• using R Under development (unstable) (2025-12-22 r89219)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-15 (Debian 15.2.0-11) 15.2.0     GNU Fortran (Debian 15.2.0-11) 15.2.0
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘hydroloom/DESCRIPTION’ ... OK
• this is package ‘hydroloom’ version ‘1.1.1’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [2s/2s] OK
• 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 ‘hydroloom’ can be installed ... OK See the install log for details.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ 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 ... [1s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the package can be unloaded cleanly ... [1s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [1s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [1s/2s] OK
• checking loading without being on the library search path ... [2s/3s] 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 ... [12s/15s] OK
• checking Rd files ... [0s/0s] 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 installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [9s/12s] ERROR Running examples in ‘hydroloom-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: disambiguate_indexes > ### Title: Disambiguate Flowline Indexes > ### Aliases: disambiguate_indexes > > ### ** Examples > > if(require(nhdplusTools)) { + source(system.file("extdata", "sample_flines.R", package = "nhdplusTools")) + + hydro_location <- sf::st_sf(id = c(1, 2, 3), + geom = sf::st_sfc(list(sf::st_point(c(-76.86934, 39.49328)), + sf::st_point(c(-76.91711, 39.40884)), + sf::st_point(c(-76.88081, 39.36354))), + crs = 4326), + totda = c(23.6, 7.3, 427.9), + nameid = c("Patapsco", "", "Falls Run River")) + + indexes <- index_points_to_lines(sample_flines, + hydro_location, + search_radius = units::set_units(0.2, "degrees"), + max_matches = 10) + + disambiguate_indexes(indexes, + dplyr::select(sample_flines, COMID, TotDASqKM), + dplyr::select(hydro_location, id, totda)) + + result <- disambiguate_indexes(indexes, + dplyr::select(sample_flines, COMID, GNIS_NAME), + dplyr::select(hydro_location, id, nameid)) + + result[result$point_id == 1, ] + + result[result$point_id == 2, ] + + result[result$point_id == 3, ] + } Loading required package: nhdplusTools Attaching package: ‘nhdplusTools’ The following object is masked from ‘package:hydroloom’:     make_node_topology Warning in index_points_to_lines.hy(x, points, search_radius = search_radius, :   converting to LINESTRING, this may be slow, check results Error in `[.data.table`(matched, , `:=`(N, seq_len(.N)), by = list(point_id)) :   attempt access index 4/4 in VECTOR_ELT Calls: index_points_to_lines ... index_points_to_lines.hy -> left_join -> matcher_dt -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [51s/28s] ERROR   Running ‘testthat.R’ [51s/28s] 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/tests.html   > # * https://testthat.r-lib.org/reference/test_package.html#special-files   >   > library(testthat)   > library(hydroloom)   >   > test_check("hydroloom")   Starting 2 test processes.   > test_check_hy_graph.R:     |     | | 0%   > test_check_hy_graph.R:     |     |========================================================== | 83%   > test_check_hy_graph.R: found loop at 3   > test_check_hy_graph.R: found loop at 3   > test_check_hy_graph.R:     |     | | 0%     |     |========================================================== | 83%   > test_check_hy_graph.R: found loop at 3   > test_check_hy_graph.R: found loop at 3   > test_check_hy_graph.R:     |     | | 0%     |     |=================================== | 50%   > test_check_hy_graph.R:     |     | | 0%     |     |=================================== | 50%   > test_check_hy_graph.R:     |     | | 0%     |     |======================================================================| 100%   > test_check_hy_graph.R:     |   > test_check_hy_graph.R:     | | 0%     |     |======================================================================| 100%   > test_check_hy_graph.R:     |     | | 0%   > test_check_hy_graph.R:     |     |========= | 13%   > test_check_hy_graph.R:     |     |=================== | 27%   > test_check_hy_graph.R:     |     |============================ | 40%   > test_check_hy_graph.R:     |     |====================================== | 54%   > test_check_hy_graph.R:     |     |=============================================== | 67%     |     |======================================================== | 80%     |     |================================================================== | 94%   > test_check_hy_graph.R:     |     |======================================================================| 100%   > test_check_hy_graph.R:     |     | | 0%   > test_check_hy_graph.R:     |     |===== | 8%   > test_check_hy_graph.R:     |     |=========== | 15%   > test_check_hy_graph.R:     |     |================ | 23%   > test_check_hy_graph.R:     |     |===================== | 30%   > test_check_hy_graph.R:     |     |========================== | 38%   > test_check_hy_graph.R:     |     |================================ | 45%   > test_check_hy_graph.R:     |     |===================================== | 53%   > test_check_hy_graph.R:     |   > test_check_hy_graph.R:     |========================================== | 60%   > test_check_hy_graph.R:     |     |=============================================== | 68%   > test_check_hy_graph.R:     |     |===================================================== | 75%   > test_check_hy_graph.R:     |     |========================================================== | 83%   > test_check_hy_graph.R:     |     |=============================================================== | 90%   > test_check_hy_graph.R:     |     |===================================================================== | 98%     |     |======================================================================| 100%   > test_check_hy_graph.R:     |     | | 0%   > test_check_hy_graph.R:     |     |========= | 13%   > test_check_hy_graph.R:     |     |================== | 26%   > test_check_hy_graph.R:     |     |=========================== | 38%   > test_check_hy_graph.R:     |     |==================================== | 51%   > test_check_hy_graph.R:     |     |============================================= | 64%   > test_check_hy_graph.R:     |   > test_check_hy_graph.R:     |====================================================== | 77%   > test_check_hy_graph.R:     |     |=============================================================== | 90%   > test_check_hy_graph.R:     |   > test_check_hy_graph.R:     |======================================================================| 100%   > test_check_hy_graph.R:     |     | | 0%     |     |======================================================================| 100%   Saving _problems/test_get_hydro_location-13.R   > test_hydroloom.R: no hy class attribute   > test_hydroloom.R: some na toids   > test_hydroloom.R: no original names attribute   > test_hydroloom.R: no hy class attribute   Saving _problems/test_index-17.R   Saving _problems/test_index-77.R   Saving _problems/test_index-132.R   Saving _problems/test_index-156.R   Saving _problems/test_index-211.R   Saving _problems/test_index-245.R   Saving _problems/test_index-269.R   [ FAIL 8 | WARN 4 | SKIP 1 | PASS 343 ]      ══ Skipped tests (1) ═══════════════════════════════════════════════════════════   • On CRAN (1): 'test_add_levelpaths.R:158:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_get_hydro_location.R:13:3'): get location ──────────────────────   Error in ``[.data.table`(matched, , `:=`(N, seq_len(.N)), by = list(point_id))`: attempt access index 4/4 in VECTOR_ELT   Backtrace:       ▆    1. ├─hydroloom::index_points_to_lines(sample_flines, points) at test_get_hydro_location.R:13:3    2. └─hydroloom:::index_points_to_lines.data.frame(sample_flines, points)    3. ├─hydroloom::index_points_to_lines(...)    4. └─hydroloom:::index_points_to_lines.hy(...)    5. ├─dplyr::left_join(...)    6. └─hydroloom:::matcher_dt(x, points, search_radius, max_matches = max_matches)    7. ├─matched[, `:=`(N, seq_len(.N)), by = list(point_id)]    8. └─data.table:::`[.data.table`(...)   ── Error ('test_index.R:16:3'): index to waterbodies ───────────────────────────   Error in ``[.data.table`(matched, , `:=`(N, seq_len(.N)), by = list(point_id))`: attempt access index 4/4 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::expect_warning(...) at test_index.R:16:3     2. │ └─testthat:::expect_condition_matching_(...)     3. │ └─testthat:::quasi_capture(...)     4. │ ├─testthat (local) .capture(...)     5. │ │ └─base::withCallingHandlers(...)     6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))     7. └─hydroloom::index_points_to_waterbodies(wb, gage_l)     8. └─hydroloom:::matcher_dt(waterbodies, st_coordinates(points), search_radius)     9. ├─matched[, `:=`(N, seq_len(.N)), by = list(point_id)]    10. └─data.table:::`[.data.table`(...)   ── Error ('test_index.R:72:3'): point indexing to nearest existing node works as expected ──   Error in ``[.data.table`(matched, , `:=`(N, seq_len(.N)), by = list(point_id))`: attempt access index 4/4 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::expect_equal(...) at test_index.R:72:3     2. │ └─testthat::quasi_label(enquo(object), label)     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))     4. ├─hydroloom::index_points_to_lines(flines_in, point)     5. └─hydroloom:::index_points_to_lines.data.frame(flines_in, point)     6. ├─hydroloom::index_points_to_lines(...)     7. └─hydroloom:::index_points_to_lines.hy(...)     8. ├─dplyr::left_join(...)     9. └─hydroloom:::matcher_dt(x, points, search_radius, max_matches = max_matches)    10. ├─matched[, `:=`(N, seq_len(.N)), by = list(point_id)]    11. └─data.table:::`[.data.table`(...)   ── Error ('test_index.R:128:5'): point indexing works without measures ─────────   Error in ``[.data.table`(matched, , `:=`(N, seq_len(.N)), by = list(point_id))`: attempt access index 4/4 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::expect_equal(...) at test_index.R:128:5     2. │ └─testthat::quasi_label(enquo(object), label)     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))     4. ├─hydroloom::index_points_to_lines(flines_in, point)     5. └─hydroloom:::index_points_to_lines.data.frame(flines_in, point)     6. ├─hydroloom::index_points_to_lines(...)     7. └─hydroloom:::index_points_to_lines.hy(...)     8. ├─dplyr::left_join(...)     9. └─hydroloom:::matcher_dt(x, points, search_radius, max_matches = max_matches)    10. ├─matched[, `:=`(N, seq_len(.N)), by = list(point_id)]    11. └─data.table:::`[.data.table`(...)   ── Error ('test_index.R:147:3'): point indexing to for multiple points works ───   Error in ``[.data.table`(matched, , `:=`(N, seq_len(.N)), by = list(point_id))`: attempt access index 4/4 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::expect_equal(...) at test_index.R:147:3     2. │ └─testthat::quasi_label(enquo(object), label)     3. │ └─rlang::eval_bare(expr, quo_get_env(quo))     4. ├─hydroloom::index_points_to_lines(flines_in, point, search_radius = sr)     5. └─hydroloom:::index_points_to_lines.data.frame(...)     6. ├─hydroloom::index_points_to_lines(...)     7. └─hydroloom:::index_points_to_lines.hy(...)     8. ├─dplyr::left_join(...)     9. └─hydroloom:::matcher_dt(x, points, search_radius, max_matches = max_matches)    10. ├─matched[, `:=`(N, seq_len(.N)), by = list(point_id)]    11. └─data.table:::`[.data.table`(...)   ── Error ('test_index.R:210:3'): multipart indexing ────────────────────────────   Error in ``[.data.table`(matched, , `:=`(N, seq_len(.N)), by = list(point_id))`: attempt access index 4/4 in VECTOR_ELT   Backtrace:        ▆     1. ├─testthat::capture_warnings(...) at test_index.R:210:3     2. │ └─base::withCallingHandlers(...)     3. ├─hydroloom::index_points_to_lines(lines, points, search_radius = 500)     4. └─hydroloom:::index_points_to_lines.data.frame(lines, points, search_radius = 500)     5. ├─hydroloom::index_points_to_lines(...)     6. └─hydroloom:::index_points_to_lines.hy(...)     7. ├─dplyr::left_join(...)     8. └─hydroloom:::matcher_dt(x, points, search_radius, max_matches = max_matches)     9. ├─matched[, `:=`(N, seq_len(.N)), by = list(point_id)]    10. └─data.table:::`[.data.table`(...)   ── Error ('test_index.R:241:3'): no duplicates when using precision ────────────   Error in ``[.data.table`(matched, , `:=`(N, seq_len(.N)), by = list(point_id))`: attempt access index 4/4 in VECTOR_ELT   Backtrace:       ▆    1. ├─dplyr::filter(...) at test_index.R:241:3    2. ├─hydroloom::index_points_to_lines(...)    3. └─hydroloom:::index_points_to_lines.data.frame(...)    4. ├─hydroloom::index_points_to_lines(...)    5. └─hydroloom:::index_points_to_lines.hy(...)    6. ├─dplyr::left_join(...)    7. └─hydroloom:::matcher_dt(x, points, search_radius, max_matches = max_matches)    8. ├─matched[, `:=`(N, seq_len(.N)), by = list(point_id)]    9. └─data.table:::`[.data.table`(...)   ── Error ('test_index.R:266:3'): disambiguate ──────────────────────────────────   Error in ``[.data.table`(matched, , `:=`(N, seq_len(.N)), by = list(point_id))`: attempt access index 4/4 in VECTOR_ELT   Backtrace:       ▆    1. ├─hydroloom::index_points_to_lines(...) at test_index.R:266:3    2. └─hydroloom:::index_points_to_lines.data.frame(...)    3. ├─hydroloom::index_points_to_lines(...)    4. └─hydroloom:::index_points_to_lines.hy(...)    5. ├─dplyr::left_join(...)    6. └─hydroloom:::matcher_dt(x, points, search_radius, max_matches = max_matches)    7. ├─matched[, `:=`(N, seq_len(.N)), by = list(point_id)]    8. └─data.table:::`[.data.table`(...)      [ FAIL 8 | WARN 4 | SKIP 1 | PASS 343 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [21s/27s] OK
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [2s/3s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs