CRAN Package Check Results for Package simphony

Last updated on 2025-12-20 09:50:02 CET.

Flavor	Version	T_install	T_check	T_total	Status
r-devel-linux-x86_64-debian-clang	1.0.3	2.57	56.06	58.63	OK
r-devel-linux-x86_64-debian-gcc	1.0.3	1.89	28.55	30.44	ERROR
r-devel-linux-x86_64-fedora-clang	1.0.3			62.95	ERROR
r-devel-linux-x86_64-fedora-gcc	1.0.3			74.47	ERROR
r-devel-windows-x86_64	1.0.3	4.00	66.00	70.00	OK
r-patched-linux-x86_64	1.0.3	2.47	50.18	52.65	OK
r-release-linux-x86_64	1.0.3	2.37	50.13	52.50	OK
r-release-macos-arm64	1.0.3				OK
r-release-macos-x86_64	1.0.3	2.00	75.00	77.00	OK
r-release-windows-x86_64	1.0.3	4.00	65.00	69.00	OK
r-oldrel-macos-arm64	1.0.3				OK
r-oldrel-macos-x86_64	1.0.3	2.00	45.00	47.00	OK
r-oldrel-windows-x86_64	1.0.3	5.00	77.00	82.00	OK

Check Details

Version: 1.0.3
Check: examples
Result: ERROR Running examples in ‘simphony-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: mergeSimData > ### Title: Merge abundance data, feature metadata, and sample metadata > ### Aliases: mergeSimData > > ### ** Examples > > library('data.table') Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% > featureGroups = data.table(amp = c(0, 1)) > simData = simphony(featureGroups) Error in `[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * : attempt access index 13/13 in VECTOR_ELT Calls: simphony -> getExpectedAbund -> [ -> [.data.table Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.3
Check: tests
Result: ERROR Running ‘testthat.R’ [2s/2s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(simphony) > > test_check('simphony') Saving _problems/test-functional-simphony-9.R Saving _problems/test-functional-simphony-33.R Saving _problems/test-functional-simphony-47.R Saving _problems/test-unit-simphony-32.R Saving _problems/test-unit-simphony-59.R Saving _problems/test-unit-simphony-72.R Saving _problems/test-unit-simphony-83.R [ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-functional-simphony.R:7:3'): Abundances are sampled from the correct trend ── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(...) at test-functional-simphony.R:7:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-functional-simphony.R:33:3'): Time-independent statistics from NBD are as expected ── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(...) at test-functional-simphony.R:33:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-functional-simphony.R:46:3'): Time-dependent statistics from NBD are as expected ── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(...) at test-functional-simphony.R:46:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-functional-simphony.R:77:3'): Amplitude and base can be passed as functions ── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_silent(simphony(featureGroups)) at test-functional-simphony.R:77:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─simphony::simphony(featureGroups) 10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 11. ├─...[] 12. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:6:18'): Single condition simulation works ────── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-unit-simphony.R:6:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:6:18 10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 11. ├─...[] 12. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:15:3'): Multiple condition simulation works ──── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_silent(simphony(featureGroupsList)) at test-unit-simphony.R:15:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─simphony::simphony(featureGroupsList) 10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 11. ├─...[] 12. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:30:3'): Number of features and samples simulated are predictable ── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(...) at test-unit-simphony.R:30:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:59:3'): Condition names are as expected ──────── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:59:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:71:3'): Sample names are as expected ─────────── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(...) at test-unit-simphony.R:71:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:83:3'): Feature names are as expected ────────── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(featureGroups, nFeatures = 20) at test-unit-simphony.R:83:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) [ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ] Error: ! Test failures. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘examples.Rmd’ using rmarkdown Quitting from examples.Rmd:23-43 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 14/14 in VECTOR_ELT --- Backtrace: ▆ 1. └─simphony::simphony(featureGroups) 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'examples.Rmd' failed with diagnostics: attempt access index 14/14 in VECTOR_ELT --- failed re-building ‘examples.Rmd’ --- re-building ‘introduction.Rmd’ using rmarkdown Quitting from introduction.Rmd:35-39 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 14/14 in VECTOR_ELT --- Backtrace: ▆ 1. └─simphony::simphony(...) 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'introduction.Rmd' failed with diagnostics: attempt access index 14/14 in VECTOR_ELT --- failed re-building ‘introduction.Rmd’ SUMMARY: processing the following files failed: ‘examples.Rmd’ ‘introduction.Rmd’ Error: Vignette re-building failed. Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.0.3
Check: examples
Result: ERROR Running examples in ‘simphony-Ex.R’ failed The error most likely occurred in: > ### Name: mergeSimData > ### Title: Merge abundance data, feature metadata, and sample metadata > ### Aliases: mergeSimData > > ### ** Examples > > library('data.table') Attaching package: ‘data.table’ The following object is masked from ‘package:base’: %notin% > featureGroups = data.table(amp = c(0, 1)) > simData = simphony(featureGroups) Error in `[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * : attempt access index 13/13 in VECTOR_ELT Calls: simphony -> getExpectedAbund -> [ -> [.data.table Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.3
Check: tests
Result: ERROR Running ‘testthat.R’ Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(simphony) > > test_check('simphony') Saving _problems/test-functional-simphony-9.R Saving _problems/test-functional-simphony-33.R Saving _problems/test-functional-simphony-47.R Saving _problems/test-unit-simphony-32.R Saving _problems/test-unit-simphony-59.R Saving _problems/test-unit-simphony-72.R Saving _problems/test-unit-simphony-83.R [ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-functional-simphony.R:7:3'): Abundances are sampled from the correct trend ── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(...) at test-functional-simphony.R:7:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-functional-simphony.R:33:3'): Time-independent statistics from NBD are as expected ── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(...) at test-functional-simphony.R:33:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-functional-simphony.R:46:3'): Time-dependent statistics from NBD are as expected ── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(...) at test-functional-simphony.R:46:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-functional-simphony.R:77:3'): Amplitude and base can be passed as functions ── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_silent(simphony(featureGroups)) at test-functional-simphony.R:77:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─simphony::simphony(featureGroups) 10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 11. ├─...[] 12. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:6:18'): Single condition simulation works ────── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_silent(...) at test-unit-simphony.R:6:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:6:18 10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 11. ├─...[] 12. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:15:3'): Multiple condition simulation works ──── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. ├─testthat::expect_silent(simphony(featureGroupsList)) at test-unit-simphony.R:15:3 2. │ └─testthat:::quasi_capture(enquo(object), NULL, evaluate_promise) 3. │ ├─testthat (local) .capture(...) 4. │ │ ├─withr::with_output_sink(...) 5. │ │ │ └─base::force(code) 6. │ │ ├─base::withCallingHandlers(...) 7. │ │ └─base::withVisible(code) 8. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo)) 9. └─simphony::simphony(featureGroupsList) 10. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 11. ├─...[] 12. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:30:3'): Number of features and samples simulated are predictable ── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(...) at test-unit-simphony.R:30:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:59:3'): Condition names are as expected ──────── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(featureGroupsList) at test-unit-simphony.R:59:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:71:3'): Sample names are as expected ─────────── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(...) at test-unit-simphony.R:71:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ── Error ('test-unit-simphony.R:83:3'): Feature names are as expected ────────── Error in ``[.data.table`(d, , `:=`(mu, base[[1]](time) + amp[[1]](time) * rhyFunc[[1]]((time + phase) * 2 * pi/period)), by = c("cond", "group"))`: attempt access index 13/13 in VECTOR_ELT Backtrace: ▆ 1. └─simphony::simphony(featureGroups, nFeatures = 20) at test-unit-simphony.R:83:3 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) [ FAIL 10 | WARN 0 | SKIP 0 | PASS 1 ] Error: ! Test failures. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.3
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building ‘examples.Rmd’ using rmarkdown Quitting from examples.Rmd:23-43 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 14/14 in VECTOR_ELT --- Backtrace: ▆ 1. └─simphony::simphony(featureGroups) 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'examples.Rmd' failed with diagnostics: attempt access index 14/14 in VECTOR_ELT --- failed re-building ‘examples.Rmd’ --- re-building ‘introduction.Rmd’ using rmarkdown Quitting from introduction.Rmd:35-39 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 14/14 in VECTOR_ELT --- Backtrace: ▆ 1. └─simphony::simphony(...) 2. └─simphony::getExpectedAbund(fm, sampleMetadata = sm) 3. ├─...[] 4. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'introduction.Rmd' failed with diagnostics: attempt access index 14/14 in VECTOR_ELT --- failed re-building ‘introduction.Rmd’ SUMMARY: processing the following files failed: ‘examples.Rmd’ ‘introduction.Rmd’ Error: Vignette re-building failed. Execution halted Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc