CRAN Package Check Results for Package OpenSpecy

Last updated on 2025-12-20 17:50:35 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.5.3	17.39	181.18	198.57	ERROR
r-devel-linux-x86_64-debian-gcc	1.5.3	9.96	122.55	132.51	ERROR
r-devel-linux-x86_64-fedora-clang	1.5.3	28.00	276.60	304.60	ERROR
r-devel-linux-x86_64-fedora-gcc	1.5.3	28.00	290.55	318.55	ERROR
r-devel-windows-x86_64	1.5.3	18.00	183.00	201.00	OK
r-patched-linux-x86_64	1.5.3	15.24	174.04	189.28	OK
r-release-linux-x86_64	1.5.3	15.30	173.59	188.89	OK
r-release-macos-arm64	1.5.3				OK
r-release-macos-x86_64	1.5.3	10.00	198.00	208.00	OK
r-release-windows-x86_64	1.5.3	18.00	177.00	195.00	OK
r-oldrel-macos-arm64	1.5.3				OK
r-oldrel-macos-x86_64	1.5.3	10.00	193.00	203.00	OK
r-oldrel-windows-x86_64	1.5.3	27.00	237.00	264.00	OK

Check Details

Version: 1.5.3
Check: CRAN incoming feasibility
Result: NOTE Maintainer: ‘Win Cowger <wincowger@gmail.com>’ Found the following (possibly) invalid URLs: URL: https://app.gitter.im/#/room/#Open-Specy_community:gitter.im From: README.md Message: Invalid URL: '#' not allowed in fragment Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.5.3
Check: examples
Result: ERROR Running examples in ‘OpenSpecy-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: collapse_spec > ### Title: Define features > ### Aliases: collapse_spec collapse_spec.default collapse_spec.OpenSpecy > ### def_features def_features.default def_features.OpenSpecy > > ### ** Examples > > ## Don't show: > data.table::setDTthreads(2) > ## End(Don't show) > tiny_map <- read_extdata("CA_tiny_map.zip") |> read_any() > identified_map <- def_features(tiny_map, tiny_map$metadata$x == 0) Error in `[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id") : attempt access index 26/26 in VECTOR_ELT Calls: def_features -> def_features.OpenSpecy -> [ -> [.data.table Execution halted Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Version: 1.5.3
Check: tests
Result: ERROR Running ‘testthat.R’ [33s/39s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(OpenSpecy) > > library(data.table) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > setDTthreads(2) > > test_check("OpenSpecy") Saving _problems/test-def_features-15.R Saving _problems/test-def_features-30.R Saving _problems/test-def_features-93.R Saving _problems/test-def_features-208.R [ FAIL 4 | WARN 0 | SKIP 6 | PASS 470 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (6): 'test-def_features.R:118:3', 'test-def_features.R:139:3', 'test-manage_lib.R:7:3', 'test-manage_lib.R:28:3', 'test-match_spec.R:63:3', 'test-match_spec.R:201:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-def_features.R:15:3'): features are identified when given logical ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 27/27 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$particles) at test-def_features.R:15:3 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$particles) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:30:5'): features are identified with sig_noise and smoothing with closing ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 28/28 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$snr > 0.1) at test-def_features.R:30:5 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$snr > 0.1) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:93:3'): particles are identified when given character ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 28/28 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$particles) at test-def_features.R:93:3 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$particles) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:208:5'): RGB values are correctly extracted and stored in metadata ── Error in ``[.data.table`(md, , `:=`(mean_r = as.integer(sqrt(mean(r^2))), mean_g = as.integer(sqrt(mean(g^2))), mean_b = as.integer(sqrt(mean(b^2)))), by = "feature_id")`: attempt access index 25/25 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(...) at test-def_features.R:208:5 2. └─OpenSpecy:::def_features.OpenSpecy(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) [ FAIL 4 | WARN 0 | SKIP 6 | PASS 470 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.5.3
Check: tests
Result: ERROR Running ‘testthat.R’ [20s/24s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(OpenSpecy) > > library(data.table) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > setDTthreads(2) > > test_check("OpenSpecy") Saving _problems/test-def_features-15.R Saving _problems/test-def_features-30.R Saving _problems/test-def_features-93.R Saving _problems/test-def_features-208.R [ FAIL 4 | WARN 0 | SKIP 6 | PASS 470 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (6): 'test-def_features.R:118:3', 'test-def_features.R:139:3', 'test-manage_lib.R:7:3', 'test-manage_lib.R:28:3', 'test-match_spec.R:63:3', 'test-match_spec.R:201:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-def_features.R:15:3'): features are identified when given logical ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 27/27 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$particles) at test-def_features.R:15:3 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$particles) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:30:5'): features are identified with sig_noise and smoothing with closing ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 28/28 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$snr > 0.1) at test-def_features.R:30:5 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$snr > 0.1) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:93:3'): particles are identified when given character ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 28/28 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$particles) at test-def_features.R:93:3 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$particles) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:208:5'): RGB values are correctly extracted and stored in metadata ── Error in ``[.data.table`(md, , `:=`(mean_r = as.integer(sqrt(mean(r^2))), mean_g = as.integer(sqrt(mean(g^2))), mean_b = as.integer(sqrt(mean(b^2)))), by = "feature_id")`: attempt access index 25/25 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(...) at test-def_features.R:208:5 2. └─OpenSpecy:::def_features.OpenSpecy(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) [ FAIL 4 | WARN 0 | SKIP 6 | PASS 470 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.5.3
Check: examples
Result: ERROR Running examples in ‘OpenSpecy-Ex.R’ failed The error most likely occurred in: > ### Name: collapse_spec > ### Title: Define features > ### Aliases: collapse_spec collapse_spec.default collapse_spec.OpenSpecy > ### def_features def_features.default def_features.OpenSpecy > > ### ** Examples > > ## Don't show: > data.table::setDTthreads(2) > ## End(Don't show) > tiny_map <- read_extdata("CA_tiny_map.zip") |> read_any() > identified_map <- def_features(tiny_map, tiny_map$metadata$x == 0) Error in `[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id") : attempt access index 26/26 in VECTOR_ELT Calls: def_features -> def_features.OpenSpecy -> [ -> [.data.table Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.5.3
Check: tests
Result: ERROR Running ‘testthat.R’ [50s/52s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(OpenSpecy) > > library(data.table) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > setDTthreads(2) > > test_check("OpenSpecy") Saving _problems/test-def_features-15.R Saving _problems/test-def_features-30.R Saving _problems/test-def_features-93.R Saving _problems/test-def_features-208.R [ FAIL 4 | WARN 0 | SKIP 6 | PASS 470 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (6): 'test-def_features.R:118:3', 'test-def_features.R:139:3', 'test-manage_lib.R:7:3', 'test-manage_lib.R:28:3', 'test-match_spec.R:63:3', 'test-match_spec.R:201:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-def_features.R:15:3'): features are identified when given logical ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 27/27 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$particles) at test-def_features.R:15:3 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$particles) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:30:5'): features are identified with sig_noise and smoothing with closing ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 28/28 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$snr > 0.1) at test-def_features.R:30:5 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$snr > 0.1) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:93:3'): particles are identified when given character ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 28/28 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$particles) at test-def_features.R:93:3 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$particles) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:208:5'): RGB values are correctly extracted and stored in metadata ── Error in ``[.data.table`(md, , `:=`(mean_r = as.integer(sqrt(mean(r^2))), mean_g = as.integer(sqrt(mean(g^2))), mean_b = as.integer(sqrt(mean(b^2)))), by = "feature_id")`: attempt access index 25/25 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(...) at test-def_features.R:208:5 2. └─OpenSpecy:::def_features.OpenSpecy(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) [ FAIL 4 | WARN 0 | SKIP 6 | PASS 470 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.5.3
Check: tests
Result: ERROR Running ‘testthat.R’ [62s/72s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(OpenSpecy) > > library(data.table) Attaching package: 'data.table' The following object is masked from 'package:base': %notin% > setDTthreads(2) > > test_check("OpenSpecy") Saving _problems/test-def_features-15.R Saving _problems/test-def_features-30.R Saving _problems/test-def_features-93.R Saving _problems/test-def_features-208.R [ FAIL 4 | WARN 0 | SKIP 6 | PASS 470 ] ══ Skipped tests (6) ═══════════════════════════════════════════════════════════ • On CRAN (6): 'test-def_features.R:118:3', 'test-def_features.R:139:3', 'test-manage_lib.R:7:3', 'test-manage_lib.R:28:3', 'test-match_spec.R:63:3', 'test-match_spec.R:201:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-def_features.R:15:3'): features are identified when given logical ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 27/27 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$particles) at test-def_features.R:15:3 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$particles) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:30:5'): features are identified with sig_noise and smoothing with closing ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 28/28 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$snr > 0.1) at test-def_features.R:30:5 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$snr > 0.1) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:93:3'): particles are identified when given character ── Error in ``[.data.table`(md, , `:=`("rand_x", sample(x, 1)), by = "feature_id")`: attempt access index 28/28 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(map, map$metadata$particles) at test-def_features.R:93:3 2. └─OpenSpecy:::def_features.OpenSpecy(map, map$metadata$particles) 3. ├─md[, `:=`("rand_x", sample(x, 1)), by = "feature_id"] 4. └─data.table:::`[.data.table`(...) ── Error ('test-def_features.R:208:5'): RGB values are correctly extracted and stored in metadata ── Error in ``[.data.table`(md, , `:=`(mean_r = as.integer(sqrt(mean(r^2))), mean_g = as.integer(sqrt(mean(g^2))), mean_b = as.integer(sqrt(mean(b^2)))), by = "feature_id")`: attempt access index 25/25 in VECTOR_ELT Backtrace: ▆ 1. ├─OpenSpecy::def_features(...) at test-def_features.R:208:5 2. └─OpenSpecy:::def_features.OpenSpecy(...) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) [ FAIL 4 | WARN 0 | SKIP 6 | PASS 470 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc