CRAN Package Check Results for Maintainer ‘Isaac Vock <isaac.vock at gmail.com>’

Last updated on 2025-12-28 01:49:11 CET.

Package	ERROR	NOTE	OK
bakR		5	8
EZbakR	3		10

Package bakR

Current CRAN status: NOTE: 5, OK: 8

Version: 1.0.1
Check: dependencies in R code
Result: NOTE Namespaces in Imports field not imported from: ‘RcppParallel’ ‘rstantools’ All declared Imports should be used. Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Version: 1.0.1
Check: installed package size
Result: NOTE installed size is 103.3Mb sub-directories of 1Mb or more: libs 101.5Mb Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

Version: 1.0.1
Check: for GNU extensions in Makefiles
Result: NOTE GNU make is a SystemRequirements. Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Package EZbakR

Current CRAN status: ERROR: 3, OK: 10

Version: 0.1.0
Check: examples
Result: ERROR Running examples in 'EZbakR-Ex.R' failed The error most likely occurred in: > ### Name: AverageAndRegularize > ### Title: Average parameter estimates across replicates, and regularize > ### variance estimates > ### Aliases: AverageAndRegularize > > ### ** Examples > > > # Simulate data to analyze > simdata <- EZSimulate(30) > > # Create EZbakR input > ezbdo <- EZbakRData(simdata$cB, simdata$metadf) > > # Estimate Fractions > ezbdo <- EstimateFractions(ezbdo) Estimating mutation rates Error in `[.data.table`(mutest_temp, , `:=`(c("pold", "pnew"), .(min(c(p1, : attempt access index 4/4 in VECTOR_ELT Calls: EstimateFractions ... EstimateMutRates -> EstimateMutRates.EZbakRData -> [ -> [.data.table Execution halted Flavor: r-devel-windows-x86_64

Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR Error(s) in re-building vignettes: --- re-building 'EZDynamics.Rmd' using rmarkdown Quitting from EZDynamics.Rmd:68-103 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 4/4 in VECTOR_ELT --- Backtrace: ▆ 1. ├─EZbakR::EstimateFractions(ezbdo) 2. └─EZbakR:::EstimateFractions.EZbakRData(ezbdo) 3. ├─EZbakR::EstimateMutRates(...) 4. └─EZbakR:::EstimateMutRates.EZbakRData(...) 5. ├─...[] 6. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EZDynamics.Rmd' failed with diagnostics: attempt access index 4/4 in VECTOR_ELT --- failed re-building 'EZDynamics.Rmd' --- re-building 'EZQC.Rmd' using rmarkdown Quitting from EZQC.Rmd:37-50 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 4/4 in VECTOR_ELT --- Backtrace: ▆ 1. ├─EZbakR::EZQC(ezbdo) 2. └─EZbakR:::EZQC.EZbakRData(ezbdo) 3. ├─EZbakR::EstimateMutRates(obj, populations = mutrate_populations) 4. └─EZbakR:::EstimateMutRates.EZbakRData(obj, populations = mutrate_populations) 5. ├─...[] 6. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EZQC.Rmd' failed with diagnostics: attempt access index 4/4 in VECTOR_ELT --- failed re-building 'EZQC.Rmd' --- re-building 'EZget.Rmd' using rmarkdown Quitting from EZget.Rmd:33-49 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 4/4 in VECTOR_ELT --- Backtrace: ▆ 1. ├─EZbakR::EstimateFractions(ezbdo) 2. └─EZbakR:::EstimateFractions.EZbakRData(ezbdo) 3. ├─EZbakR::EstimateMutRates(...) 4. └─EZbakR:::EstimateMutRates.EZbakRData(...) 5. ├─...[] 6. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EZget.Rmd' failed with diagnostics: attempt access index 4/4 in VECTOR_ELT --- failed re-building 'EZget.Rmd' --- re-building 'EstimateFractions.Rmd' using rmarkdown Quitting from EstimateFractions.Rmd:52-61 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 4/4 in VECTOR_ELT --- Backtrace: ▆ 1. ├─EZbakR::EstimateFractions(ezbdo, features = "feature") 2. └─EZbakR:::EstimateFractions.EZbakRData(ezbdo, features = "feature") 3. ├─EZbakR::EstimateMutRates(...) 4. └─EZbakR:::EstimateMutRates.EZbakRData(...) 5. ├─...[] 6. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EstimateFractions.Rmd' failed with diagnostics: attempt access index 4/4 in VECTOR_ELT --- failed re-building 'EstimateFractions.Rmd' --- re-building 'EstimateKinetics.Rmd' using rmarkdown Quitting from EstimateKinetics.Rmd:39-52 [unnamed-chunk-2] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 4/4 in VECTOR_ELT --- Backtrace: ▆ 1. ├─EZbakR::EstimateFractions(ezbdo) 2. └─EZbakR:::EstimateFractions.EZbakRData(ezbdo) 3. ├─EZbakR::EstimateMutRates(...) 4. └─EZbakR:::EstimateMutRates.EZbakRData(...) 5. ├─...[] 6. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'EstimateKinetics.Rmd' failed with diagnostics: attempt access index 4/4 in VECTOR_ELT --- failed re-building 'EstimateKinetics.Rmd' --- re-building 'Linear-modeling.Rmd' using rmarkdown Quitting from Linear-modeling.Rmd:74-125 [unnamed-chunk-4] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 4/4 in VECTOR_ELT --- Backtrace: ▆ 1. ├─EZbakR::EstimateFractions(ezbdo) 2. └─EZbakR:::EstimateFractions.EZbakRData(ezbdo) 3. ├─EZbakR::EstimateMutRates(...) 4. └─EZbakR:::EstimateMutRates.EZbakRData(...) 5. ├─...[] 6. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Linear-modeling.Rmd' failed with diagnostics: attempt access index 4/4 in VECTOR_ELT --- failed re-building 'Linear-modeling.Rmd' --- re-building 'Quickstart.Rmd' using rmarkdown Quitting from Quickstart.Rmd:134-141 [unnamed-chunk-5] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rlang_error> Error in `[.data.table`: ! attempt access index 4/4 in VECTOR_ELT --- Backtrace: ▆ 1. ├─EZbakR::EstimateFractions(ezbdo, features = "feature") 2. └─EZbakR:::EstimateFractions.EZbakRData(ezbdo, features = "feature") 3. ├─EZbakR::EstimateMutRates(...) 4. └─EZbakR:::EstimateMutRates.EZbakRData(...) 5. ├─...[] 6. └─data.table:::`[.data.table`(...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'Quickstart.Rmd' failed with diagnostics: attempt access index 4/4 in VECTOR_ELT --- failed re-building 'Quickstart.Rmd' SUMMARY: processing the following files failed: 'EZDynamics.Rmd' 'EZQC.Rmd' 'EZget.Rmd' 'EstimateFractions.Rmd' 'EstimateKinetics.Rmd' 'Linear-modeling.Rmd' 'Quickstart.Rmd' Error: Vignette re-building failed. Execution halted Flavor: r-devel-windows-x86_64

Version: 0.1.0
Check: package dependencies
Result: ERROR Package required but not available: ‘tximport’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual. Flavors: r-release-macos-arm64, r-oldrel-macos-arm64