Last updated on 2025-12-20 11:50:21 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.1.0 | 15.12 | 192.28 | 207.40 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.1.0 | 8.61 | 134.16 | 142.77 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.1.0 | 28.00 | 273.60 | 301.60 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.1.0 | 27.00 | 267.59 | 294.59 | ERROR | |
| r-devel-windows-x86_64 | 0.1.0 | 17.00 | 572.00 | 589.00 | OK | |
| r-patched-linux-x86_64 | 0.1.0 | 15.98 | 603.27 | 619.25 | OK | |
| r-release-linux-x86_64 | 0.1.0 | 16.83 | 592.90 | 609.73 | OK | |
| r-release-macos-arm64 | 0.1.0 | 4.00 | ERROR | |||
| r-release-macos-x86_64 | 0.1.0 | 8.00 | 292.00 | 300.00 | OK | |
| r-release-windows-x86_64 | 0.1.0 | 18.00 | 536.00 | 554.00 | OK | |
| r-oldrel-macos-arm64 | 0.1.0 | 9.00 | ERROR | |||
| r-oldrel-macos-x86_64 | 0.1.0 | 8.00 | 284.00 | 292.00 | OK | |
| r-oldrel-windows-x86_64 | 0.1.0 | 25.00 | 713.00 | 738.00 | OK |
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