• using R Under development (unstable) (2025-12-18 r89199)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     Debian clang version 21.1.7 (1)     Debian flang version 21.1.7 (1)
• running under: Debian GNU/Linux forky/sid
• using session charset: UTF-8
• checking for file ‘simphony/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘simphony’ version ‘1.0.3’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [0s/1s] 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 serialization versions ... OK
• checking whether package ‘simphony’ 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 ... [0s/1s] OK
• checking whether the package can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the package can be unloaded cleanly ... [0s/1s] OK
• checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
• checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
• checking loading without being on the library search path ... [0s/1s] 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 ... [4s/6s] 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/0s] 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 ... [1s/1s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [4s/4s] ERROR   Running ‘testthat.R’ [4s/3s] 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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [7s/8s] 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
• checking PDF version of manual ... [4s/6s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 3 ERRORs