Last updated on 2025-12-21 11:50:30 CET.
| Package | ERROR | OK |
|---|---|---|
| MEAanalysis | 4 | 9 |
Current CRAN status: ERROR: 4, OK: 9
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘MEAanalysis-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_electrode_dataset
> ### Title: Create Electrode Data Set
> ### Aliases: create_electrode_dataset
>
> ### ** Examples
>
> output_electrode_burst <- create_electrode_dataset(
+ data_path = system.file("extdata", "input_electrode_burst.csv",
+ package = "MEAanalysis"),
+ recording_identifier = "burst_recording_1")
New names:
• `` -> `...7`
• `` -> `...8`
• `` -> `...9`
• `` -> `...10`
• `` -> `...11`
• `` -> `...12`
• `` -> `...13`
• `` -> `...14`
• `` -> `...15`
• `` -> `...16`
• `` -> `...17`
• `` -> `...18`
• `` -> `...19`
• `` -> `...20`
• `` -> `...21`
• `` -> `...22`
• `` -> `...23`
• `` -> `...24`
• `` -> `...25`
Error in `[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), :
attempt access index 4/4 in VECTOR_ELT
Calls: create_electrode_dataset -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [7s/7s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(MEAanalysis)
>
> test_check("MEAanalysis")
New names:
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
* `` -> `...13`
* `` -> `...14`
* `` -> `...15`
* `` -> `...16`
* `` -> `...17`
* `` -> `...18`
* `` -> `...19`
* `` -> `...20`
* `` -> `...21`
* `` -> `...22`
* `` -> `...23`
* `` -> `...24`
* `` -> `...25`
Saving _problems/test-create_electrode_dataset-4.R
New names:
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
* `` -> `...13`
* `` -> `...14`
* `` -> `...15`
* `` -> `...16`
* `` -> `...17`
* `` -> `...18`
* `` -> `...19`
* `` -> `...20`
* `` -> `...21`
* `` -> `...22`
* `` -> `...23`
* `` -> `...24`
* `` -> `...25`
Saving _problems/test-create_electrode_dataset-12.R
New names:
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
* `` -> `...13`
* `` -> `...14`
* `` -> `...15`
* `` -> `...16`
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* `` -> `...20`
* `` -> `...21`
* `` -> `...22`
* `` -> `...23`
* `` -> `...24`
* `` -> `...25`
Saving _problems/test-create_electrode_dataset-31.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 11 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-create_electrode_dataset.R:4:3'): create_electrode_dataset output is a datatable ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:4:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
── Error ('test-create_electrode_dataset.R:12:3'): create_electrode_dataset column classes are correct ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:12:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
── Error ('test-create_electrode_dataset.R:31:3'): create_electrode_dataset output does not contain missing values ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:31:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 11 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘MEA_single_electrode_barchart.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-19 13:58:04 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
Quitting from MEA_single_electrode_barchart.Rmd:46-54 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...)
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MEA_single_electrode_barchart.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘MEA_single_electrode_barchart.Rmd’
--- re-building ‘MEA_synchrony_index_heatmap.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-19 13:58:04 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘MEA_synchrony_index_heatmap.Rmd’
--- re-building ‘MEA_well_barchart.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-19 13:58:04 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
Quitting from MEA_well_barchart.Rmd:46-54 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...)
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MEA_well_barchart.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘MEA_well_barchart.Rmd’
SUMMARY: processing the following files failed:
‘MEA_single_electrode_barchart.Rmd’ ‘MEA_well_barchart.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(MEAanalysis)
>
> test_check("MEAanalysis")
New names:
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
* `` -> `...13`
* `` -> `...14`
* `` -> `...15`
* `` -> `...16`
* `` -> `...17`
* `` -> `...18`
* `` -> `...19`
* `` -> `...20`
* `` -> `...21`
* `` -> `...22`
* `` -> `...23`
* `` -> `...24`
* `` -> `...25`
Saving _problems/test-create_electrode_dataset-4.R
New names:
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
* `` -> `...13`
* `` -> `...14`
* `` -> `...15`
* `` -> `...16`
* `` -> `...17`
* `` -> `...18`
* `` -> `...19`
* `` -> `...20`
* `` -> `...21`
* `` -> `...22`
* `` -> `...23`
* `` -> `...24`
* `` -> `...25`
Saving _problems/test-create_electrode_dataset-12.R
New names:
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
* `` -> `...13`
* `` -> `...14`
* `` -> `...15`
* `` -> `...16`
* `` -> `...17`
* `` -> `...18`
* `` -> `...19`
* `` -> `...20`
* `` -> `...21`
* `` -> `...22`
* `` -> `...23`
* `` -> `...24`
* `` -> `...25`
Saving _problems/test-create_electrode_dataset-31.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 11 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-create_electrode_dataset.R:4:3'): create_electrode_dataset output is a datatable ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:4:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
── Error ('test-create_electrode_dataset.R:12:3'): create_electrode_dataset column classes are correct ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:12:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
── Error ('test-create_electrode_dataset.R:31:3'): create_electrode_dataset output does not contain missing values ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:31:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 11 ]
Error:
! Test failures.
Execution halted
Flavor: 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 ‘MEA_single_electrode_barchart.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-20 11:07:40 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
Quitting from MEA_single_electrode_barchart.Rmd:46-54 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...)
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MEA_single_electrode_barchart.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘MEA_single_electrode_barchart.Rmd’
--- re-building ‘MEA_synchrony_index_heatmap.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-20 11:07:40 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘MEA_synchrony_index_heatmap.Rmd’
--- re-building ‘MEA_well_barchart.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-20 11:07:40 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
Quitting from MEA_well_barchart.Rmd:46-54 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...)
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MEA_well_barchart.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘MEA_well_barchart.Rmd’
SUMMARY: processing the following files failed:
‘MEA_single_electrode_barchart.Rmd’ ‘MEA_well_barchart.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.1.0
Check: dependencies in R code
Result: NOTE
Namespaces in Imports field not imported from:
‘kableExtra’ ‘knitr’ ‘reshape2’ ‘tidyverse’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: examples
Result: ERROR
Running examples in ‘MEAanalysis-Ex.R’ failed
The error most likely occurred in:
> ### Name: create_electrode_dataset
> ### Title: Create Electrode Data Set
> ### Aliases: create_electrode_dataset
>
> ### ** Examples
>
> output_electrode_burst <- create_electrode_dataset(
+ data_path = system.file("extdata", "input_electrode_burst.csv",
+ package = "MEAanalysis"),
+ recording_identifier = "burst_recording_1")
New names:
• `` -> `...7`
• `` -> `...8`
• `` -> `...9`
• `` -> `...10`
• `` -> `...11`
• `` -> `...12`
• `` -> `...13`
• `` -> `...14`
• `` -> `...15`
• `` -> `...16`
• `` -> `...17`
• `` -> `...18`
• `` -> `...19`
• `` -> `...20`
• `` -> `...21`
• `` -> `...22`
• `` -> `...23`
• `` -> `...24`
• `` -> `...25`
Error in `[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), :
attempt access index 4/4 in VECTOR_ELT
Calls: create_electrode_dataset -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(MEAanalysis)
>
> test_check("MEAanalysis")
New names:
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
* `` -> `...13`
* `` -> `...14`
* `` -> `...15`
* `` -> `...16`
* `` -> `...17`
* `` -> `...18`
* `` -> `...19`
* `` -> `...20`
* `` -> `...21`
* `` -> `...22`
* `` -> `...23`
* `` -> `...24`
* `` -> `...25`
Saving _problems/test-create_electrode_dataset-4.R
New names:
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
* `` -> `...13`
* `` -> `...14`
* `` -> `...15`
* `` -> `...16`
* `` -> `...17`
* `` -> `...18`
* `` -> `...19`
* `` -> `...20`
* `` -> `...21`
* `` -> `...22`
* `` -> `...23`
* `` -> `...24`
* `` -> `...25`
Saving _problems/test-create_electrode_dataset-12.R
New names:
* `` -> `...7`
* `` -> `...8`
* `` -> `...9`
* `` -> `...10`
* `` -> `...11`
* `` -> `...12`
* `` -> `...13`
* `` -> `...14`
* `` -> `...15`
* `` -> `...16`
* `` -> `...17`
* `` -> `...18`
* `` -> `...19`
* `` -> `...20`
* `` -> `...21`
* `` -> `...22`
* `` -> `...23`
* `` -> `...24`
* `` -> `...25`
Saving _problems/test-create_electrode_dataset-31.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 11 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-create_electrode_dataset.R:4:3'): create_electrode_dataset output is a datatable ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:4:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
── Error ('test-create_electrode_dataset.R:12:3'): create_electrode_dataset column classes are correct ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:12:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
── Error ('test-create_electrode_dataset.R:31:3'): create_electrode_dataset output does not contain missing values ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:31:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 11 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘MEA_single_electrode_barchart.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-19 09:10:21 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/data/gannet/ripley/R/packages/tests-clang/MEAanalysis.Rcheck/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
Quitting from MEA_single_electrode_barchart.Rmd:46-54 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...)
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MEA_single_electrode_barchart.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘MEA_single_electrode_barchart.Rmd’
--- re-building ‘MEA_synchrony_index_heatmap.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-19 09:10:21 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/data/gannet/ripley/R/packages/tests-clang/MEAanalysis.Rcheck/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘MEA_synchrony_index_heatmap.Rmd’
--- re-building ‘MEA_well_barchart.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-19 09:10:21 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/data/gannet/ripley/R/packages/tests-clang/MEAanalysis.Rcheck/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
Quitting from MEA_well_barchart.Rmd:46-54 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...)
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MEA_well_barchart.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘MEA_well_barchart.Rmd’
SUMMARY: processing the following files failed:
‘MEA_single_electrode_barchart.Rmd’ ‘MEA_well_barchart.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.1.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [10s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
>
> library(testthat)
> library(MEAanalysis)
>
> test_check("MEAanalysis")
New names:
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Saving _problems/test-create_electrode_dataset-4.R
New names:
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Saving _problems/test-create_electrode_dataset-12.R
New names:
* `` -> `...7`
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Saving _problems/test-create_electrode_dataset-31.R
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 11 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-create_electrode_dataset.R:4:3'): create_electrode_dataset output is a datatable ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:4:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
── Error ('test-create_electrode_dataset.R:12:3'): create_electrode_dataset column classes are correct ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:12:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
── Error ('test-create_electrode_dataset.R:31:3'): create_electrode_dataset output does not contain missing values ──
Error in ``[.data.table`(data_1, , `:=`(Recording_identifier, recording_identifier), by = Electrode)`: attempt access index 4/4 in VECTOR_ELT
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...) at test-create_electrode_dataset.R:31:3
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 11 ]
Error:
! Test failures.
Execution halted
Flavor: 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 ‘MEA_single_electrode_barchart.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-19 09:36:34 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/data/gannet/ripley/R/packages/tests-devel/MEAanalysis.Rcheck/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
Quitting from MEA_single_electrode_barchart.Rmd:46-54 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...)
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MEA_single_electrode_barchart.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘MEA_single_electrode_barchart.Rmd’
--- re-building ‘MEA_synchrony_index_heatmap.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-19 09:36:34 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/data/gannet/ripley/R/packages/tests-devel/MEAanalysis.Rcheck/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘MEA_synchrony_index_heatmap.Rmd’
--- re-building ‘MEA_well_barchart.Rmd’ using rmarkdown
Information on package 'MEAanalysis'
Description:
Package: MEAanalysis
Version: 0.1.0
Title: Analyse and Visualise Multi Electrode Array
Burst Data
Authors@R: person(given = "Emily", family = "Gordon",
role = c("aut", "cre"), email =
"emily.gordon@wadham.ox.ac.uk")
Maintainer: Emily Gordon <emily.gordon@wadham.ox.ac.uk>
Description: Analyse and visualise multi electrode array
data at the single electrode and whole well
level, downstream of 'AxIS Navigator 3.6.2
Software' processing. Compare bursting
parameters between time intervals and
recordings using the bar chart visualisation
functions. Compatible with 12- and 24- well
plates.
License: GPL (>= 2)
Imports: data.table (>= 1.15.4), dplyr (>= 1.1.4),
ggplot2 (>= 3.5.0), janitor (>= 2.2.0),
kableExtra (>= 1.4.0), knitr (>= 1.46),
readr (>= 2.1.5), readxl (>= 1.4.3),
reshape2 (>= 1.4.4), stringr (>= 1.5.1),
tidyr (>= 1.3.1), tidyverse (>= 2.0.0)
Depends: R (>= 4.3.0)
Encoding: UTF-8
RoxygenNote: 7.3.1
LazyData: true
Suggests: rmarkdown (>= 2.26), testthat (>= 3.2.1)
VignetteBuilder: knitr
Config/testthat/edition: 3
URL: https://egordon2.github.io/MEA-analysis-package/
BugReports: https://github.com/egordon2/MEA-analysis-package/issues
NeedsCompilation: no
Packaged: 2025-05-02 14:34:24 UTC; Emily Gordon
Author: Emily Gordon [aut, cre]
Repository: CRAN
Date/Publication: 2025-05-06 08:30:06 UTC
Built: R 4.6.0; ; 2025-12-19 09:36:34 UTC; unix
Index:
MEA_heatmap MEA_heatmap
create_electrode_dataset
Create Electrode Data Set
create_synchrony_dataset
Create Synchrony Data Set
electrode_burst_duration
Electrode Burst Duration
electrode_mean_burst_ISI
Electrode Mean Burst ISI
electrode_number_of_bursts
Electrode Number of Bursts
electrode_spikes_per_burst
Electrode Spikes per Burst
input_MEA_data Input dataset for electrode and well MEA
parameter functions.
input_electrode_barchart
Input dataset for single_electrode_barchart
function
input_heatmap_data Input dataset for MEA_heatmap function
input_well_barchart Input dataset for well_barchart function
single_electrode_barchart
Single Electrode Bar chart
well_barchart Well Bar chart
well_burst_duration Well Burst Duration
well_mean_burst_ISI Well Mean Burst ISI
well_number_of_bursts Well Number of Bursts
well_spikes_per_burst Well Spikes per Burst
Further information is available in the following vignettes in
directory
'/data/gannet/ripley/R/packages/tests-devel/MEAanalysis.Rcheck/MEAanalysis/doc':
MEA_single_electrode_barchart: MEA_single_electrode_barchart (source,
pdf)
MEA_synchrony_index_heatmap: MEA_synchrony_index_heatmap (source, pdf)
MEA_well_barchart: MEA_well_barchart (source, pdf)
Quitting from MEA_well_barchart.Rmd:46-54 [unnamed-chunk-3]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 4/4 in VECTOR_ELT
---
Backtrace:
▆
1. └─MEAanalysis::create_electrode_dataset(...)
2. ├─data_1[, `:=`(Recording_identifier, recording_identifier), by = Electrode]
3. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'MEA_well_barchart.Rmd' failed with diagnostics:
attempt access index 4/4 in VECTOR_ELT
--- failed re-building ‘MEA_well_barchart.Rmd’
SUMMARY: processing the following files failed:
‘MEA_single_electrode_barchart.Rmd’ ‘MEA_well_barchart.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc