• 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 ‘MEAanalysis/DESCRIPTION’ ... OK
• this is package ‘MEAanalysis’ version ‘0.1.0’
• package encoding: UTF-8
• checking CRAN incoming feasibility ... [0s/1s] OK
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• checking package dependencies ... OK
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• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking whether package ‘MEAanalysis’ 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
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• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
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• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
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• checking R code for possible problems ... [14s/20s] OK
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• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [4s/6s] 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
• checking for unstated dependencies in ‘tests’ ... OK
• checking tests ... [7s/7s] 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`   * `` -> `...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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [16s/22s] 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
• 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