• using R Under development (unstable) (2026-04-23 r89960)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     clang version 22.1.4 (https://github.com/llvm/llvm-project 35990504507d79e0b9deb809c8ee5e1b34ceef20)     flang version 22.1.4 (https://github.com/llvm/llvm-project 35990504507d79e0b9deb809c8ee5e1b34ceef20)
• running under: Fedora Linux 42 (Workstation Edition)
• using session charset: UTF-8 * current time: 2026-04-26 00:09:42 UTC
• using option ‘--no-stop-on-test-error’
• checking for file ‘duckh3/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘duckh3’ version ‘0.1.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘duckh3’ can be installed ... OK See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking examples ... [6s/38s] ERROR Running examples in ‘duckh3-Ex.R’ failed The error most likely occurred in: > ### Name: ddbh3_get_child_pos > ### Title: Get the position of an H3 cell within its parent > ### Aliases: ddbh3_get_child_pos > > ### ** Examples > > ## Load needed packages > library(duckh3) > library(dplyr) Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’:     filter, lag The following objects are masked from ‘package:base’:     intersect, setdiff, setequal, union > > ## Setup the default connection with h3 and spatial extensions > ## This is a mandatory step to use duckh3 functions > ddbh3_default_conn(threads = 1) [gannet:1499538:0:1499538] Caught signal 11 (Segmentation fault: Sent by the kernel at address (nil)) ==== backtrace (tid:1499538) ====  0 /lib64/libucs.so.0(ucs_handle_error+0x2e4) [0x7fc5749e4df4]  1 /lib64/libucs.so.0(+0x17aed) [0x7fc5749e6aed]  2 /lib64/libucs.so.0(+0x17cbd) [0x7fc5749e6cbd]  3 /lib64/libc.so.6(+0x1a040) [0x7fc58a328040]  4 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1181e00) [0x7fc45cd81e00]  5 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x1152a28) [0x7fc45cd52a28]  6 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75c104) [0x7fc45c35c104]  7 /data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension(+0x75a499) [0x7fc45c35a499]  8 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper29LoadExternalExtensionInternalERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEERNS_19ExtensionActiveLoadE+0x18f) [0x7fc4ad679e3f]  9 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb15ExtensionHelper21LoadExternalExtensionERNS_16DatabaseInstanceERNS_10FileSystemERKNSt3__112basic_stringIcNS5_11char_traitsIcEENS5_9allocatorIcEEEE+0x4a) [0x7fc4ad679bea] 10 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZNK6duckdb12PhysicalLoad15GetDataInternalERNS_16ExecutionContextERNS_9DataChunkERNS_19OperatorSourceInputE+0x151) [0x7fc4ae45e831] 11 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor15FetchFromSourceERNS_9DataChunkE+0x9b) [0x7fc4aec8d8eb] 12 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb16PipelineExecutor7ExecuteEm+0x146) [0x7fc4aec8a4c6] 13 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12PipelineTask11ExecuteTaskENS_17TaskExecutionModeE+0x112) [0x7fc4aec8a0f2] 14 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb12ExecutorTask7ExecuteENS_17TaskExecutionModeE+0xa0) [0x7fc4aec83d90] 15 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb8Executor11ExecuteTaskEb+0x1c0) [0x7fc4aec890f0] 16 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext19ExecuteTaskInternalERNS_17ClientContextLockERNS_15BaseQueryResultEb+0x40) [0x7fc4aea981f0] 17 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb18PendingQueryResult15ExecuteInternalERNS_17ClientContextLockE+0x7a) [0x7fc4aea9a97a] 18 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb13ClientContext7ExecuteERKNSt3__112basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEERNS_10shared_ptrINS_21PreparedStatementDataELb1EEERKNS_22PendingQueryParametersE+0xa0) [0x7fc4aea9a6c0] 19 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNSt3__113unordered_mapINS1_12basic_stringIcNS1_11char_traitsIcEENS1_9allocatorIcEEEENS_18BoundParameterDataENS_33CaseInsensitiveStringHashFunctionENS_29CaseInsensitiveStringEqualityENS6_INS1_4pairIKS8_S9_EEEEEEb+0x1c3) [0x7fc4aeabd473] 20 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_ZN6duckdb17PreparedStatement7ExecuteERNS_6vectorINS_5ValueELb1ENSt3__19allocatorIS2_EEEEb+0x172) [0x7fc4aeabd712] 21 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_Z12rapi_executeN5cpp1116external_pointerIN6duckdb10RStatementEXadL_ZNS_15default_deleterIS2_EEvPT_EEEENS1_11ConvertOptsE+0x115) [0x7fc4ad307f75] 22 /data/gannet/ripley/R/test-clang/duckdb/libs/duckdb.so(_duckdb_rapi_execute+0x66) [0x7fc4ad3704a6] 23 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8f4d4) [0x564bfbeb14d4] 24 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdaff8) [0x564bfbefcff8] 25 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc914c) [0x564bfbeeb14c] 26 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x564bfbeea8f5] 27 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93a4) [0x564bfbeeb3a4] 28 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x26e) [0x564bfbeea9be] 29 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93a4) [0x564bfbeeb3a4] 30 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd100) [0x564bfbeff100] 31 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd7d9) [0x564bfbeef7d9] 32 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc914c) [0x564bfbeeb14c] 33 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x564bfbeea8f5] 34 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0949) [0x564bfbf02949] 35 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdfe4c) [0x564bfbf01e4c] 36 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x564bfbeead46] 37 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc93a4) [0x564bfbeeb3a4] 38 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdd100) [0x564bfbeff100] 39 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcd7d9) [0x564bfbeef7d9] 40 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc914c) [0x564bfbeeb14c] 41 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x564bfbeea8f5] 42 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0949) [0x564bfbf02949] 43 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdfe4c) [0x564bfbf01e4c] 44 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x564bfbeead46] 45 /data/gannet/ripley/R/test-clang/rlang/libs/rlang.so(+0x4983) [0x7fc587d01983] 46 /data/gannet/ripley/R/R-clang/bin/exec/R(+0x8d623) [0x564bfbeaf623] 47 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcfdc4) [0x564bfbef1dc4] 48 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc914c) [0x564bfbeeb14c] 49 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x564bfbeea8f5] 50 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0949) [0x564bfbf02949] 51 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdfe4c) [0x564bfbf01e4c] 52 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x5f6) [0x564bfbeead46] 53 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe5e48) [0x564bfbf07e48] 54 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x564bfbeeab20] 55 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe4f8b) [0x564bfbf06f8b] 56 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x3d0) [0x564bfbeeab20] 57 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xe0949) [0x564bfbf02949] 58 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xdfe4c) [0x564bfbf01e4c] 59 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xcf653) [0x564bfbef1653] 60 /data/gannet/ripley/R/R-clang/bin/exec/R(+0xc914c) [0x564bfbeeb14c] 61 /data/gannet/ripley/R/R-clang/bin/exec/R(Rf_eval+0x1a5) [0x564bfbeea8f5] =================================  *** caught segfault *** address 0x4d20016e192, cause 'unknown' Traceback:  1: rapi_execute(stmt, convert_opts)  2: withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }})  3: doTryCatch(return(expr), name, parentenv, handler)  4: tryCatchOne(expr, names, parentenv, handlers[[1L]])  5: tryCatchList(expr, classes, parentenv, handlers)  6: tryCatch(withCallingHandlers(expr, condition = function(cnd) { { .__handler_frame__. <- TRUE .__setup_frame__. <- frame if (inherits(cnd, "message")) { except <- c("warning", "error") } else if (inherits(cnd, "warning")) { except <- "error" } else { except <- "" } } while (!is_null(cnd)) { if (inherits(cnd, "error")) { out <- handlers[[1L]](cnd) if (!inherits(out, "rlang_zap")) throw(out) } inherit <- .subset2(.subset2(cnd, "rlang"), "inherit") if (is_false(inherit)) { return() } cnd <- .subset2(cnd, "parent") }}), stackOverflowError = handlers[[1L]])  7: rlang::try_fetch(rapi_execute(stmt, convert_opts), error = function(e) { rethrow_error_from_rapi(e, call)})  8: rethrow_rapi_execute(res@stmt_lst$ref, duckdb_convert_opts_impl(res@connection@convert_opts, arrow = res@arrow))  9: duckdb_execute(res) 10: duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow) 11: .local(conn, statement, ...) 12: dbSendQuery(conn, statement, ...) 13: dbSendQuery(conn, statement, ...) 14: dbSendStatement(conn, statement, ...) 15: dbSendStatement(conn, statement, ...) 16: DBI::dbExecute(conn, glue::glue("LOAD {extension};")) 17: DBI::dbExecute(conn, glue::glue("LOAD {extension};")) 18: withCallingHandlers(expr, message = function(c) if (inherits(c, classes)) tryInvokeRestart("muffleMessage")) 19: suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};"))) 20: ddbs_load(conn, quiet = TRUE) 21: duckspatial::ddbs_create_conn(dbdir = "memory", bigint = "integer64", ...) 22: ddbh3_default_conn(threads = 1) An irrecoverable exception occurred. R is aborting now ...
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... ERROR   Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output:   > # This file is part of the standard setup for testthat.   > # It is recommended that you do not modify it.   > #   > # Where should you do additional test configuration?   > # Learn more about the roles of various files in:   > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview   > # * https://testthat.r-lib.org/articles/special-files.html   >   > library(testthat)   > library(duckh3)   >   > test_check("duckh3")   Error in `source_dir()`:   ! Failed to evaluate './setup.R'.   Caused by error in `duckdb_result()`:   ! Invalid Error: Invalid Input Error: Initialization function "spatial_duckdb_cpp_init" from file "/data/gannet/ripley/.local/share/R/duckdb/extensions/v1.5.2/linux_amd64/spatial.duckdb_extension" threw an exception: "Attempted to dereference shared_ptr that is NULL!"   ℹ Context: rapi_execute   ℹ Error type: INVALID   Backtrace:        ▆     1. ├─testthat::test_check("duckh3")     2. │ └─testthat::test_dir(...)     3. │ └─testthat:::test_files(...)     4. │ └─testthat:::test_files_serial(...)     5. │ └─testthat:::test_files_setup_state(...)     6. │ └─testthat::source_test_setup(".", env)     7. │ └─testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)     8. │ └─base::lapply(...)     9. │ └─testthat (local) FUN(X[[i]], ...)    10. │ └─testthat::source_file(...)    11. │ ├─base::withCallingHandlers(...)    12. │ └─base::eval(exprs, env)    13. │ └─base::eval(exprs, env)    14. │ └─duckh3::ddbh3_default_conn() at ./setup.R:12:1    15. │ └─duckspatial::ddbs_create_conn(...)    16. │ └─duckspatial::ddbs_load(conn, quiet = TRUE)    17. │ ├─base::suppressMessages(DBI::dbExecute(conn, glue::glue("LOAD {extension};")))    18. │ │ └─base::withCallingHandlers(...)    19. │ ├─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))    20. │ └─DBI::dbExecute(conn, glue::glue("LOAD {extension};"))    21. │ ├─DBI::dbSendStatement(conn, statement, ...)    22. │ └─DBI::dbSendStatement(conn, statement, ...)    23. │ ├─DBI::dbSendQuery(conn, statement, ...)    24. │ └─duckdb::dbSendQuery(conn, statement, ...)    25. │ └─duckdb (local) .local(conn, statement, ...)    26. │ └─duckdb:::duckdb_result(connection = conn, stmt_lst = stmt_lst, arrow = arrow)    27. │ └─duckdb:::duckdb_execute(res)    28. │ └─duckdb:::rethrow_rapi_execute(...)    29. │ ├─rlang::try_fetch(...)    30. │ │ ├─base::tryCatch(...)    31. │ │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)    32. │ │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])    33. │ │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)    34. │ │ └─base::withCallingHandlers(...)    35. │ └─duckdb:::rapi_execute(stmt, convert_opts)    36. ├─duckdb (local) `<fn>`(...)    37. │ └─rlang::abort(error_parts, class = "duckdb_error", !!!fields)    38. │ └─rlang:::signal_abort(cnd, .file)    39. │ └─base::signalCondition(cnd)    40. └─rlang (local) `<fn>`(`<dckdb_rr>`)    41. └─handlers[[1L]](cnd)    42. └─duckdb:::rethrow_error_from_rapi(e, call)    43. └─rlang::abort(msg, call = call)   Execution halted
• checking PDF version of manual ... OK
• checking HTML version of manual ... OK
• checking for non-standard things in the check directory ... OK
• checking for detritus in the temp directory ... OK
• DONE

Status: 2 ERRORs