 1 4 traitaff_table pId ClassCnt PenCnt locus_link affectclass_table 1 9 affectclass_table pId MaleDef FemaleDef AutoDef MalePen FemalePen AutoPen locus_link class_link phenotype_table 69 4 phenotype_table pId person_link bytes data genotype_table 69 5 genotype_table pId person_link chr bytes data > Mega2SKAT(ENV$phe[, 3] - 1 ~ 1, "D", gs=1:1) Sample size (non-missing y and X) = 69, which is < 2000. The small sample adjustment is applied! tryFn() No markers in range: NM_005286, NPBWR2, 20, 62737182, 62738184 > > > # DOSKAT is called internally to Mega2SKAT. init_SKAT and Mega2SKAT need to be > # called to set up the environment for DOSKAT to run. You should ignore DOSKAT > # and use Mega2SKAT instead > # > applyFnToRanges(DOSKAT, ENV$refRanges[50:60, ], ENV$refIndices) tryFn() No markers in range: NR_052010, IL11RA, 9, 34653893, 34661898 tryFn() No markers in range: NR_045785, CHIT1, 1, 203185206, 203198860 tryFn() No markers in range: NM_017799, TMEM260, 14, 57046510, 57116232 tryFn() No markers in range: NM_014705, DOCK4, 7, 111366163, 111846462 tryFn() No markers in range: NM_003759, SLC4A4, 4, 72204769, 72437804 tryFn() No markers in range: NM_002192, INHBA, 7, 41728600, 41742706 tryFn() No markers in range: NM_002202, ISL1, 5, 50678957, 50690563 tryFn() No markers in range: NM_003659, AGPS, 2, 178257470, 178408564 tryFn() No markers in range: NM_003658, BARX2, 11, 129245880, 129322174 tryFn() No markers in range: NM_018051, WDR60, 7, 158649268, 158738883 CEP104 snp24037 34 35 0 CEP104 snp24039 69 0 0 CEP104 snp24041 49 20 0 CEP104 snp24048 37 30 2 CEP104 snp24494 60 8 1 CEP104 snp24499 56 13 0 CEP104 snp24506 24 36 9 CEP104 snp24507 48 18 3 chr gene nvariants start end skat 1 1 CEP104 7 3728644 3773797 0.3886462 > > > > > cleanEx() > nameEx("DOfamSKATRC") > ### * DOfamSKATRC > > flush(stderr()); flush(stdout()) > > ### Name: DOfamSKATRC > ### Title: DofamSKATRC call back function > ### Aliases: DOfamSKATRC > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = init_famSKATRC(db, verbose = TRUE) int_table 35 3 int_table pId key value charstar_table 9 3 charstar_table pId key value pedigree_table 1 8 pedigree_table pId Num EntryCnt Name PedPre OriginalID origped pedigree_link person_table 69 11 person_table pId UniqueID OrigID FamName PerPre ID Father Mother Sex pedigree_link person_link pedigree_brkloop_table 1 8 pedigree_brkloop_table pId Num EntryCnt Name PedPre OriginalID origped pedigree_link person_brkloop_table 69 11 person_brkloop_table pId UniqueID OrigID FamName PerPre ID Father Mother Sex pedigree_link person_link locus_table 17 5 locus_table pId LocusName Type AlleleCnt locus_link allele_table 34 5 allele_table pId AlleleName Frequency indexX locus_link marker_table 16 7 marker_table pId MarkerName pos_avg pos_female pos_male chromosome locus_link map_table 32 6 map_table pId marker map position pos_female pos_male mapnames_table 2 6 mapnames_table pId map sex_averaged_map male_sex_map female_sex_map name traitaff_table 1 4 traitaff_table pId ClassCnt PenCnt locus_link affectclass_table 1 9 affectclass_table pId MaleDef FemaleDef AutoDef MalePen FemalePen AutoPen locus_link class_link phenotype_table 69 4 phenotype_table pId person_link bytes data genotype_table 69 5 genotype_table pId person_link chr bytes data > ENV$famSKATRC_results = ENV$famSKATRC_results[0, ] > Mega2famSKATRC(gs=1:1, envir=ENV, pheno=3) tryFn() No markers in range: NM_005286, NPBWR2, 20, 62737182, 62738184 > # this sets one of the many arguments for DOfamSKATRC > # but basically prepares the ENV for the direct use of DOfamSKATRC (below). > > > # DOfamSKATRC is called within Mega2famSKATRC. init_famSKATRC and Mega2famSKATRC need to be > # called to set up the environment for famSKAT_RC to run. BUT, you should ignore DOfamSKATRC > # and use Mega2famSKATRC instead. > # > applyFnToRanges(DOfamSKATRC, ENV$refRanges[50:60, ], ENV$refIndices, envir=ENV) tryFn() No markers in range: NR_052010, IL11RA, 9, 34653893, 34661898 tryFn() No markers in range: NR_045785, CHIT1, 1, 203185206, 203198860 tryFn() No markers in range: NM_017799, TMEM260, 14, 57046510, 57116232 tryFn() No markers in range: NM_014705, DOCK4, 7, 111366163, 111846462 tryFn() No markers in range: NM_003759, SLC4A4, 4, 72204769, 72437804 tryFn() No markers in range: NM_002192, INHBA, 7, 41728600, 41742706 tryFn() No markers in range: NM_002202, ISL1, 5, 50678957, 50690563 tryFn() No markers in range: NM_003659, AGPS, 2, 178257470, 178408564 tryFn() No markers in range: NM_003658, BARX2, 11, 129245880, 129322174 tryFn() No markers in range: NM_018051, WDR60, 7, 158649268, 158738883 CEP104 snp24037 34 35 0 CEP104 snp24039 69 0 0 CEP104 snp24041 49 20 0 CEP104 snp24048 37 30 2 CEP104 snp24494 60 8 1 CEP104 snp24499 56 13 0 CEP104 snp24506 24 36 9 CEP104 snp24507 48 18 3 tryFn() tryFn() tryFn() tryFn() chr gene nvariants start end user.self sys.self elapsed famSKATRC1 1 1 CEP104 7 3728644 3773797 2.422 0.026 2.641 0.3368337 famSKATRC2 famSKATRC3 famSKATRC4 1 0.3368337 0.3368337 0.3368337 > # this will use all the default argument values for DOfamSKATRC > > > > > cleanEx() > nameEx("DOpedgene") > ### * DOpedgene > > flush(stderr()); flush(stdout()) > > ### Name: DOpedgene > ### Title: pedgene call back function > ### Aliases: DOpedgene > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = init_pedgene(db) > ENV$verbose = TRUE > applyFnToRanges(DOpedgene, ENV$refRanges[50:60,], ENV$refIndices) tryFn() No markers in range: NR_052010, IL11RA, 9, 34653893, 34661898 tryFn() No markers in range: NR_045785, CHIT1, 1, 203185206, 203198860 tryFn() No markers in range: NM_017799, TMEM260, 14, 57046510, 57116232 tryFn() No markers in range: NM_014705, DOCK4, 7, 111366163, 111846462 tryFn() No markers in range: NM_003759, SLC4A4, 4, 72204769, 72437804 tryFn() No markers in range: NM_002192, INHBA, 7, 41728600, 41742706 tryFn() No markers in range: NM_002202, ISL1, 5, 50678957, 50690563 tryFn() No markers in range: NM_003659, AGPS, 2, 178257470, 178408564 tryFn() No markers in range: NM_003658, BARX2, 11, 129245880, 129322174 tryFn() No markers in range: NM_018051, WDR60, 7, 158649268, 158738883 CEP104 snp24037 34 35 0 CEP104 snp24039 69 0 0 CEP104 snp24041 49 20 0 CEP104 snp24048 37 30 2 CEP104 snp24494 60 8 1 CEP104 snp24499 56 13 0 CEP104 snp24506 24 36 9 CEP104 snp24507 48 18 3 chr gene nvariants start end sKernel_BT pKernel_BT sBurden_BT 1 1 CEP104 7 3728644 3773797 6.528463 0.5192704 -0.1875224 pBurden_BT sKernel_MB pKernel_MB sBurden_MB pBurden_MB sKernel_UW pKernel_UW 1 0.8512511 52.16311 0.3215774 -0.5778388 0.563373 8.347616 0.2846234 sBurden_UW pBurden_UW 1 -0.6058099 0.544641 > > > > > > cleanEx() > nameEx("Mega2ENVGenABEL") > ### * Mega2ENVGenABEL > > flush(stderr()); flush(stdout()) > > ### Name: Mega2ENVGenABEL > ### Title: generate gwaa.data-class object > ### Aliases: Mega2ENVGenABEL > > ### ** Examples > > ## Not run: > ##D require("GenABEL") > ##D db = system.file("exdata", "seqsimm.db", package="Mega2R") > ##D ENV = read.Mega2DB(db) > ##D gwaa = Mega2ENVGenABEL(markers=ENV$markers[1:10,]) > ##D > ##D str(gwaa) > ##D head(summary(gwaa)) > ## End(Not run) > > > > > cleanEx() > nameEx("Mega2GenABEL") > ### * Mega2GenABEL > > flush(stderr()); flush(stdout()) > > ### Name: Mega2GenABEL > ### Title: generate gwaa.data-class object from a *Mega2R* database > ### Aliases: Mega2GenABEL > > ### ** Examples > > ## Not run: > ##D require("GenABEL") > ##D db = system.file("exdata", "seqsimm.db", package="Mega2R") > ##D ENV = read.Mega2DB(db) > ##D seqsimgwaa = Mega2GenABEL(markers=ENV$markers[1:10,]) > ##D > ##D str(seqsimgwaa) > ##D head(summary(seqsimgwaa)) > ## End(Not run) > > > > > cleanEx() > nameEx("Mega2GenABELClean") > ### * Mega2GenABELClean > > flush(stderr()); flush(stdout()) > > ### Name: Mega2GenABELClean > ### Title: delete temporary PLINK tped files processed by GenABEL > ### Aliases: Mega2GenABELClean > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D > ##D Mega2GenABELClean() > ## End(Not run) > > > > cleanEx() > nameEx("Mega2GenABELtst") > ### * Mega2GenABELtst > > flush(stderr()); flush(stdout()) > > ### Name: Mega2GenABELtst > ### Title: compare two gwaa.data-class objects > ### Aliases: Mega2GenABELtst > > ### ** Examples > > ## Not run: > ##D db = system.file("exdata", "seqsimm.db", package="Mega2R") > ##D require("GenABEL") > ##D ENV = read.Mega2DB(db) > ##D > ##D y = Mega2ENVGenABEL() > ##D Mega2GenABELtst(y, y, full = FALSE) > ## End(Not run) > > ## Not run: > ##D # donttestcheck: if you have more time, try ... > ##D x = Mega2GenABEL() > ##D Mega2GenABELtst(x, y, full = FALSE) > ## End(Not run) > > > > > cleanEx() > nameEx("Mega2SKAT") > ### * Mega2SKAT > > flush(stderr()); flush(stdout()) > > ### Name: Mega2SKAT > ### Title: execute the CRAN SKAT function on a subset of the gene > ### transcripts > ### Aliases: Mega2SKAT > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = init_SKAT(db, verbose = FALSE, allMarkers = FALSE) > ENV$verbose = FALSE > ENV$SKAT_results = ENV$SKAT_results[0, ] > Mega2SKAT(ENV$phe[, 3] - 1 ~ 1, "D", kernel = "linear.weighted", + weights.beta = c(0.5, 0.5), gs=50:60 ) Sample size (non-missing y and X) = 69, which is < 2000. The small sample adjustment is applied! > > > ENV$SKAT_results chr gene nvariants start end skat 1 1 CEP104 7 3728644 3773797 0.2663667 > > > > > cleanEx() > nameEx("Mega2VCF") > ### * Mega2VCF > > flush(stderr()); flush(stdout()) > > ### Name: Mega2VCF > ### Title: generate a VCF file set for a collection of markers > ### Aliases: Mega2VCF > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > vcfdir = file.path(where_mega2rtutorial_data(), "vcfr") > if (!dir.exists(vcfdir)) dir.create(vcfdir) > vcffile = file.path(where_mega2rtutorial_data(), "vcfr", "vcf.01") > Mega2VCF(vcffile, ENV$markers[ENV$markers$chromosome == 1, ][1:10,], envir = ENV) > list.files(vcfdir) [1] "vcf.01.fam" "vcf.01.freq" "vcf.01.map" "vcf.01.pen" "vcf.01.phe" [6] "vcf.01.vcf" > > > > > cleanEx() > nameEx("Mega2famSKATRC") > ### * Mega2famSKATRC > > flush(stderr()); flush(stdout()) > > ### Name: Mega2famSKATRC > ### Title: execute the CRAN famSKAT_RC function on a subset of the gene > ### transcripts > ### Aliases: Mega2famSKATRC > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = init_famSKATRC(db, verbose = FALSE) > ENV$verbose = FALSE > ENV$famSKATRC_results = ENV$famSKATRC_results[0, ] > Mega2famSKATRC(gs=50:60, envir=ENV, pheno=3) tryFn() tryFn() tryFn() tryFn() > > > ENV$famSKATRC_results chr gene nvariants start end user.self sys.self elapsed famSKATRC1 1 1 CEP104 7 3728644 3773797 2.845 0.02 2.899 0.3368337 famSKATRC2 famSKATRC3 famSKATRC4 1 0.3368337 0.3368337 0.3368337 > > > > > cleanEx() > nameEx("Mega2gdsfmt") > ### * Mega2gdsfmt > > flush(stderr()); flush(stdout()) > > ### Name: Mega2gdsfmt > ### Title: transcode mega2 to gdsfmt/SNP_ARRAY > ### Aliases: Mega2gdsfmt > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > gdsfmtfile = file.path(where_mega2rtutorial_data(), "test.gds") > append_genotype_a = TRUE > append_genotype_b = append_genotype_c = FALSE > gn = Mega2gdsfmt(gdsfmtfile, envir=ENV) Clean up the fragments of GDS file: open the file '/tmp/RtmpWSj9QF/Mega2Rtutorial/test.gds' (5.5K) # of fragments: 72 save to '/tmp/RtmpWSj9QF/Mega2Rtutorial/test.gds.tmp' rename '/tmp/RtmpWSj9QF/Mega2Rtutorial/test.gds.tmp' (5.0K, reduced: 516B) # of fragments: 29 > gn File: /tmp/RtmpWSj9QF/Mega2Rtutorial/test.gds (5.0K) + [ ] * |--+ description [ ] |--+ sample.id { Str8 69 LZMA_ra(39.4%), 265B } |--+ snp.id { Int32 16 LZMA_ra(171.9%), 117B } |--+ snp.rs.id { Str8 16 LZMA_ra(93.1%), 141B } |--+ snp.position { Int32 16 LZMA_ra(184.4%), 125B } |--+ snp.chromosome { Int32 16 LZMA_ra(134.4%), 93B } * |--+ snp.allele { Str8 16 LZMA_ra(144.1%), 105B } |--+ genotype { Bit2 69x16 LZMA_ra(109.4%), 309B } * \--+ sample.annot [ data.frame ] * |--+ sample.id { Str8 69 LZMA_ra(39.4%), 265B } |--+ family.id { Str8 69 LZMA_ra(17.8%), 105B } |--+ father.id { Str8 69 LZMA_ra(24.8%), 145B } |--+ mother.id { Str8 69 LZMA_ra(25.5%), 149B } |--+ sex.id { Str8 69 LZMA_ra(29.9%), 133B } \--+ cc.id { Int32 69 LZMA_ra(35.5%), 105B } > > > > > cleanEx() > nameEx("Mega2pedgene") > ### * Mega2pedgene > > flush(stderr()); flush(stdout()) > > ### Name: Mega2pedgene > ### Title: Execute the pedgene function on a transcript ranges > ### Aliases: Mega2pedgene > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = init_pedgene(db) > ENV$verbose = TRUE > Mega2pedgene(gs = 50:60) tryFn() No markers in range: NR_052010, IL11RA, 9, 34653893, 34661898 tryFn() No markers in range: NR_045785, CHIT1, 1, 203185206, 203198860 tryFn() No markers in range: NM_017799, TMEM260, 14, 57046510, 57116232 tryFn() No markers in range: NM_014705, DOCK4, 7, 111366163, 111846462 tryFn() No markers in range: NM_003759, SLC4A4, 4, 72204769, 72437804 tryFn() No markers in range: NM_002192, INHBA, 7, 41728600, 41742706 tryFn() No markers in range: NM_002202, ISL1, 5, 50678957, 50690563 tryFn() No markers in range: NM_003659, AGPS, 2, 178257470, 178408564 tryFn() No markers in range: NM_003658, BARX2, 11, 129245880, 129322174 tryFn() No markers in range: NM_018051, WDR60, 7, 158649268, 158738883 CEP104 snp24037 34 35 0 CEP104 snp24039 69 0 0 CEP104 snp24041 49 20 0 CEP104 snp24048 37 30 2 CEP104 snp24494 60 8 1 CEP104 snp24499 56 13 0 CEP104 snp24506 24 36 9 CEP104 snp24507 48 18 3 chr gene nvariants start end sKernel_BT pKernel_BT sBurden_BT 1 1 CEP104 7 3728644 3773797 6.528463 0.5192704 -0.1875224 pBurden_BT sKernel_MB pKernel_MB sBurden_MB pBurden_MB sKernel_UW pKernel_UW 1 0.8512511 52.16311 0.3215774 -0.5778388 0.563373 8.347616 0.2846234 sBurden_UW pBurden_UW 1 -0.6058099 0.544641 > > > > > cleanEx() > nameEx("applyFnToGenes") > ### * applyFnToGenes > > flush(stderr()); flush(stdout()) > > ### Name: applyFnToGenes > ### Title: apply a function to the genotypes (markers) in each gene > ### transcript and/or base pair range > ### Aliases: applyFnToGenes > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > show = function(m, r, e) { + print(r) + print(m) + print(head(getgenotypes(m, envir = e))) + } > > # apply function "show" to all transcripts on genes ELL2 and CARD15 > > # apply function "show" to all genotypes on chromosomes 11 for two base > # pair ranges > applyFnToGenes(show, ranges_arg = matrix(c(1, 5000000, 10000000, + 1, 10000000, 15000000), ncol = 3, nrow = 2, byrow = TRUE)) ENTREZID ALIAS SYMBOL TXID TXNAME TXCHROM TXSTRAND TXSTART TXEND 1 - - chr1:5e+06-1e+07 0 - 1 - 5e+06 1e+07 locus_link locus_link_fill MarkerName chromosome position 14 14 14 snp30480 1 8264348 15 15 15 snp30484 1 8264352 16 16 16 snp30487 1 8264355 [,1] [,2] [,3] [1,] "11" "11" "12" [2,] "22" "12" "11" [3,] "11" "11" "11" [4,] "12" "11" "11" [5,] "12" "22" "11" [6,] "22" "12" "11" > > # apply function "show" to all genotypes for first marker in each chromosome > applyFnToGenes(show, markers_arg = ENV$markers[! duplicated(ENV$markers$chromosome), 3]) NULL locus_link locus_link_fill MarkerName chromosome position 1 1 1 snp22735 1 2243901 [,1] [1,] "11" [2,] "11" [3,] "12" [4,] "11" [5,] "12" [6,] "12" > > # apply function "show" to all genotypes on chromosomes 24 and 26 > applyFnToGenes(show, chrs_arg=c(24, 26)) > > > > > > cleanEx() > nameEx("applyFnToMarkers") > ### * applyFnToMarkers > > flush(stderr()); flush(stdout()) > > ### Name: applyFnToMarkers > ### Title: apply a function to the genotypes from a set of markers > ### Aliases: applyFnToMarkers > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > show = function(m, r, e) { + print(r) + print(m) + print(head(getgenotypes(m, envir = e))) + } > > # apply function "show" to all genotypes > 5,000,000 bp > applyFnToMarkers(show, ENV$markers[ENV$markers$position > 5000000,]) NULL locus_link locus_link_fill MarkerName chromosome position 14 14 14 snp30480 1 8264348 15 15 15 snp30484 1 8264352 16 16 16 snp30487 1 8264355 [,1] [,2] [,3] [1,] "11" "11" "12" [2,] "22" "12" "11" [3,] "11" "11" "11" [4,] "12" "11" "11" [5,] "12" "22" "11" [6,] "22" "12" "11" > > > > > > cleanEx() > nameEx("applyFnToRanges") > ### * applyFnToRanges > > flush(stderr()); flush(stdout()) > > ### Name: applyFnToRanges > ### Title: apply a function to all the genotypes for markers found in > ### several specified ranges > ### Aliases: applyFnToRanges > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > show = function(m, r, e) { + print(r) + print(m) + print(head(getgenotypesraw(m, envir = e))) + } > > # apply function "show" to all genotypes on chromosomes 1 for two base pair > # ranges > applyFnToRanges(show, + ranges_arg = + matrix(c(1, 2244000, 2245000, + 1, 3762500, 3765000), + ncol = 3, nrow = 2, byrow = TRUE), + indices_arg = 1:3) X1 X2 X3 ChrStartEnd 1 1 2244000 2245000 chr1:2244000-2245000 locus_link locus_link_fill MarkerName chromosome position 2 2 2 snp23360 1 2244526 3 3 3 snp23361 1 2244527 4 4 4 snp23362 1 2244528 5 5 5 snp23364 1 2244530 [,1] [,2] [,3] [,4] [1,] 65538 65538 65538 65538 [2,] 65537 65538 65538 65538 [3,] 65537 65537 65537 65537 [4,] 65537 65538 65538 65537 [5,] 65538 65537 65537 65537 [6,] 65538 65537 65537 65538 X1 X2 X3 ChrStartEnd 2 1 3762500 3765000 chr1:3762500-3765000 locus_link locus_link_fill MarkerName chromosome position 10 10 10 snp24494 1 3762638 11 11 11 snp24499 1 3762643 12 12 12 snp24506 1 3762650 13 13 13 snp24507 1 3762651 [,1] [,2] [,3] [,4] [1,] 65538 65537 65537 65538 [2,] 65538 65538 65538 65538 [3,] 65537 65537 65537 65537 [4,] 65537 65538 65537 65538 [5,] 65537 65537 131074 65537 [6,] 65537 65538 65538 65538 > > # apply function "show" to all genotypes on chromosomes 1 for two base pair > # ranges > applyFnToRanges(show, + ranges_arg = + matrix(c(1, 2240000, 2245000, "range1", + 1, 3760000, 3765000, "range2"), + ncol = 4, nrow = 2, byrow = TRUE), + indices_arg = 1:4) X1 X2 X3 X4 1 1 2240000 2245000 range1 locus_link locus_link_fill MarkerName chromosome position 1 1 1 snp22735 1 2243901 2 2 2 snp23360 1 2244526 3 3 3 snp23361 1 2244527 4 4 4 snp23362 1 2244528 5 5 5 snp23364 1 2244530 [,1] [,2] [,3] [,4] [,5] [1,] 65537 65538 65538 65538 65538 [2,] 65537 65537 65538 65538 65538 [3,] 65538 65537 65537 65537 65537 [4,] 65537 65537 65538 65538 65537 [5,] 65538 65538 65537 65537 65537 [6,] 65538 65538 65537 65537 65538 X1 X2 X3 X4 2 1 3760000 3765000 range2 locus_link locus_link_fill MarkerName chromosome position 6 6 6 snp24037 1 3762181 7 7 7 snp24039 1 3762183 8 8 8 snp24041 1 3762185 9 9 9 snp24048 1 3762192 10 10 10 snp24494 1 3762638 11 11 11 snp24499 1 3762643 12 12 12 snp24506 1 3762650 13 13 13 snp24507 1 3762651 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [1,] 65538 65537 65537 65538 65538 65537 65537 65538 [2,] 65537 65537 65538 65538 65538 65538 65538 65538 [3,] 65537 65537 65537 65537 65537 65537 65537 65537 [4,] 65537 65537 65538 65537 65537 65538 65537 65538 [5,] 65537 65537 65537 65538 65537 65537 131074 65537 [6,] 65538 65537 65538 65538 65537 65538 65538 65538 > > > > > cleanEx() > nameEx("clean_mega2rtutorial_data") > ### * clean_mega2rtutorial_data > > flush(stderr()); flush(stdout()) > > ### Name: clean_mega2rtutorial_data > ### Title: remove tutorial data > ### Aliases: clean_mega2rtutorial_data > > ### ** Examples > > clean_mega2rtutorial_data() > > > > > cleanEx() > nameEx("computeDosage") > ### * computeDosage > > flush(stderr()); flush(stdout()) > > ### Name: computeDosage > ### Title: computeDosage function > ### Aliases: computeDosage > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = init_famSKATRC(db, verbose = TRUE) int_table 35 3 int_table pId key value charstar_table 9 3 charstar_table pId key value pedigree_table 1 8 pedigree_table pId Num EntryCnt Name PedPre OriginalID origped pedigree_link person_table 69 11 person_table pId UniqueID OrigID FamName PerPre ID Father Mother Sex pedigree_link person_link pedigree_brkloop_table 1 8 pedigree_brkloop_table pId Num EntryCnt Name PedPre OriginalID origped pedigree_link person_brkloop_table 69 11 person_brkloop_table pId UniqueID OrigID FamName PerPre ID Father Mother Sex pedigree_link person_link locus_table 17 5 locus_table pId LocusName Type AlleleCnt locus_link allele_table 34 5 allele_table pId AlleleName Frequency indexX locus_link marker_table 16 7 marker_table pId MarkerName pos_avg pos_female pos_male chromosome locus_link map_table 32 6 map_table pId marker map position pos_female pos_male mapnames_table 2 6 mapnames_table pId map sex_averaged_map male_sex_map female_sex_map name traitaff_table 1 4 traitaff_table pId ClassCnt PenCnt locus_link affectclass_table 1 9 affectclass_table pId MaleDef FemaleDef AutoDef MalePen FemalePen AutoPen locus_link class_link phenotype_table 69 4 phenotype_table pId person_link bytes data genotype_table 69 5 genotype_table pId person_link chr bytes data > dimDosage = function(m, r, e) {print(dim(computeDosage(m, r, e)))} > applyFnToRanges(dimDosage, ENV$refRanges[50:60, ], ENV$refIndices, envir=ENV) tryFn() No markers in range: NR_052010, IL11RA, 9, 34653893, 34661898 tryFn() No markers in range: NR_045785, CHIT1, 1, 203185206, 203198860 tryFn() No markers in range: NM_017799, TMEM260, 14, 57046510, 57116232 tryFn() No markers in range: NM_014705, DOCK4, 7, 111366163, 111846462 tryFn() No markers in range: NM_003759, SLC4A4, 4, 72204769, 72437804 tryFn() No markers in range: NM_002192, INHBA, 7, 41728600, 41742706 tryFn() No markers in range: NM_002202, ISL1, 5, 50678957, 50690563 tryFn() No markers in range: NM_003659, AGPS, 2, 178257470, 178408564 tryFn() No markers in range: NM_003658, BARX2, 11, 129245880, 129322174 tryFn() No markers in range: NM_018051, WDR60, 7, 158649268, 158738883 CEP104 snp24037 34 35 0 CEP104 snp24039 69 0 0 CEP104 snp24041 49 20 0 CEP104 snp24048 37 30 2 CEP104 snp24494 60 8 1 CEP104 snp24499 56 13 0 CEP104 snp24506 24 36 9 CEP104 snp24507 48 18 3 [1] 69 7 > # This will use return dosage matrices for the markers in the ranges 50 - 60, > # but is basically ignores the results. > > > > > cleanEx() > nameEx("dbmega2_import") > ### * dbmega2_import > > flush(stderr()); flush(stdout()) > > ### Name: dbmega2_import > ### Title: read Mega2 SQLite database into R > ### Aliases: dbmega2_import > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = dbmega2_import(db, verbose = TRUE) int_table 35 3 int_table pId key value charstar_table 9 3 charstar_table pId key value pedigree_table 1 8 pedigree_table pId Num EntryCnt Name PedPre OriginalID origped pedigree_link person_table 69 11 person_table pId UniqueID OrigID FamName PerPre ID Father Mother Sex pedigree_link person_link pedigree_brkloop_table 1 8 pedigree_brkloop_table pId Num EntryCnt Name PedPre OriginalID origped pedigree_link person_brkloop_table 69 11 person_brkloop_table pId UniqueID OrigID FamName PerPre ID Father Mother Sex pedigree_link person_link locus_table 17 5 locus_table pId LocusName Type AlleleCnt locus_link allele_table 34 5 allele_table pId AlleleName Frequency indexX locus_link marker_table 16 7 marker_table pId MarkerName pos_avg pos_female pos_male chromosome locus_link map_table 32 6 map_table pId marker map position pos_female pos_male mapnames_table 2 6 mapnames_table pId map sex_averaged_map male_sex_map female_sex_map name traitaff_table 1 4 traitaff_table pId ClassCnt PenCnt locus_link affectclass_table 1 9 affectclass_table pId MaleDef FemaleDef AutoDef MalePen FemalePen AutoPen locus_link class_link phenotype_table 69 4 phenotype_table pId person_link bytes data genotype_table 69 5 genotype_table pId person_link chr bytes data > > ENV = dbmega2_import(db) > > > > cleanEx() > nameEx("dmpPed") > ### * dmpPed > > flush(stderr()); flush(stdout()) > > ### Name: dmpPed > ### Title: generate the .ped, .fam and .map files of PLINK PED > ### representation of a gwaa.data-class object > ### Aliases: dmpPed > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D dmpPed() > ##D or > ##D dmpPed(mygwaa, "name", "cc") > ## End(Not run) > > > > cleanEx() > nameEx("dump_mega2rtutorial_data") > ### * dump_mega2rtutorial_data > > flush(stderr()); flush(stdout()) > > ### Name: dump_mega2rtutorial_data > ### Title: dump tutorial data > ### Aliases: dump_mega2rtutorial_data > > ### ** Examples > > dump_mega2rtutorial_data() > > > > > cleanEx() > nameEx("getAlleles") > ### * getAlleles > > flush(stderr()); flush(stdout()) > > ### Name: getAlleles > ### Title: pull allele pairs > ### Aliases: getAlleles > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D getAlleles(envir) > ## End(Not run) > > > > cleanEx() > nameEx("getgenotype_person") > ### * getgenotype_person > > flush(stderr()); flush(stdout()) > > ### Name: getgenotype_person > ### Title: return the genotypes for all markers of a given person > ### Aliases: getgenotype_person > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D # genotypes for all markers for n'th person in genotype table > ##D getgenotype_person(1) > ##D > ##D # genotypes for all markers for range of persons in genotype table > ##D getgenotype_person(m:n) > ## End(Not run) > > > > cleanEx() > nameEx("getgenotypes") > ### * getgenotypes > > flush(stderr()); flush(stdout()) > > ### Name: getgenotypes > ### Title: fetch genotype character matrix for specified markers > ### Aliases: getgenotypes > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > getgenotypes(ENV$markers) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [1,] "11" "12" "12" "12" "12" "12" "11" "11" "12" "12" "11" "11" "12" [2,] "11" "11" "12" "12" "12" "11" "11" "12" "12" "12" "12" "12" "12" [3,] "12" "11" "11" "11" "11" "11" "11" "11" "11" "11" "11" "11" "11" [4,] "11" "11" "12" "12" "11" "11" "11" "12" "11" "11" "12" "11" "12" [5,] "12" "12" "11" "11" "11" "11" "11" "11" "12" "11" "11" "22" "11" [6,] "12" "12" "11" "11" "12" "12" "11" "12" "12" "11" "12" "12" "12" [7,] "12" "12" "11" "11" "11" "11" "11" "12" "11" "11" "12" "11" "12" [8,] "11" "12" "11" "12" "22" "12" "11" "12" "11" "11" "12" "11" "12" [9,] "11" "11" "12" "12" "12" "11" "11" "11" "11" "11" "11" "11" "11" [10,] "12" "11" "11" "22" "22" "11" "11" "11" "12" "11" "11" "12" "11" [11,] "12" "12" "11" "11" "12" "12" "11" "11" "12" "11" "11" "22" "11" [12,] "12" "12" "11" "12" "22" "12" "11" "12" "12" "11" "11" "12" "11" [13,] "11" "12" "12" "12" "11" "12" "11" "11" "12" "12" "11" "11" "12" [14,] "12" "12" "11" "12" "12" "12" "11" "11" "11" "11" "11" "12" "11" [15,] "12" "12" "11" "12" "12" "12" "11" "11" "12" "12" "11" "11" "12" [16,] "11" "12" "12" "12" "22" "12" "11" "12" "12" "22" "12" "11" "22" [17,] "11" "11" "11" "12" "12" "11" "11" "12" "11" "11" "12" "11" "12" [18,] "11" "12" "11" "11" "12" "12" "11" "12" "11" "12" "12" "11" "12" [19,] "11" "11" "11" "12" "12" "11" "11" "12" "12" "12" "12" "11" "22" [20,] "11" "12" "11" "11" "12" "12" "11" "11" "12" "11" "11" "12" "11" [21,] "12" "12" "11" "11" "11" "11" "11" "11" "12" "11" "11" "12" "11" [22,] "12" "12" "11" "11" "11" "11" "11" "11" "11" "11" "11" "11" "12" [23,] "11" "12" "11" "11" "12" "12" "11" "11" "12" "11" "11" "12" "11" [24,] "11" "12" "11" "11" "11" "11" "11" "11" "11" "11" "11" "11" "11" [25,] "11" "11" "11" "12" "12" "11" "11" "11" "11" "11" "11" "11" "11" [26,] "11" "11" "12" "22" "12" "11" "11" "12" "11" "11" "12" "11" "22" [27,] "12" "11" "11" "12" "12" "11" "11" "12" "11" "11" "12" "11" "12" [28,] "12" "12" "11" "11" "12" "12" "11" "11" "11" "11" "11" "12" "12" [29,] "12" "11" "11" "12" "12" "11" "11" "11" "11" "11" "11" "12" "12" [30,] "12" "11" "11" "12" "12" "11" "11" "12" "11" "11" "12" "11" "12" [31,] "12" "12" "11" "11" "12" "12" "11" "11" "11" "11" "11" "12" "11" [32,] "12" "12" "11" "11" "11" "11" "11" "11" "12" "11" "11" "12" "11" [33,] "11" "12" "12" "12" "11" "11" "11" "11" "12" "11" "11" "12" "11" [34,] "12" "12" "11" "11" "11" "11" "11" "11" "12" "11" "11" "12" "11" [35,] "11" "12" "12" "12" "12" "12" "11" "12" "22" "11" "11" "22" "11" [36,] "12" "12" "11" "11" "12" "12" "11" "11" "12" "11" "11" "12" "11" [37,] "11" "12" "12" "12" "11" "11" "11" "11" "12" "11" "11" "12" "11" [38,] "11" "12" "12" "12" "12" "12" "11" "12" "22" "11" "11" "22" "11" [39,] "12" "12" "11" "11" "11" "11" "11" "11" "11" "11" "11" "12" "11" [40,] "12" "12" "11" "11" "11" "11" "11" "11" "11" "11" "11" "12" "11" [41,] "12" "12" "11" "11" "11" "11" "11" "11" "11" "11" "11" "12" "11" [42,] "12" "12" "11" "12" "12" "11" "11" "11" "11" "11" "11" "11" "11" [43,] "12" "12" "11" "11" "12" "12" "11" "12" "12" "11" "11" "12" "11" [44,] "12" "11" "11" "11" "12" "12" "11" "11" "12" "11" "11" "22" "11" [45,] "12" "11" "11" "12" "22" "12" "11" "12" "12" "11" "11" "12" "11" [46,] "12" "12" "11" "11" "12" "12" "11" "11" "11" "11" "11" "12" "11" [47,] "12" "11" "11" "22" "22" "11" "11" "11" "11" "11" "11" "12" "11" [48,] "12" "12" "11" "11" "12" "12" "11" "11" "11" "11" "11" "12" "11" [49,] "12" "12" "11" "12" "22" "12" "11" "11" "12" "11" "11" "22" "11" [50,] "12" "11" "11" "12" "12" "11" "11" "11" "12" "11" "11" "22" "11" [51,] "12" "11" "11" "22" "22" "11" "11" "12" "12" "11" "11" "12" "11" [52,] "12" "12" "11" "11" "12" "12" "11" "11" "12" "11" "11" "22" "11" [53,] "12" "11" "11" "12" "12" "11" "11" "11" "11" "11" "11" "12" "11" [54,] "12" "11" "11" "12" "12" "11" "11" "11" "12" "11" "11" "22" "11" [55,] "12" "11" "11" "22" "22" "11" "11" "11" "11" "11" "11" "12" "11" [56,] "12" "11" "11" "12" "12" "11" "11" "12" "12" "11" "11" "12" "11" [57,] "22" "11" "11" "22" "22" "12" "11" "11" "11" "11" "11" "11" "11" [58,] "22" "11" "11" "22" "22" "12" "11" "11" "11" "11" "11" "11" "11" [59,] "22" "11" "11" "22" "22" "12" "11" "11" "11" "11" "11" "11" "11" [60,] "22" "11" "11" "22" "22" "12" "11" "11" "11" "11" "11" "11" "11" [61,] "12" "11" "11" "12" "12" "11" "11" "11" "11" "11" "11" "12" "11" [62,] "12" "11" "11" "12" "12" "11" "11" "11" "11" "11" "11" "12" "11" [63,] "12" "12" "11" "12" "22" "12" "11" "11" "11" "11" "11" "12" "11" [64,] "12" "12" "11" "11" "12" "12" "11" "12" "11" "11" "12" "11" "12" [65,] "12" "12" "11" "12" "22" "12" "11" "11" "11" "11" "11" "12" "11" [66,] "12" "12" "11" "11" "12" "12" "11" "11" "11" "11" "11" "12" "11" [67,] "12" "12" "11" "11" "12" "12" "11" "11" "12" "12" "11" "12" "12" [68,] "12" "12" "11" "12" "22" "12" "11" "11" "11" "11" "11" "12" "11" [69,] "12" "12" "11" "11" "12" "12" "11" "11" "12" "12" "11" "12" "12" [,14] [,15] [,16] [1,] "11" "11" "12" [2,] "22" "12" "11" [3,] "11" "11" "11" [4,] "12" "11" "11" [5,] "12" "22" "11" [6,] "22" "12" "11" [7,] "12" "11" "11" [8,] "12" "11" "11" [9,] "11" "11" "11" [10,] "12" "12" "11" [11,] "12" "22" "11" [12,] "11" "12" "11" [13,] "11" "11" "12" [14,] "11" "12" "11" [15,] "11" "11" "12" [16,] "12" "11" "12" [17,] "12" "11" "11" [18,] "12" "11" "11" [19,] "12" "11" "12" [20,] "12" "12" "11" [21,] "12" "12" "11" [22,] "11" "11" "12" [23,] "12" "12" "11" [24,] "11" "11" "11" [25,] "11" "11" "11" [26,] "12" "11" "12" [27,] "12" "11" "12" [28,] "11" "12" "22" [29,] "11" "12" "22" [30,] "12" "11" "12" [31,] "11" "12" "12" [32,] "12" "12" "12" [33,] "12" "12" "11" [34,] "12" "12" "12" [35,] "12" "22" "11" [36,] "12" "12" "12" [37,] "12" "12" "11" [38,] "12" "22" "12" [39,] "11" "12" "11" [40,] "11" "12" "11" [41,] "11" "12" "11" [42,] "11" "11" "11" [43,] "11" "12" "11" [44,] "12" "22" "11" [45,] "11" "12" "11" [46,] "11" "12" "11" [47,] "11" "12" "11" [48,] "11" "12" "11" [49,] "12" "22" "11" [50,] "12" "22" "11" [51,] "11" "12" "11" [52,] "12" "22" "11" [53,] "11" "12" "11" [54,] "12" "22" "11" [55,] "11" "12" "11" [56,] "11" "12" "11" [57,] "11" "11" "11" [58,] "11" "11" "11" [59,] "11" "11" "11" [60,] "11" "11" "11" [61,] "11" "12" "11" [62,] "11" "12" "11" [63,] "11" "12" "11" [64,] "12" "11" "11" [65,] "11" "12" "11" [66,] "11" "12" "11" [67,] "11" "12" "12" [68,] "11" "12" "11" [69,] "11" "12" "12" > > > > > cleanEx() > nameEx("getgenotypes_R") > ### * getgenotypes_R > > flush(stderr()); flush(stdout()) > > ### Name: getgenotypes_R > ### Title: fetch genotype matrix for specified markers (assemble by rows) > ### Aliases: getgenotypes_R > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D # genotypes for all persons in markers data.frame argument > ##D getgenotypes_R(ENV$markers) > ##D > ##D # genotypes for all persons in chromosome n > ##D getgenotypes_R(ENV$markers[ENV$markers$chromosome == n,]) > ## End(Not run) > > > > cleanEx() > nameEx("getgenotypesdos") > ### * getgenotypesdos > > flush(stderr()); flush(stdout()) > > ### Name: getgenotypesdos > ### Title: fetch dosage integer matrix for specified markers > ### Aliases: getgenotypesdos > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > getgenotypesdos(ENV$markers[ENV$markers$chromosome == 1,]) $ncol [1] 15 $zero [1] 1 2 3 4 5 6 0 7 8 9 10 11 12 13 14 15 $geno [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [1,] 0 1 1 1 1 1 0 1 1 0 0 1 0 [2,] 0 0 1 1 1 0 1 1 1 1 1 1 2 [3,] 1 0 0 0 2 0 0 0 0 0 0 0 0 [4,] 0 0 1 1 2 0 1 0 0 1 0 1 1 [5,] 1 1 0 0 2 0 0 1 0 0 2 0 1 [6,] 1 1 0 0 1 1 1 1 0 1 1 1 2 [7,] 1 1 0 0 2 0 1 0 0 1 0 1 1 [8,] 0 1 0 1 0 1 1 0 0 1 0 1 1 [9,] 0 0 1 1 1 0 0 0 0 0 0 0 0 [10,] 1 0 0 2 0 0 0 1 0 0 1 0 1 [11,] 1 1 0 0 1 1 0 1 0 0 2 0 1 [12,] 1 1 0 1 0 1 1 1 0 0 1 0 0 [13,] 0 1 1 1 2 1 0 1 1 0 0 1 0 [14,] 1 1 0 1 1 1 0 0 0 0 1 0 0 [15,] 1 1 0 1 1 1 0 1 1 0 0 1 0 [16,] 0 1 1 1 0 1 1 1 2 1 0 2 1 [17,] 0 0 0 1 1 0 1 0 0 1 0 1 1 [18,] 0 1 0 0 1 1 1 0 1 1 0 1 1 [19,] 0 0 0 1 1 0 1 1 1 1 0 2 1 [20,] 0 1 0 0 1 1 0 1 0 0 1 0 1 [21,] 1 1 0 0 2 0 0 1 0 0 1 0 1 [22,] 1 1 0 0 2 0 0 0 0 0 0 1 0 [23,] 0 1 0 0 1 1 0 1 0 0 1 0 1 [24,] 0 1 0 0 2 0 0 0 0 0 0 0 0 [25,] 0 0 0 1 1 0 0 0 0 0 0 0 0 [26,] 0 0 1 2 1 0 1 0 0 1 0 2 1 [27,] 1 0 0 1 1 0 1 0 0 1 0 1 1 [28,] 1 1 0 0 1 1 0 0 0 0 1 1 0 [29,] 1 0 0 1 1 0 0 0 0 0 1 1 0 [30,] 1 0 0 1 1 0 1 0 0 1 0 1 1 [31,] 1 1 0 0 1 1 0 0 0 0 1 0 0 [32,] 1 1 0 0 2 0 0 1 0 0 1 0 1 [33,] 0 1 1 1 2 0 0 1 0 0 1 0 1 [34,] 1 1 0 0 2 0 0 1 0 0 1 0 1 [35,] 0 1 1 1 1 1 1 2 0 0 2 0 1 [36,] 1 1 0 0 1 1 0 1 0 0 1 0 1 [37,] 0 1 1 1 2 0 0 1 0 0 1 0 1 [38,] 0 1 1 1 1 1 1 2 0 0 2 0 1 [39,] 1 1 0 0 2 0 0 0 0 0 1 0 0 [40,] 1 1 0 0 2 0 0 0 0 0 1 0 0 [41,] 1 1 0 0 2 0 0 0 0 0 1 0 0 [42,] 1 1 0 1 1 0 0 0 0 0 0 0 0 [43,] 1 1 0 0 1 1 1 1 0 0 1 0 0 [44,] 1 0 0 0 1 1 0 1 0 0 2 0 1 [45,] 1 0 0 1 0 1 1 1 0 0 1 0 0 [46,] 1 1 0 0 1 1 0 0 0 0 1 0 0 [47,] 1 0 0 2 0 0 0 0 0 0 1 0 0 [48,] 1 1 0 0 1 1 0 0 0 0 1 0 0 [49,] 1 1 0 1 0 1 0 1 0 0 2 0 1 [50,] 1 0 0 1 1 0 0 1 0 0 2 0 1 [51,] 1 0 0 2 0 0 1 1 0 0 1 0 0 [52,] 1 1 0 0 1 1 0 1 0 0 2 0 1 [53,] 1 0 0 1 1 0 0 0 0 0 1 0 0 [54,] 1 0 0 1 1 0 0 1 0 0 2 0 1 [55,] 1 0 0 2 0 0 0 0 0 0 1 0 0 [56,] 1 0 0 1 1 0 1 1 0 0 1 0 0 [57,] 2 0 0 2 0 1 0 0 0 0 0 0 0 [58,] 2 0 0 2 0 1 0 0 0 0 0 0 0 [59,] 2 0 0 2 0 1 0 0 0 0 0 0 0 [60,] 2 0 0 2 0 1 0 0 0 0 0 0 0 [61,] 1 0 0 1 1 0 0 0 0 0 1 0 0 [62,] 1 0 0 1 1 0 0 0 0 0 1 0 0 [63,] 1 1 0 1 0 1 0 0 0 0 1 0 0 [64,] 1 1 0 0 1 1 1 0 0 1 0 1 1 [65,] 1 1 0 1 0 1 0 0 0 0 1 0 0 [66,] 1 1 0 0 1 1 0 0 0 0 1 0 0 [67,] 1 1 0 0 1 1 0 1 1 0 1 1 0 [68,] 1 1 0 1 0 1 0 0 0 0 1 0 0 [69,] 1 1 0 0 1 1 0 1 1 0 1 1 0 [,14] [,15] [,16] [1,] 0 1 0 [2,] 1 0 0 [3,] 0 0 0 [4,] 0 0 0 [5,] 2 0 0 [6,] 1 0 0 [7,] 0 0 0 [8,] 0 0 0 [9,] 0 0 0 [10,] 1 0 0 [11,] 2 0 0 [12,] 1 0 0 [13,] 0 1 0 [14,] 1 0 0 [15,] 0 1 0 [16,] 0 1 0 [17,] 0 0 0 [18,] 0 0 0 [19,] 0 1 0 [20,] 1 0 0 [21,] 1 0 0 [22,] 0 1 0 [23,] 1 0 0 [24,] 0 0 0 [25,] 0 0 0 [26,] 0 1 0 [27,] 0 1 0 [28,] 1 2 0 [29,] 1 2 0 [30,] 0 1 0 [31,] 1 1 0 [32,] 1 1 0 [33,] 1 0 0 [34,] 1 1 0 [35,] 2 0 0 [36,] 1 1 0 [37,] 1 0 0 [38,] 2 1 0 [39,] 1 0 0 [40,] 1 0 0 [41,] 1 0 0 [42,] 0 0 0 [43,] 1 0 0 [44,] 2 0 0 [45,] 1 0 0 [46,] 1 0 0 [47,] 1 0 0 [48,] 1 0 0 [49,] 2 0 0 [50,] 2 0 0 [51,] 1 0 0 [52,] 2 0 0 [53,] 1 0 0 [54,] 2 0 0 [55,] 1 0 0 [56,] 1 0 0 [57,] 0 0 0 [58,] 0 0 0 [59,] 0 0 0 [60,] 0 0 0 [61,] 1 0 0 [62,] 1 0 0 [63,] 1 0 0 [64,] 0 0 0 [65,] 1 0 0 [66,] 1 0 0 [67,] 1 1 0 [68,] 1 0 0 [69,] 1 1 0 > > > > > cleanEx() > nameEx("getgenotypesgenabel") > ### * getgenotypesgenabel > > flush(stderr()); flush(stdout()) > > ### Name: getgenotypesgenabel > ### Title: process the genotype matrix for specified markers and return the > ### corresponding GenABEL genotype matrix > ### Aliases: getgenotypesgenabel > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > aa = getgenotypesgenabel(ENV$markers[ENV$markers$chromosome == 1,]) > > aa [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13] [1,] 59 95 a6 a6 af 95 55 66 a5 a5 66 65 a6 [2,] a9 aa 55 56 ed 66 55 6a a5 55 6a e5 6a [3,] 6a 5a 95 b6 99 5a 55 56 6a 55 55 6e 55 [4,] 69 aa 96 aa e9 aa 55 56 9a 9b 56 65 9b [5,] 55 66 55 99 aa 66 55 a9 5a 69 a9 56 ad [6,] a5 aa 55 55 fb 59 55 55 99 55 55 99 65 [7,] 5a 56 65 b9 aa 56 55 69 55 55 69 56 7a [8,] aa 5a 55 a5 ab 59 55 65 56 55 65 9a a5 [9,] 66 aa 99 99 fa 5a 55 59 ae 55 55 ae 55 [10,] 5a aa a5 a5 ef 65 55 65 b5 55 55 ba 55 [11,] aa a9 55 65 ea 5a 55 59 5a 55 55 9b 55 [12,] aa 66 55 9d 66 a6 55 95 95 55 55 aa 55 [13,] aa 96 55 ad 66 96 55 59 aa 55 55 fb 55 [14,] aa 55 55 ae a6 55 55 56 66 55 55 ba 55 [15,] ff 55 55 ff 55 aa 55 55 55 55 55 55 55 [16,] aa 5a 55 a9 a6 5a 55 56 55 55 56 a9 56 [17,] aa aa 55 96 69 aa 55 55 59 59 55 aa 59 [18,] 80 80 40 40 80 80 40 40 80 80 40 80 80 [,14] [,15] [,16] [1,] 76 65 95 [2,] ba e5 55 [3,] 69 6e 55 [4,] 56 65 9a [5,] aa 56 59 [6,] 99 99 65 [7,] 69 56 6b [8,] 66 9a ea [9,] aa ae 66 [10,] a5 ba 65 [11,] 56 9b 55 [12,] 55 aa 55 [13,] a6 fb 55 [14,] 65 ba 55 [15,] 55 55 55 [16,] 56 a9 55 [17,] 55 aa 59 [18,] 40 80 80 > > > > > cleanEx() > nameEx("getgenotypesraw") > ### * getgenotypesraw > > flush(stderr()); flush(stdout()) > > ### Name: getgenotypesraw > ### Title: fetch genotype integer matrix for specified markers > ### Aliases: getgenotypesraw > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > # two ints in upper/lower half integer representing allele # for all persons in chromosome 1 > getgenotypesraw(ENV$markers[ENV$markers$chromosome == 1,]) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [1,] 65537 65538 65538 65538 65538 65538 65537 65537 65538 65538 65537 [2,] 65537 65537 65538 65538 65538 65537 65537 65538 65538 65538 65538 [3,] 65538 65537 65537 65537 65537 65537 65537 65537 65537 65537 65537 [4,] 65537 65537 65538 65538 65537 65537 65537 65538 65537 65537 65538 [5,] 65538 65538 65537 65537 65537 65537 65537 65537 65538 65537 65537 [6,] 65538 65538 65537 65537 65538 65538 65537 65538 65538 65537 65538 [7,] 65538 65538 65537 65537 65537 65537 65537 65538 65537 65537 65538 [8,] 65537 65538 65537 65538 131074 65538 65537 65538 65537 65537 65538 [9,] 65537 65537 65538 65538 65538 65537 65537 65537 65537 65537 65537 [10,] 65538 65537 65537 131074 131074 65537 65537 65537 65538 65537 65537 [11,] 65538 65538 65537 65537 65538 65538 65537 65537 65538 65537 65537 [12,] 65538 65538 65537 65538 131074 65538 65537 65538 65538 65537 65537 [13,] 65537 65538 65538 65538 65537 65538 65537 65537 65538 65538 65537 [14,] 65538 65538 65537 65538 65538 65538 65537 65537 65537 65537 65537 [15,] 65538 65538 65537 65538 65538 65538 65537 65537 65538 65538 65537 [16,] 65537 65538 65538 65538 131074 65538 65537 65538 65538 131074 65538 [17,] 65537 65537 65537 65538 65538 65537 65537 65538 65537 65537 65538 [18,] 65537 65538 65537 65537 65538 65538 65537 65538 65537 65538 65538 [19,] 65537 65537 65537 65538 65538 65537 65537 65538 65538 65538 65538 [20,] 65537 65538 65537 65537 65538 65538 65537 65537 65538 65537 65537 [21,] 65538 65538 65537 65537 65537 65537 65537 65537 65538 65537 65537 [22,] 65538 65538 65537 65537 65537 65537 65537 65537 65537 65537 65537 [23,] 65537 65538 65537 65537 65538 65538 65537 65537 65538 65537 65537 [24,] 65537 65538 65537 65537 65537 65537 65537 65537 65537 65537 65537 [25,] 65537 65537 65537 65538 65538 65537 65537 65537 65537 65537 65537 [26,] 65537 65537 65538 131074 65538 65537 65537 65538 65537 65537 65538 [27,] 65538 65537 65537 65538 65538 65537 65537 65538 65537 65537 65538 [28,] 65538 65538 65537 65537 65538 65538 65537 65537 65537 65537 65537 [29,] 65538 65537 65537 65538 65538 65537 65537 65537 65537 65537 65537 [30,] 65538 65537 65537 65538 65538 65537 65537 65538 65537 65537 65538 [31,] 65538 65538 65537 65537 65538 65538 65537 65537 65537 65537 65537 [32,] 65538 65538 65537 65537 65537 65537 65537 65537 65538 65537 65537 [33,] 65537 65538 65538 65538 65537 65537 65537 65537 65538 65537 65537 [34,] 65538 65538 65537 65537 65537 65537 65537 65537 65538 65537 65537 [35,] 65537 65538 65538 65538 65538 65538 65537 65538 131074 65537 65537 [36,] 65538 65538 65537 65537 65538 65538 65537 65537 65538 65537 65537 [37,] 65537 65538 65538 65538 65537 65537 65537 65537 65538 65537 65537 [38,] 65537 65538 65538 65538 65538 65538 65537 65538 131074 65537 65537 [39,] 65538 65538 65537 65537 65537 65537 65537 65537 65537 65537 65537 [40,] 65538 65538 65537 65537 65537 65537 65537 65537 65537 65537 65537 [41,] 65538 65538 65537 65537 65537 65537 65537 65537 65537 65537 65537 [42,] 65538 65538 65537 65538 65538 65537 65537 65537 65537 65537 65537 [43,] 65538 65538 65537 65537 65538 65538 65537 65538 65538 65537 65537 [44,] 65538 65537 65537 65537 65538 65538 65537 65537 65538 65537 65537 [45,] 65538 65537 65537 65538 131074 65538 65537 65538 65538 65537 65537 [46,] 65538 65538 65537 65537 65538 65538 65537 65537 65537 65537 65537 [47,] 65538 65537 65537 131074 131074 65537 65537 65537 65537 65537 65537 [48,] 65538 65538 65537 65537 65538 65538 65537 65537 65537 65537 65537 [49,] 65538 65538 65537 65538 131074 65538 65537 65537 65538 65537 65537 [50,] 65538 65537 65537 65538 65538 65537 65537 65537 65538 65537 65537 [51,] 65538 65537 65537 131074 131074 65537 65537 65538 65538 65537 65537 [52,] 65538 65538 65537 65537 65538 65538 65537 65537 65538 65537 65537 [53,] 65538 65537 65537 65538 65538 65537 65537 65537 65537 65537 65537 [54,] 65538 65537 65537 65538 65538 65537 65537 65537 65538 65537 65537 [55,] 65538 65537 65537 131074 131074 65537 65537 65537 65537 65537 65537 [56,] 65538 65537 65537 65538 65538 65537 65537 65538 65538 65537 65537 [57,] 131074 65537 65537 131074 131074 65538 65537 65537 65537 65537 65537 [58,] 131074 65537 65537 131074 131074 65538 65537 65537 65537 65537 65537 [59,] 131074 65537 65537 131074 131074 65538 65537 65537 65537 65537 65537 [60,] 131074 65537 65537 131074 131074 65538 65537 65537 65537 65537 65537 [61,] 65538 65537 65537 65538 65538 65537 65537 65537 65537 65537 65537 [62,] 65538 65537 65537 65538 65538 65537 65537 65537 65537 65537 65537 [63,] 65538 65538 65537 65538 131074 65538 65537 65537 65537 65537 65537 [64,] 65538 65538 65537 65537 65538 65538 65537 65538 65537 65537 65538 [65,] 65538 65538 65537 65538 131074 65538 65537 65537 65537 65537 65537 [66,] 65538 65538 65537 65537 65538 65538 65537 65537 65537 65537 65537 [67,] 65538 65538 65537 65537 65538 65538 65537 65537 65538 65538 65537 [68,] 65538 65538 65537 65538 131074 65538 65537 65537 65537 65537 65537 [69,] 65538 65538 65537 65537 65538 65538 65537 65537 65538 65538 65537 [,12] [,13] [,14] [,15] [,16] [1,] 65537 65538 65537 65537 65538 [2,] 65538 65538 131074 65538 65537 [3,] 65537 65537 65537 65537 65537 [4,] 65537 65538 65538 65537 65537 [5,] 131074 65537 65538 131074 65537 [6,] 65538 65538 131074 65538 65537 [7,] 65537 65538 65538 65537 65537 [8,] 65537 65538 65538 65537 65537 [9,] 65537 65537 65537 65537 65537 [10,] 65538 65537 65538 65538 65537 [11,] 131074 65537 65538 131074 65537 [12,] 65538 65537 65537 65538 65537 [13,] 65537 65538 65537 65537 65538 [14,] 65538 65537 65537 65538 65537 [15,] 65537 65538 65537 65537 65538 [16,] 65537 131074 65538 65537 65538 [17,] 65537 65538 65538 65537 65537 [18,] 65537 65538 65538 65537 65537 [19,] 65537 131074 65538 65537 65538 [20,] 65538 65537 65538 65538 65537 [21,] 65538 65537 65538 65538 65537 [22,] 65537 65538 65537 65537 65538 [23,] 65538 65537 65538 65538 65537 [24,] 65537 65537 65537 65537 65537 [25,] 65537 65537 65537 65537 65537 [26,] 65537 131074 65538 65537 65538 [27,] 65537 65538 65538 65537 65538 [28,] 65538 65538 65537 65538 131074 [29,] 65538 65538 65537 65538 131074 [30,] 65537 65538 65538 65537 65538 [31,] 65538 65537 65537 65538 65538 [32,] 65538 65537 65538 65538 65538 [33,] 65538 65537 65538 65538 65537 [34,] 65538 65537 65538 65538 65538 [35,] 131074 65537 65538 131074 65537 [36,] 65538 65537 65538 65538 65538 [37,] 65538 65537 65538 65538 65537 [38,] 131074 65537 65538 131074 65538 [39,] 65538 65537 65537 65538 65537 [40,] 65538 65537 65537 65538 65537 [41,] 65538 65537 65537 65538 65537 [42,] 65537 65537 65537 65537 65537 [43,] 65538 65537 65537 65538 65537 [44,] 131074 65537 65538 131074 65537 [45,] 65538 65537 65537 65538 65537 [46,] 65538 65537 65537 65538 65537 [47,] 65538 65537 65537 65538 65537 [48,] 65538 65537 65537 65538 65537 [49,] 131074 65537 65538 131074 65537 [50,] 131074 65537 65538 131074 65537 [51,] 65538 65537 65537 65538 65537 [52,] 131074 65537 65538 131074 65537 [53,] 65538 65537 65537 65538 65537 [54,] 131074 65537 65538 131074 65537 [55,] 65538 65537 65537 65538 65537 [56,] 65538 65537 65537 65538 65537 [57,] 65537 65537 65537 65537 65537 [58,] 65537 65537 65537 65537 65537 [59,] 65537 65537 65537 65537 65537 [60,] 65537 65537 65537 65537 65537 [61,] 65538 65537 65537 65538 65537 [62,] 65538 65537 65537 65538 65537 [63,] 65538 65537 65537 65538 65537 [64,] 65537 65538 65538 65537 65537 [65,] 65538 65537 65537 65538 65537 [66,] 65538 65537 65537 65538 65537 [67,] 65538 65538 65537 65538 65538 [68,] 65538 65537 65537 65538 65537 [69,] 65538 65538 65537 65538 65538 > > > > > cleanEx() > nameEx("init_SKAT") > ### * init_SKAT > > flush(stderr()); flush(stdout()) > > ### Name: init_SKAT > ### Title: load Mega2 SQLite database and perform initialization for SKAT > ### usage > ### Aliases: init_SKAT > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = init_SKAT(db, verbose = FALSE, allMarkers = FALSE) > ls(ENV) [1] "DBMega2Version" "DBcompress" "LocusCnt" [4] "MARKER_SCHEME" "Mega2R" "PhenoCnt" [7] "SKAT_results" "affectclass_table" "allMarkers" [10] "allele_table" "charstar_table" "chr2int" [13] "dosage" "dosageRaw" "entrezGene" [16] "fam" "int_table" "locus_allele_table" [19] "locus_table" "map_table" "mapnames_table" [22] "marker_table" "markers" "mt1" [25] "mt2" "pedigree_brkloop_table" "pedigree_table" [28] "person_brkloop_table" "person_table" "phe" [31] "phenotype_table" "positionVsName" "refIndices" [34] "refRanges" "traitaff_table" "txdb" [37] "unified_genotype_table" "verbose" > > > > > cleanEx() > nameEx("init_famSKATRC") > ### * init_famSKATRC > > flush(stderr()); flush(stdout()) > > ### Name: init_famSKATRC > ### Title: load Mega2 SQLite database and perform initialization for > ### famSKATRC usage > ### Aliases: init_famSKATRC > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = init_famSKATRC(db, verbose = FALSE) > ls(ENV) [1] "ALPHA" "DBMega2Version" "DBcompress" [4] "KIN" "LocusCnt" "MARKER_SCHEME" [7] "Mega2R" "PhenoCnt" "affectclass_table" [10] "allele_table" "charstar_table" "chr2int" [13] "dosage" "dosageRaw" "entrezGene" [16] "fam" "famSKATRC_results" "int_table" [19] "locus_allele_table" "locus_table" "map_table" [22] "mapnames_table" "marker_table" "markers" [25] "pedigree_brkloop_table" "pedigree_table" "person_brkloop_table" [28] "person_table" "phe" "phenotype_table" [31] "positionVsName" "refIndices" "refRanges" [34] "traitaff_table" "txdb" "unified_genotype_table" [37] "verbose" "wuweights_c" "wuweights_r" > > > > > cleanEx() > nameEx("init_pedgene") > ### * init_pedgene > > flush(stderr()); flush(stdout()) > > ### Name: init_pedgene > ### Title: load Mega2 SQLite database and perform initialization for > ### pedgene usage > ### Aliases: init_pedgene > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = init_pedgene(db, traitname = "default") > ls(ENV) [1] "DBMega2Version" "DBcompress" "LocusCnt" [4] "MARKER_SCHEME" "Mega2R" "PhenoCnt" [7] "affectclass_table" "allele_table" "charstar_table" [10] "chr2int" "dosage" "dosageRaw" [13] "entrezGene" "fam" "int_table" [16] "locus_allele_table" "locus_table" "map_table" [19] "mapnames_table" "marker_table" "markers" [22] "mt1" "mt2" "pedPer" [25] "pedgene_results" "pedigree_brkloop_table" "pedigree_table" [28] "person_brkloop_table" "person_table" "phenotype_table" [31] "positionVsName" "refIndices" "refRanges" [34] "schaidPed" "traitaff_table" "txdb" [37] "unified_genotype_table" "verbose" > > > > > cleanEx() > nameEx("mkAlleles") > ### * mkAlleles > > flush(stderr()); flush(stdout()) > > ### Name: mkAlleles > ### Title: generate allele pairs in with MAJ(or) allele first > ### Aliases: mkAlleles > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D mkAlleles(envir) > ## End(Not run) > > > > cleanEx() > nameEx("mkGenABELcoding") > ### * mkGenABELcoding > > flush(stderr()); flush(stdout()) > > ### Name: mkGenABELcoding > ### Title: generate GenABEL coding vector > ### Aliases: mkGenABELcoding > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D mkGenABELcoding(envir) > ## End(Not run) > > > > cleanEx() > nameEx("mkGenABELgenotype") > ### * mkGenABELgenotype > > flush(stderr()); flush(stdout()) > > ### Name: mkGenABELgenotype > ### Title: generate GenABEL compressed genotype matrix > ### Aliases: mkGenABELgenotype > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D mkGenABELgenotype(envir) > ## End(Not run) > > > > cleanEx() > nameEx("mkGenABELphenotype") > ### * mkGenABELphenotype > > flush(stderr()); flush(stdout()) > > ### Name: mkGenABELphenotype > ### Title: generate required PLINK (.phe) file > ### Aliases: mkGenABELphenotype > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D db = system.file("exdata", "seqsimm.db", package="Mega2R") > ##D ENV = read.Mega2DB(db) > ##D mkGenABELphenotype(ENV) > ## End(Not run) > > > > cleanEx() > nameEx("mkGenABELtfam") > ### * mkGenABELtfam > > flush(stderr()); flush(stdout()) > > ### Name: mkGenABELtfam > ### Title: generate required fam family for PLINK TPED (.tfam) file > ### Aliases: mkGenABELtfam > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D db = system.file("exdata", "seqsimm.db", package="Mega2R") > ##D ENV = read.Mega2DB(db) > ##D mkGenABELtfam("foo", ENV) > ## End(Not run) > > > > cleanEx() > nameEx("mkGenABELtped") > ### * mkGenABELtped > > flush(stderr()); flush(stdout()) > > ### Name: mkGenABELtped > ### Title: generate a PLINK TPED file for GenABEL > ### Aliases: mkGenABELtped > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D db = system.file("exdata", "seqsimm.db", package="Mega2R") > ##D ENV = read.Mega2DB(db) > ##D mkGenABELtped("foo", NULL, 0, ENV) > ## End(Not run) > > > > cleanEx() > nameEx("mkMarkers") > ### * mkMarkers > > flush(stderr()); flush(stdout()) > > ### Name: mkMarkers > ### Title: create "markers" data frame > ### Aliases: mkMarkers > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db, verbose = FALSE) > > mkMarkers(1) > > ENV$markers locus_link locus_link_fill MarkerName chromosome position 1 1 1 snp22735 1 2243901 2 2 2 snp23360 1 2244526 3 3 3 snp23361 1 2244527 4 4 4 snp23362 1 2244528 5 5 5 snp23364 1 2244530 6 6 6 snp24037 1 3762181 7 7 7 snp24039 1 3762183 8 8 8 snp24041 1 3762185 9 9 9 snp24048 1 3762192 10 10 10 snp24494 1 3762638 11 11 11 snp24499 1 3762643 12 12 12 snp24506 1 3762650 13 13 13 snp24507 1 3762651 14 14 14 snp30480 1 8264348 15 15 15 snp30484 1 8264352 16 16 16 snp30487 1 8264355 > > > > > cleanEx() > nameEx("mkVCFfam") > ### * mkVCFfam > > flush(stderr()); flush(stdout()) > > ### Name: mkVCFfam > ### Title: generate required VCF family (.fam) file > ### Aliases: mkVCFfam > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D mkVCFfam(prefix, envir) > ## End(Not run) > > > > cleanEx() > nameEx("mkVCFfreq") > ### * mkVCFfreq > > flush(stderr()); flush(stdout()) > > ### Name: mkVCFfreq > ### Title: generate required VCF frequency (.freq) file > ### Aliases: mkVCFfreq > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D mkVCFfreq(prefix, NULL, FALSE, envir) > ## End(Not run) > > > > cleanEx() > nameEx("mkVCFhdr") > ### * mkVCFhdr > > flush(stderr()); flush(stdout()) > > ### Name: mkVCFhdr > ### Title: generate required VCF header > ### Aliases: mkVCFhdr > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D mkVCFhdr(prefix, NULL, envir) > ## End(Not run) > > > > cleanEx() > nameEx("mkVCFmap") > ### * mkVCFmap > > flush(stderr()); flush(stdout()) > > ### Name: mkVCFmap > ### Title: generate required Mega2 map (.map) file > ### Aliases: mkVCFmap > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D mkVCFmap(prefix, NULL, envir) > ## End(Not run) > > > > cleanEx() > nameEx("mkVCFpen") > ### * mkVCFpen > > flush(stderr()); flush(stdout()) > > ### Name: mkVCFpen > ### Title: generate required Mega2 penetrance (.pen) file > ### Aliases: mkVCFpen > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D mkVCFpen(prefix, envir) > ## End(Not run) > > > > cleanEx() > nameEx("mkVCFphe") > ### * mkVCFphe > > flush(stderr()); flush(stdout()) > > ### Name: mkVCFphe > ### Title: generate required PLINK (.phe) file > ### Aliases: mkVCFphe > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D mkVCFphe(prefix, envir) > ## End(Not run) > > > > cleanEx() > nameEx("mk_markers_with_skip") > ### * mk_markers_with_skip > > flush(stderr()); flush(stdout()) > > ### Name: mk_markers_with_skip > ### Title: make the derived "markers" data frame and store it in the > ### environment. > ### Aliases: mk_markers_with_skip > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D mk_markers_with_skip(1) > ## End(Not run) > > > > cleanEx() > nameEx("mkfam") > ### * mkfam > > flush(stderr()); flush(stdout()) > > ### Name: mkfam > ### Title: assemble pedigree information into a data frame > ### Aliases: mkfam > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > fam = mkfam() > > fam person_link pedigree_link PedPre PerPre Father Mother Sex trait 1 0 0 1SAP039 H05-0107 0 0 2 1 2 1 0 1SAP039 H05-0106 0 0 1 1 3 2 0 1SAP039 SAP039F14 0 0 1 1 4 3 0 1SAP039 SAP039F13 0 0 1 1 5 4 0 1SAP039 SAP039F12 0 0 1 1 6 5 0 1SAP039 SAP039M11 0 0 2 1 7 6 0 1SAP039 SAP039M4 0 0 2 1 8 7 0 1SAP039 SAP039M3 0 0 2 1 9 8 0 1SAP039 SAP039M2 0 0 2 1 10 9 0 1SAP039 SAP039M1 0 0 2 1 11 10 0 1SAP039 SAP039F0 0 0 1 1 12 11 0 1SAP039 SAP039M0 0 0 2 1 13 12 0 1SAP039 SAP039M39 H05-0105 H05-0107 2 1 14 13 0 1SAP039 H05-0120 H05-0105 H05-0107 2 1 15 14 0 1SAP039 SAP039M38 H05-0105 H05-0107 2 1 16 15 0 1SAP039 H05-0119 H05-0106 SAP039M15 1 1 17 16 0 1SAP039 SAP039M37 H05-0106 SAP039M15 2 1 18 17 0 1SAP039 SAP039F36 H05-0106 SAP039M15 1 1 19 18 0 1SAP039 SAP039M35 H05-0106 SAP039M15 2 1 20 19 0 1SAP039 SAP039F34 SAP039F14 H05-0103 1 1 21 20 0 1SAP039 SAP039M33 SAP039F14 H05-0103 2 1 22 21 0 1SAP039 SAP039M32 SAP039F14 H05-0103 2 1 23 22 0 1SAP039 H05-0118 SAP039F14 H05-0103 2 1 24 23 0 1SAP039 H05-0117 SAP039F13 SAP039M13 1 1 25 24 0 1SAP039 SAP039M31 SAP039F13 SAP039M13 2 1 26 25 0 1SAP039 H05-0116 SAP039F13 SAP039M13 1 1 27 26 0 1SAP039 SAP039M30 SAP039F12 SAP039M12 2 1 28 27 0 1SAP039 H06-0007 SAP039F12 SAP039M12 1 1 29 28 0 1SAP039 H06-0006 SAP039F12 SAP039M12 2 1 30 29 0 1SAP039 H06-0005 SAP039F12 SAP039M12 2 1 31 30 0 1SAP039 H06-0004 SAP039F12 SAP039M12 1 2 32 31 0 1SAP039 SAP039F29 SAP039F11 SAP039M11 1 1 33 32 0 1SAP039 SAP039M28 SAP039F11 SAP039M11 2 1 34 33 0 1SAP039 SAP039M27 SAP039F11 SAP039M11 2 1 35 34 0 1SAP039 SAP039M26 SAP039F11 SAP039M11 2 1 36 35 0 1SAP039 SAP039F25 SAP039F11 SAP039M11 1 1 37 36 0 1SAP039 H05-0115 SAP039F11 SAP039M11 1 1 38 37 0 1SAP039 SAP039M24 SAP039F11 SAP039M11 2 1 39 38 0 1SAP039 SAP039M23 SAP039F4 SAP039M4 2 1 40 39 0 1SAP039 H05-0114 SAP039F4 SAP039M4 1 1 41 40 0 1SAP039 H05-0113 SAP039F4 SAP039M4 1 1 42 41 0 1SAP039 SAP039F22 SAP039F4 SAP039M4 1 1 43 42 0 1SAP039 H05-0111 SAP039F3 SAP039M3 1 1 44 43 0 1SAP039 SAP039M21 SAP039F3 SAP039M3 2 1 45 44 0 1SAP039 SAP039M20 SAP039F3 SAP039M3 2 1 46 45 0 1SAP039 SAP039F19 SAP039F3 SAP039M3 1 1 47 46 0 1SAP039 H05-0105 SAP039F1 SAP039M1 1 1 48 47 0 1SAP039 SAP039M18 SAP039F1 SAP039M1 2 1 49 48 0 1SAP039 H05-0104 SAP039F1 SAP039M1 2 1 50 49 0 1SAP039 SAP039M17 SAP039F1 SAP039M1 2 1 51 50 0 1SAP039 SAP039M15 SAP039F1 SAP039M1 2 1 52 51 0 1SAP039 H05-0103 SAP039F1 SAP039M1 2 1 53 52 0 1SAP039 SAP039M13 SAP039F1 SAP039M1 2 1 54 53 0 1SAP039 SAP039M16 SAP039F1 SAP039M1 2 1 55 54 0 1SAP039 SAP039M12 SAP039F1 SAP039M1 2 1 56 55 0 1SAP039 SAP039F11 SAP039F1 SAP039M1 1 1 57 56 0 1SAP039 H05-0110 SAP039F2 SAP039M2 2 1 58 57 0 1SAP039 H05-0109 SAP039F2 SAP039M2 1 2 59 58 0 1SAP039 H05-0108 SAP039F2 SAP039M2 1 2 60 59 0 1SAP039 SAP039M10 SAP039F2 SAP039M2 2 1 61 60 0 1SAP039 SAP039M9 SAP039F2 SAP039M2 2 1 62 61 0 1SAP039 SAP039F8 SAP039F2 SAP039M2 1 1 63 62 0 1SAP039 SAP039F7 SAP039F0 SAP039M0 1 1 64 63 0 1SAP039 SAP039F6 SAP039F0 SAP039M0 1 1 65 64 0 1SAP039 SAP039M5 SAP039F0 SAP039M0 2 1 66 65 0 1SAP039 SAP039F4 SAP039F0 SAP039M0 1 1 67 66 0 1SAP039 SAP039F3 SAP039F0 SAP039M0 1 1 68 67 0 1SAP039 SAP039F2 SAP039F0 SAP039M0 1 1 69 68 0 1SAP039 SAP039F1 SAP039F0 SAP039M0 1 2 > > > > > cleanEx() > nameEx("mkphenotype") > ### * mkphenotype > > flush(stderr()); flush(stdout()) > > ### Name: mkphenotype > ### Title: generate a phenotype data frame > ### Aliases: mkphenotype > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > out = mkphenotype() > > out FID IID default 1 1SAP039 H05-0107 1 2 1SAP039 H05-0106 1 3 1SAP039 SAP039F14 1 4 1SAP039 SAP039F13 1 5 1SAP039 SAP039F12 1 6 1SAP039 SAP039M11 1 7 1SAP039 SAP039M4 1 8 1SAP039 SAP039M3 1 9 1SAP039 SAP039M2 1 10 1SAP039 SAP039M1 1 11 1SAP039 SAP039F0 1 12 1SAP039 SAP039M0 1 13 1SAP039 SAP039M39 1 14 1SAP039 H05-0120 1 15 1SAP039 SAP039M38 1 16 1SAP039 H05-0119 1 17 1SAP039 SAP039M37 1 18 1SAP039 SAP039F36 1 19 1SAP039 SAP039M35 1 20 1SAP039 SAP039F34 1 21 1SAP039 SAP039M33 1 22 1SAP039 SAP039M32 1 23 1SAP039 H05-0118 1 24 1SAP039 H05-0117 1 25 1SAP039 SAP039M31 1 26 1SAP039 H05-0116 1 27 1SAP039 SAP039M30 1 28 1SAP039 H06-0007 1 29 1SAP039 H06-0006 1 30 1SAP039 H06-0005 1 31 1SAP039 H06-0004 2 32 1SAP039 SAP039F29 1 33 1SAP039 SAP039M28 1 34 1SAP039 SAP039M27 1 35 1SAP039 SAP039M26 1 36 1SAP039 SAP039F25 1 37 1SAP039 H05-0115 1 38 1SAP039 SAP039M24 1 39 1SAP039 SAP039M23 1 40 1SAP039 H05-0114 1 41 1SAP039 H05-0113 1 42 1SAP039 SAP039F22 1 43 1SAP039 H05-0111 1 44 1SAP039 SAP039M21 1 45 1SAP039 SAP039M20 1 46 1SAP039 SAP039F19 1 47 1SAP039 H05-0105 1 48 1SAP039 SAP039M18 1 49 1SAP039 H05-0104 1 50 1SAP039 SAP039M17 1 51 1SAP039 SAP039M15 1 52 1SAP039 H05-0103 1 53 1SAP039 SAP039M13 1 54 1SAP039 SAP039M16 1 55 1SAP039 SAP039M12 1 56 1SAP039 SAP039F11 1 57 1SAP039 H05-0110 1 58 1SAP039 H05-0109 2 59 1SAP039 H05-0108 2 60 1SAP039 SAP039M10 1 61 1SAP039 SAP039M9 1 62 1SAP039 SAP039F8 1 63 1SAP039 SAP039F7 1 64 1SAP039 SAP039F6 1 65 1SAP039 SAP039M5 1 66 1SAP039 SAP039F4 1 67 1SAP039 SAP039F3 1 68 1SAP039 SAP039F2 1 69 1SAP039 SAP039F1 2 > > > > cleanEx() > nameEx("read.Mega2DB") > ### * read.Mega2DB > > flush(stderr()); flush(stdout()) > > ### Name: read.Mega2DB > ### Title: load Mega2 database and initialize family data frame and markers > ### data frame > ### Aliases: read.Mega2DB > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db, verbose = TRUE) int_table 35 3 int_table pId key value charstar_table 9 3 charstar_table pId key value pedigree_table 1 8 pedigree_table pId Num EntryCnt Name PedPre OriginalID origped pedigree_link person_table 69 11 person_table pId UniqueID OrigID FamName PerPre ID Father Mother Sex pedigree_link person_link pedigree_brkloop_table 1 8 pedigree_brkloop_table pId Num EntryCnt Name PedPre OriginalID origped pedigree_link person_brkloop_table 69 11 person_brkloop_table pId UniqueID OrigID FamName PerPre ID Father Mother Sex pedigree_link person_link locus_table 17 5 locus_table pId LocusName Type AlleleCnt locus_link allele_table 34 5 allele_table pId AlleleName Frequency indexX locus_link marker_table 16 7 marker_table pId MarkerName pos_avg pos_female pos_male chromosome locus_link map_table 32 6 map_table pId marker map position pos_female pos_male mapnames_table 2 6 mapnames_table pId map sex_averaged_map male_sex_map female_sex_map name traitaff_table 1 4 traitaff_table pId ClassCnt PenCnt locus_link affectclass_table 1 9 affectclass_table pId MaleDef FemaleDef AutoDef MalePen FemalePen AutoPen locus_link class_link phenotype_table 69 4 phenotype_table pId person_link bytes data genotype_table 69 5 genotype_table pId person_link chr bytes data > > > > > cleanEx() > nameEx("resetMega2ENV") > ### * resetMega2ENV > > flush(stderr()); flush(stdout()) > > ### Name: resetMega2ENV > ### Title: return an initialized environment > ### Aliases: resetMega2ENV > ### Keywords: internal > > ### ** Examples > > ## Not run: > ##D resetMega2ENV() > ## End(Not run) > > > > cleanEx() > nameEx("setAnnotations") > ### * setAnnotations > > flush(stderr()); flush(stdout()) > > ### Name: setAnnotations > ### Title: set default name of transcription database and name of database > ### mapping gene name to entrez gene id > ### Aliases: setAnnotations > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > setAnnotations("TxDb.Hsapiens.UCSC.hg19.knownGene", "org.Hs.eg.db") > > ENV$txdb [1] "TxDb.Hsapiens.UCSC.hg19.knownGene" > ENV$entrezGene [1] "org.Hs.eg.db" > > > > > cleanEx() > nameEx("setRanges") > ### * setRanges > > flush(stderr()); flush(stdout()) > > ### Name: setRanges > ### Title: set default range data: chromosome and start/end base pair > ### Aliases: setRanges > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > ranges = matrix(c(1, 2240000, 2245000, + 1, 2245000, 2250000, + 1, 3760000, 3761000, + 1, 3761000, 3762000, + 1, 3762000, 3763000, + 1, 3763000, 3764000, + 1, 3764000, 3765000, + 1, 3765000, 3763760, + 1, 3763760, 3767000, + 1, 3767000, 3768000, + 1, 3768000, 3769000, + 1, 3769000, 3770000), + ncol = 3, nrow = 12, byrow = TRUE) > > setRanges(ranges, 1:3) > > ENV$refRanges X1 X2 X3 ChrStartEnd 1 1 2240000 2245000 chr1:2240000-2245000 2 1 2245000 2250000 chr1:2245000-2250000 3 1 3760000 3761000 chr1:3760000-3761000 4 1 3761000 3762000 chr1:3761000-3762000 5 1 3762000 3763000 chr1:3762000-3763000 6 1 3763000 3764000 chr1:3763000-3764000 7 1 3764000 3765000 chr1:3764000-3765000 8 1 3765000 3763760 chr1:3765000-3763760 9 1 3763760 3767000 chr1:3763760-3767000 10 1 3767000 3768000 chr1:3767000-3768000 11 1 3768000 3769000 chr1:3768000-3769000 12 1 3769000 3770000 chr1:3769000-3770000 > > ranges = matrix(c(1, 2240000, 2245000, + 1, 2245000, 2250000, + 1, 3760000, 3761000, + 1, 3761000, 3762000, + 1, 3762000, 3763000, + 1, 3763000, 3764000, + 1, 3764000, 3765000, + 1, 3765000, 3763760, + 1, 3763760, 3767000, + 1, 3767000, 3768000, + 1, 3768000, 3769000, + 1, 3769000, 3770000), + ncol = 3, nrow = 12, byrow = TRUE) > ranges = data.frame(ranges) > ranges$name = LETTERS[1:12] > names(ranges) = c("chr", "start", "end", "name") > > setRanges(ranges, 1:4) > > ENV$refRanges chr start end name 1 1 2240000 2245000 A 2 1 2245000 2250000 B 3 1 3760000 3761000 C 4 1 3761000 3762000 D 5 1 3762000 3763000 E 6 1 3763000 3764000 F 7 1 3764000 3765000 G 8 1 3765000 3763760 H 9 1 3763760 3767000 I 10 1 3767000 3768000 J 11 1 3768000 3769000 K 12 1 3769000 3770000 L > > > > cleanEx() > nameEx("setfam") > ### * setfam > > flush(stderr()); flush(stdout()) > > ### Name: setfam > ### Title: replace the pedigree data frame > ### Aliases: setfam > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > fam = mkfam() > # remove founders > fam = fam[ !( (fam[ , 5] == fam[ , 6]) & (fam[ , 5] == 0)), ] > setfam(fam) > > ENV$fam person_link pedigree_link PedPre PerPre Father Mother Sex trait 13 12 0 1SAP039 SAP039M39 H05-0105 H05-0107 2 1 14 13 0 1SAP039 H05-0120 H05-0105 H05-0107 2 1 15 14 0 1SAP039 SAP039M38 H05-0105 H05-0107 2 1 16 15 0 1SAP039 H05-0119 H05-0106 SAP039M15 1 1 17 16 0 1SAP039 SAP039M37 H05-0106 SAP039M15 2 1 18 17 0 1SAP039 SAP039F36 H05-0106 SAP039M15 1 1 19 18 0 1SAP039 SAP039M35 H05-0106 SAP039M15 2 1 20 19 0 1SAP039 SAP039F34 SAP039F14 H05-0103 1 1 21 20 0 1SAP039 SAP039M33 SAP039F14 H05-0103 2 1 22 21 0 1SAP039 SAP039M32 SAP039F14 H05-0103 2 1 23 22 0 1SAP039 H05-0118 SAP039F14 H05-0103 2 1 24 23 0 1SAP039 H05-0117 SAP039F13 SAP039M13 1 1 25 24 0 1SAP039 SAP039M31 SAP039F13 SAP039M13 2 1 26 25 0 1SAP039 H05-0116 SAP039F13 SAP039M13 1 1 27 26 0 1SAP039 SAP039M30 SAP039F12 SAP039M12 2 1 28 27 0 1SAP039 H06-0007 SAP039F12 SAP039M12 1 1 29 28 0 1SAP039 H06-0006 SAP039F12 SAP039M12 2 1 30 29 0 1SAP039 H06-0005 SAP039F12 SAP039M12 2 1 31 30 0 1SAP039 H06-0004 SAP039F12 SAP039M12 1 2 32 31 0 1SAP039 SAP039F29 SAP039F11 SAP039M11 1 1 33 32 0 1SAP039 SAP039M28 SAP039F11 SAP039M11 2 1 34 33 0 1SAP039 SAP039M27 SAP039F11 SAP039M11 2 1 35 34 0 1SAP039 SAP039M26 SAP039F11 SAP039M11 2 1 36 35 0 1SAP039 SAP039F25 SAP039F11 SAP039M11 1 1 37 36 0 1SAP039 H05-0115 SAP039F11 SAP039M11 1 1 38 37 0 1SAP039 SAP039M24 SAP039F11 SAP039M11 2 1 39 38 0 1SAP039 SAP039M23 SAP039F4 SAP039M4 2 1 40 39 0 1SAP039 H05-0114 SAP039F4 SAP039M4 1 1 41 40 0 1SAP039 H05-0113 SAP039F4 SAP039M4 1 1 42 41 0 1SAP039 SAP039F22 SAP039F4 SAP039M4 1 1 43 42 0 1SAP039 H05-0111 SAP039F3 SAP039M3 1 1 44 43 0 1SAP039 SAP039M21 SAP039F3 SAP039M3 2 1 45 44 0 1SAP039 SAP039M20 SAP039F3 SAP039M3 2 1 46 45 0 1SAP039 SAP039F19 SAP039F3 SAP039M3 1 1 47 46 0 1SAP039 H05-0105 SAP039F1 SAP039M1 1 1 48 47 0 1SAP039 SAP039M18 SAP039F1 SAP039M1 2 1 49 48 0 1SAP039 H05-0104 SAP039F1 SAP039M1 2 1 50 49 0 1SAP039 SAP039M17 SAP039F1 SAP039M1 2 1 51 50 0 1SAP039 SAP039M15 SAP039F1 SAP039M1 2 1 52 51 0 1SAP039 H05-0103 SAP039F1 SAP039M1 2 1 53 52 0 1SAP039 SAP039M13 SAP039F1 SAP039M1 2 1 54 53 0 1SAP039 SAP039M16 SAP039F1 SAP039M1 2 1 55 54 0 1SAP039 SAP039M12 SAP039F1 SAP039M1 2 1 56 55 0 1SAP039 SAP039F11 SAP039F1 SAP039M1 1 1 57 56 0 1SAP039 H05-0110 SAP039F2 SAP039M2 2 1 58 57 0 1SAP039 H05-0109 SAP039F2 SAP039M2 1 2 59 58 0 1SAP039 H05-0108 SAP039F2 SAP039M2 1 2 60 59 0 1SAP039 SAP039M10 SAP039F2 SAP039M2 2 1 61 60 0 1SAP039 SAP039M9 SAP039F2 SAP039M2 2 1 62 61 0 1SAP039 SAP039F8 SAP039F2 SAP039M2 1 1 63 62 0 1SAP039 SAP039F7 SAP039F0 SAP039M0 1 1 64 63 0 1SAP039 SAP039F6 SAP039F0 SAP039M0 1 1 65 64 0 1SAP039 SAP039M5 SAP039F0 SAP039M0 2 1 66 65 0 1SAP039 SAP039F4 SAP039F0 SAP039M0 1 1 67 66 0 1SAP039 SAP039F3 SAP039F0 SAP039M0 1 1 68 67 0 1SAP039 SAP039F2 SAP039F0 SAP039M0 1 1 69 68 0 1SAP039 SAP039F1 SAP039F0 SAP039M0 1 2 > > > > cleanEx() > nameEx("showMapNames") > ### * showMapNames > > flush(stderr()); flush(stdout()) > > ### Name: showMapNames > ### Title: show the association between mapno and mapname > ### Aliases: showMapNames > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > showMapNames() name map 1 Map 0 2 BP 1 > > > > > cleanEx() > nameEx("showMega2ENV") > ### * showMega2ENV > > flush(stderr()); flush(stdout()) > > ### Name: showMega2ENV > ### Title: show Mega2R environment, viz. data frames and related info. > ### Aliases: showMega2ENV > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > showMega2ENV() locus count: 17; phenotype count: 1; compression: 2 bits marker count: 16; sample count: 69 genetic and physical maps: map name map number 1 Map 0 2 BP 1 Phenotypes: Index Name Type 1 1 default affection basic tables: rows cols affectclass_table 1 9 allele_table 34 5 charstar_table 9 3 int_table 35 3 locus_table 17 5 map_table 32 6 mapnames_table 2 6 marker_table 16 8 pedigree_brkloop_table 1 8 pedigree_table 1 8 person_brkloop_table 69 11 person_table 69 11 phenotype_table 69 4 traitaff_table 1 4 derived tables: rows cols fam 69 8 markers 16 5 unified_genotype_table 69 2 > > > > > cleanEx() > nameEx("showPhenoNames") > ### * showPhenoNames > > flush(stderr()); flush(stdout()) > > ### Name: showPhenoNames > ### Title: show the association between index no and phenotype > ### Aliases: showPhenoNames > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > > showPhenoNames() Index Name Type 1 1 default affection > > > > > cleanEx() > nameEx("uniqueFamMember") > ### * uniqueFamMember > > flush(stderr()); flush(stdout()) > > ### Name: uniqueFamMember > ### Title: regenerate fam data frame with unique values in member column > ### Aliases: uniqueFamMember > > ### ** Examples > > db = system.file("exdata", "seqsimm.db", package="Mega2R") > ENV = read.Mega2DB(db) > setfam(uniqueFamMember(envir = ENV)) > > > > > cleanEx() > nameEx("where_mega2rtutorial_data") > ### * where_mega2rtutorial_data > > flush(stderr()); flush(stdout()) > > ### Name: where_mega2rtutorial_data > ### Title: show directory of tutorial data > ### Aliases: where_mega2rtutorial_data > > ### ** Examples > > directory = where_mega2rtutorial_data() > > > > > ### *