• using R Under development (unstable) (2025-12-18 r89199)
• 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 ‘nhdplusTools/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘nhdplusTools’ version ‘1.4.1’
• 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 ‘nhdplusTools’ 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 ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/3s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
• checking loading without being on the library search path ... [2s/2s] OK
• checking whether startup messages can be suppressed ... [2s/2s] 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 ... [15s/18s] OK
• checking Rd files ... [0s/1s] 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 contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/1s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/6s] ERROR Running examples in ‘nhdplusTools-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: disambiguate_flowline_indexes > ### Title: Disambiguate Flowline Indexes > ### Aliases: disambiguate_flowline_indexes > > ### ** Examples > > 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")) > > flowpath <- dplyr::select(sample_flines, + comid = COMID, + totda = TotDASqKM, + nameid = GNIS_NAME, + REACHCODE, + ToMeas, + FromMeas) > > indexes <- get_flowline_index(flowpath, + hydro_location, + search_radius = 0.2, + max_matches = 10) Warning in check_search_radius(search_radius, points) :   search_radius units not set, trying units of points CRS. 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: get_flowline_index ... index_points_to_lines.hy -> left_join -> matcher_dt -> [ -> [.data.table Execution halted
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [40s/24s] ERROR   Running ‘testthat.R’ [39s/24s] Running the tests in ‘tests/testthat.R’ failed. Complete output:   > library("testthat")   >   > test_check("nhdplusTools")   Loading required package: nhdplusTools   Starting 2 test processes.   > test_02_subset.R: All intersections performed in latitude/longitude.   > test_02_subset.R: All intersections performed in latitude/longitude.   > test_02_subset.R: All intersections performed in latitude/longitude.   > test_02_subset.R: All intersections performed in latitude/longitude.   Saving _problems/test_index-114.R   Saving _problems/test_index-151.R   Saving _problems/test_index-202.R   Saving _problems/test_wb_index-14.R   [ FAIL 4 | WARN 0 | SKIP 58 | PASS 300 ]      ══ Skipped tests (58) ══════════════════════════════════════════════════════════   • On CRAN (58): 'test_00_plot_bbox_nhdplus.R:5:3',     'test_00_plot_integration_nhdplus.R:6:3',     'test_00_plot_local_extra_nhdplus.R:9:3', 'test_00_plot_local_nhdplus.R:9:3',     'test_01_get_nldi.R:5:3', 'test_01_get_nldi.R:25:3',     'test_01_get_nldi.R:85:3', 'test_01_get_nldi.R:122:3',     'test_01_get_nldi.R:140:3', 'test_01_get_nldi.R:176:3',     'test_01_get_nldi.R:224:3', 'test_00_plot_nhdplus.R:6:3',     'test_00_plot_nhdplus.R:90:3', 'test_00_plot_nhdplus.R:134:3',     'test_00_plot_nhdplus.R:164:3', 'test_00_plot_nhdplus.R:201:3',     'test_02_subset.R:135:3', 'test_02_subset.R:191:3',     'test_03_get_functions.R:20:3', 'test_03_get_functions.R:52:3',     'test_03_get_functions.R:75:3', 'test_03_get_functions.R:129:3',     'test_03_get_functions.R:200:3', 'test_03_get_functions.R:216:3',     'test_03_get_functions.R:229:3', 'test_03_get_functions.R:247:3',     'test_03_get_functions.R:254:3', 'test_arcrest.R:51:3',     'test_02_subset_extras.R:94:3', 'test_02_subset_extras.R:149:3',     'test_geoconnex.R:3:3', 'test_geoconnex.R:14:3', 'test_get_3dhp.R:3:3',     'test_get_nhdphr.R:3:3', 'test_get_nhdplus.R:8:3', 'test_get_nhdplus.R:29:3',     'test_get_nhdplus.R:49:3', 'test_get_nhdplushr.R:3:3',     'test_get_nhdplushr.R:23:3', 'test_get_nhdplushr.R:53:3',     'test_get_nhdplushr.R:80:3', 'test_get_nhdplushr.R:101:3',     'test_get_nhdplushr.R:147:3', 'test_get_nhdplushr.R:174:3',     'test_get_nhdplushr.R:196:3', 'test_get_codes.R:4:3', 'test_get_vaa.R:4:3',     'test_get_vaa.R:38:3', 'test_index.R:13:5', 'test_index.R:61:3',     'test_map_nhdplus.R:4:3', 'test_navigate.R:4:3', 'test_navigate.R:71:3',     'test_nhdplusTools.R:41:3', 'test_nhdplusTools.R:50:3',     'test_rescale_catchments.R:3:3', 'test_get_path.R:69:3',     'test_run_plus_attributes.R:20:3'      ══ Failed tests ════════════════════════════════════════════════════════════════   ── Error ('test_index.R:113:3'): 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:113:3     2. │ └─base::withCallingHandlers(...)     3. └─nhdplusTools::get_flowline_index(lines, points, search_radius = 500)     4. ├─hydroloom::index_points_to_lines(...)     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:148:3'): disambiguate ──────────────────────────────────   Error in ``[.data.table`(matched, , `:=`(N, seq_len(.N)), by = list(point_id))`: attempt access index 4/4 in VECTOR_ELT   Backtrace:       ▆    1. └─nhdplusTools::get_flowline_index(...) at test_index.R:148:3    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:202:3'): 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. └─nhdplusTools::get_flowline_index(sample_flines, points) at test_index.R:202:3    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_wb_index.R:14:1'): 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_wb_index.R:14:1     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. └─nhdplusTools::get_waterbody_index(wb, gage_l)     8. └─hydroloom::index_points_to_waterbodies(...)     9. └─hydroloom:::matcher_dt(waterbodies, st_coordinates(points), search_radius)    10. ├─matched[, `:=`(N, seq_len(.N)), by = list(point_id)]    11. └─data.table:::`[.data.table`(...)      [ FAIL 4 | WARN 0 | SKIP 58 | PASS 300 ]   Error:   ! Test failures.   Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [20s/30s] OK
• checking PDF version of manual ... [5s/8s] OK
• checking HTML version of manual ... [3s/6s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs