Last updated on 2025-12-21 11:50:33 CET.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| bakR | 5 | 8 | |
| EZbakR | 6 | 7 |
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
Current CRAN status: ERROR: 6, OK: 7
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘EZbakR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### 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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
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
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
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