Last updated on 2025-09-28 13:49:43 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.0 | 17.12 | 160.81 | 177.93 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.0.0 | 12.17 | 105.87 | 118.04 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.0.0 | 269.66 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.0 | 272.26 | ERROR | |||
| r-devel-windows-x86_64 | 2.0.0 | 20.00 | 175.00 | 195.00 | ERROR | |
| r-patched-linux-x86_64 | 2.0.0 | 18.98 | 150.67 | 169.65 | ERROR | |
| r-release-linux-x86_64 | 2.0.0 | 17.40 | 148.64 | 166.04 | ERROR | |
| r-release-macos-arm64 | 2.0.0 | 78.00 | OK | |||
| r-release-macos-x86_64 | 2.0.0 | 158.00 | OK | |||
| r-release-windows-x86_64 | 2.0.0 | 21.00 | 167.00 | 188.00 | ERROR | |
| r-oldrel-macos-arm64 | 2.0.0 | 73.00 | OK | |||
| r-oldrel-macos-x86_64 | 2.0.0 | 99.00 | OK | |||
| r-oldrel-windows-x86_64 | 2.0.0 | 27.00 | 217.00 | 244.00 | ERROR |
Version: 2.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [36s/46s]
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(normfluodbf)
== Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
If you find this package useful, please leave a star:
https://github.com/AlphaPrime7/normfluodbf
If you want to support me in my learning and development journey:
https://www.buymeacoffee.com/tingweiadeck
If you encounter a bug or want to request an enhancement please file an issue at:
https://github.com/AlphaPrime7/normfluodbf/issues
Thank you for using normfluodbf!
Attaching package: 'normfluodbf'
The following object is masked from 'package:stats':
step
The following object is masked from 'package:utils':
demo
The following object is masked from 'package:base':
subset
>
> test_check("normfluodbf")
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "27"
Crikee, some values in your original data violate thresholds 🐷 🐫
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Data Initialized step DONE...
DONE (0 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
List of 9
$ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
..$ well : chr [1:96] "A1" "A2" "A3" "A4" ...
..$ sample : logi [1:96] NA NA NA NA NA NA ...
..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
$ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ...
..$ well_row : chr [1:1500] "A" "A" "A" "A" ...
..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
$ steps : num 0
$ status : num 5
$ dirty : logi TRUE
$ version : chr "2.0.0"
$ params :List of 3
..$ GENERAL :List of 5
.. ..$ X_VAR_ONE : chr "Time"
.. ..$ X_VAR_TWO : chr "Cycle_Number"
.. ..$ Y_VAR : chr "FLUORESCENCE"
.. ..$ X_VAR_ONE_LABEL: chr "TIME"
.. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
..$ THRESHOLDS:List of 4
.. ..$ MAX_FLUOR : num 65536
.. ..$ MIN_FLUOR : num 128
.. ..$ CUTOFF_UPPER_LIMIT: num 32768
.. ..$ CUTOFF_LOWER_LIMIT: num 4096
..$ COLORS :List of 4
.. ..$ POS : chr "#7FFFD4"
.. ..$ TEST : chr "#0000CD"
.. ..$ NEG : chr "#EE3B3B"
.. ..$ NEUTRAL: chr "#BF3EFF"
$ dataset_name: chr "dat_1"
$ data_summary: chr "36 Wells Used"
- attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:5"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: remove_outliers"
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
"gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
`actual`: "gg"
`expected`: "ggplot2::ggplot"
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/22s]
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(normfluodbf)
== Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
If you find this package useful, please leave a star:
https://github.com/AlphaPrime7/normfluodbf
If you want to support me in my learning and development journey:
https://www.buymeacoffee.com/tingweiadeck
If you encounter a bug or want to request an enhancement please file an issue at:
https://github.com/AlphaPrime7/normfluodbf/issues
Thank you for using normfluodbf!
Attaching package: 'normfluodbf'
The following object is masked from 'package:stats':
step
The following object is masked from 'package:utils':
demo
The following object is masked from 'package:base':
subset
>
> test_check("normfluodbf")
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "27"
Crikee, some values in your original data violate thresholds 🐷 🐫
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Data Initialized step DONE...
DONE (0 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
List of 9
$ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
..$ well : chr [1:96] "A1" "A2" "A3" "A4" ...
..$ sample : logi [1:96] NA NA NA NA NA NA ...
..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
$ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ...
..$ well_row : chr [1:1500] "A" "A" "A" "A" ...
..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
$ steps : num 0
$ status : num 5
$ dirty : logi TRUE
$ version : chr "2.0.0"
$ params :List of 3
..$ GENERAL :List of 5
.. ..$ X_VAR_ONE : chr "Time"
.. ..$ X_VAR_TWO : chr "Cycle_Number"
.. ..$ Y_VAR : chr "FLUORESCENCE"
.. ..$ X_VAR_ONE_LABEL: chr "TIME"
.. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
..$ THRESHOLDS:List of 4
.. ..$ MAX_FLUOR : num 65536
.. ..$ MIN_FLUOR : num 128
.. ..$ CUTOFF_UPPER_LIMIT: num 32768
.. ..$ CUTOFF_LOWER_LIMIT: num 4096
..$ COLORS :List of 4
.. ..$ POS : chr "#7FFFD4"
.. ..$ TEST : chr "#0000CD"
.. ..$ NEG : chr "#EE3B3B"
.. ..$ NEUTRAL: chr "#BF3EFF"
$ dataset_name: chr "dat_1"
$ data_summary: chr "36 Wells Used"
- attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:5"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: remove_outliers"
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
"gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
`actual`: "gg"
`expected`: "ggplot2::ggplot"
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [55s/124s]
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(normfluodbf)
== Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
If you find this package useful, please leave a star:
https://github.com/AlphaPrime7/normfluodbf
If you want to support me in my learning and development journey:
https://www.buymeacoffee.com/tingweiadeck
If you encounter a bug or want to request an enhancement please file an issue at:
https://github.com/AlphaPrime7/normfluodbf/issues
Thank you for using normfluodbf!
Attaching package: 'normfluodbf'
The following object is masked from 'package:stats':
step
The following object is masked from 'package:utils':
demo
The following object is masked from 'package:base':
subset
>
> test_check("normfluodbf")
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "27"
Crikee, some values in your original data violate thresholds 🐷 🐫
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Data Initialized step DONE...
DONE (0 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
List of 9
$ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
..$ well : chr [1:96] "A1" "A2" "A3" "A4" ...
..$ sample : logi [1:96] NA NA NA NA NA NA ...
..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
$ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ...
..$ well_row : chr [1:1500] "A" "A" "A" "A" ...
..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
$ steps : num 0
$ status : num 5
$ dirty : logi TRUE
$ version : chr "2.0.0"
$ params :List of 3
..$ GENERAL :List of 5
.. ..$ X_VAR_ONE : chr "Time"
.. ..$ X_VAR_TWO : chr "Cycle_Number"
.. ..$ Y_VAR : chr "FLUORESCENCE"
.. ..$ X_VAR_ONE_LABEL: chr "TIME"
.. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
..$ THRESHOLDS:List of 4
.. ..$ MAX_FLUOR : num 65536
.. ..$ MIN_FLUOR : num 128
.. ..$ CUTOFF_UPPER_LIMIT: num 32768
.. ..$ CUTOFF_LOWER_LIMIT: num 4096
..$ COLORS :List of 4
.. ..$ POS : chr "#7FFFD4"
.. ..$ TEST : chr "#0000CD"
.. ..$ NEG : chr "#EE3B3B"
.. ..$ NEUTRAL: chr "#BF3EFF"
$ dataset_name: chr "dat_1"
$ data_summary: chr "36 Wells Used"
- attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:5"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: remove_outliers"
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
"gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
`actual`: "gg"
`expected`: "ggplot2::ggplot"
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [54s/63s]
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(normfluodbf)
== Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
If you find this package useful, please leave a star:
https://github.com/AlphaPrime7/normfluodbf
If you want to support me in my learning and development journey:
https://www.buymeacoffee.com/tingweiadeck
If you encounter a bug or want to request an enhancement please file an issue at:
https://github.com/AlphaPrime7/normfluodbf/issues
Thank you for using normfluodbf!
Attaching package: 'normfluodbf'
The following object is masked from 'package:stats':
step
The following object is masked from 'package:utils':
demo
The following object is masked from 'package:base':
subset
>
> test_check("normfluodbf")
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "27"
Crikee, some values in your original data violate thresholds 🐷 🐫
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Data Initialized step DONE...
DONE (0 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
List of 9
$ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
..$ well : chr [1:96] "A1" "A2" "A3" "A4" ...
..$ sample : logi [1:96] NA NA NA NA NA NA ...
..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
$ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ...
..$ well_row : chr [1:1500] "A" "A" "A" "A" ...
..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
$ steps : num 0
$ status : num 5
$ dirty : logi TRUE
$ version : chr "2.0.0"
$ params :List of 3
..$ GENERAL :List of 5
.. ..$ X_VAR_ONE : chr "Time"
.. ..$ X_VAR_TWO : chr "Cycle_Number"
.. ..$ Y_VAR : chr "FLUORESCENCE"
.. ..$ X_VAR_ONE_LABEL: chr "TIME"
.. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
..$ THRESHOLDS:List of 4
.. ..$ MAX_FLUOR : num 65536
.. ..$ MIN_FLUOR : num 128
.. ..$ CUTOFF_UPPER_LIMIT: num 32768
.. ..$ CUTOFF_LOWER_LIMIT: num 4096
..$ COLORS :List of 4
.. ..$ POS : chr "#7FFFD4"
.. ..$ TEST : chr "#0000CD"
.. ..$ NEG : chr "#EE3B3B"
.. ..$ NEUTRAL: chr "#BF3EFF"
$ dataset_name: chr "dat_1"
$ data_summary: chr "36 Wells Used"
- attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:5"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: remove_outliers"
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
"gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
`actual`: "gg"
`expected`: "ggplot2::ggplot"
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [26s]
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(normfluodbf)
== Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
If you find this package useful, please leave a star:
https://github.com/AlphaPrime7/normfluodbf
If you want to support me in my learning and development journey:
https://www.buymeacoffee.com/tingweiadeck
If you encounter a bug or want to request an enhancement please file an issue at:
https://github.com/AlphaPrime7/normfluodbf/issues
Thank you for using normfluodbf!
Attaching package: 'normfluodbf'
The following object is masked from 'package:stats':
step
The following object is masked from 'package:utils':
demo
The following object is masked from 'package:base':
subset
>
> test_check("normfluodbf")
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "27"
Crikee, some values in your original data violate thresholds 🐷 🐫
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Data Initialized step DONE...
DONE (0 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
List of 9
$ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
..$ well : chr [1:96] "A1" "A2" "A3" "A4" ...
..$ sample : logi [1:96] NA NA NA NA NA NA ...
..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
$ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ...
..$ well_row : chr [1:1500] "A" "A" "A" "A" ...
..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
$ steps : num 0
$ status : num 5
$ dirty : logi TRUE
$ version : chr "2.0.0"
$ params :List of 3
..$ GENERAL :List of 5
.. ..$ X_VAR_ONE : chr "Time"
.. ..$ X_VAR_TWO : chr "Cycle_Number"
.. ..$ Y_VAR : chr "FLUORESCENCE"
.. ..$ X_VAR_ONE_LABEL: chr "TIME"
.. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
..$ THRESHOLDS:List of 4
.. ..$ MAX_FLUOR : num 65536
.. ..$ MIN_FLUOR : num 128
.. ..$ CUTOFF_UPPER_LIMIT: num 32768
.. ..$ CUTOFF_LOWER_LIMIT: num 4096
..$ COLORS :List of 4
.. ..$ POS : chr "#7FFFD4"
.. ..$ TEST : chr "#0000CD"
.. ..$ NEG : chr "#EE3B3B"
.. ..$ NEUTRAL: chr "#BF3EFF"
$ dataset_name: chr "dat_1"
$ data_summary: chr "36 Wells Used"
- attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:5"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: remove_outliers"
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
"gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
`actual`: "gg"
`expected`: "ggplot2::ggplot"
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [33s/40s]
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(normfluodbf)
== Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
If you find this package useful, please leave a star:
https://github.com/AlphaPrime7/normfluodbf
If you want to support me in my learning and development journey:
https://www.buymeacoffee.com/tingweiadeck
If you encounter a bug or want to request an enhancement please file an issue at:
https://github.com/AlphaPrime7/normfluodbf/issues
Thank you for using normfluodbf!
Attaching package: 'normfluodbf'
The following object is masked from 'package:stats':
step
The following object is masked from 'package:utils':
demo
The following object is masked from 'package:base':
subset
>
> test_check("normfluodbf")
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "27"
Crikee, some values in your original data violate thresholds 🐷 🐫
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Data Initialized step DONE...
DONE (0 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
List of 9
$ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
..$ well : chr [1:96] "A1" "A2" "A3" "A4" ...
..$ sample : logi [1:96] NA NA NA NA NA NA ...
..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
$ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ...
..$ well_row : chr [1:1500] "A" "A" "A" "A" ...
..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
$ steps : num 0
$ status : num 5
$ dirty : logi TRUE
$ version : chr "2.0.0"
$ params :List of 3
..$ GENERAL :List of 5
.. ..$ X_VAR_ONE : chr "Time"
.. ..$ X_VAR_TWO : chr "Cycle_Number"
.. ..$ Y_VAR : chr "FLUORESCENCE"
.. ..$ X_VAR_ONE_LABEL: chr "TIME"
.. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
..$ THRESHOLDS:List of 4
.. ..$ MAX_FLUOR : num 65536
.. ..$ MIN_FLUOR : num 128
.. ..$ CUTOFF_UPPER_LIMIT: num 32768
.. ..$ CUTOFF_LOWER_LIMIT: num 4096
..$ COLORS :List of 4
.. ..$ POS : chr "#7FFFD4"
.. ..$ TEST : chr "#0000CD"
.. ..$ NEG : chr "#EE3B3B"
.. ..$ NEUTRAL: chr "#BF3EFF"
$ dataset_name: chr "dat_1"
$ data_summary: chr "36 Wells Used"
- attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:5"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: remove_outliers"
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
"gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
`actual`: "gg"
`expected`: "ggplot2::ggplot"
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 2.0.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [34s/38s]
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(normfluodbf)
== Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
If you find this package useful, please leave a star:
https://github.com/AlphaPrime7/normfluodbf
If you want to support me in my learning and development journey:
https://www.buymeacoffee.com/tingweiadeck
If you encounter a bug or want to request an enhancement please file an issue at:
https://github.com/AlphaPrime7/normfluodbf/issues
Thank you for using normfluodbf!
Attaching package: 'normfluodbf'
The following object is masked from 'package:stats':
step
The following object is masked from 'package:utils':
demo
The following object is masked from 'package:base':
subset
>
> test_check("normfluodbf")
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "27"
Crikee, some values in your original data violate thresholds 🐷 🐫
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Data Initialized step DONE...
DONE (0 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
List of 9
$ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
..$ well : chr [1:96] "A1" "A2" "A3" "A4" ...
..$ sample : logi [1:96] NA NA NA NA NA NA ...
..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
$ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ...
..$ well_row : chr [1:1500] "A" "A" "A" "A" ...
..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
$ steps : num 0
$ status : num 5
$ dirty : logi TRUE
$ version : chr "2.0.0"
$ params :List of 3
..$ GENERAL :List of 5
.. ..$ X_VAR_ONE : chr "Time"
.. ..$ X_VAR_TWO : chr "Cycle_Number"
.. ..$ Y_VAR : chr "FLUORESCENCE"
.. ..$ X_VAR_ONE_LABEL: chr "TIME"
.. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
..$ THRESHOLDS:List of 4
.. ..$ MAX_FLUOR : num 65536
.. ..$ MIN_FLUOR : num 128
.. ..$ CUTOFF_UPPER_LIMIT: num 32768
.. ..$ CUTOFF_LOWER_LIMIT: num 4096
..$ COLORS :List of 4
.. ..$ POS : chr "#7FFFD4"
.. ..$ TEST : chr "#0000CD"
.. ..$ NEG : chr "#EE3B3B"
.. ..$ NEUTRAL: chr "#BF3EFF"
$ dataset_name: chr "dat_1"
$ data_summary: chr "36 Wells Used"
- attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:5"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: remove_outliers"
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
"gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
`actual`: "gg"
`expected`: "ggplot2::ggplot"
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 2.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [25s]
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(normfluodbf)
== Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
If you find this package useful, please leave a star:
https://github.com/AlphaPrime7/normfluodbf
If you want to support me in my learning and development journey:
https://www.buymeacoffee.com/tingweiadeck
If you encounter a bug or want to request an enhancement please file an issue at:
https://github.com/AlphaPrime7/normfluodbf/issues
Thank you for using normfluodbf!
Attaching package: 'normfluodbf'
The following object is masked from 'package:stats':
step
The following object is masked from 'package:utils':
demo
The following object is masked from 'package:base':
subset
>
> test_check("normfluodbf")
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "27"
Crikee, some values in your original data violate thresholds 🐷 🐫
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Data Initialized step DONE...
DONE (0 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
List of 9
$ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
..$ well : chr [1:96] "A1" "A2" "A3" "A4" ...
..$ sample : logi [1:96] NA NA NA NA NA NA ...
..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
$ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ...
..$ well_row : chr [1:1500] "A" "A" "A" "A" ...
..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
$ steps : num 0
$ status : num 5
$ dirty : logi TRUE
$ version : chr "2.0.0"
$ params :List of 3
..$ GENERAL :List of 5
.. ..$ X_VAR_ONE : chr "Time"
.. ..$ X_VAR_TWO : chr "Cycle_Number"
.. ..$ Y_VAR : chr "FLUORESCENCE"
.. ..$ X_VAR_ONE_LABEL: chr "TIME"
.. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
..$ THRESHOLDS:List of 4
.. ..$ MAX_FLUOR : num 65536
.. ..$ MIN_FLUOR : num 128
.. ..$ CUTOFF_UPPER_LIMIT: num 32768
.. ..$ CUTOFF_LOWER_LIMIT: num 4096
..$ COLORS :List of 4
.. ..$ POS : chr "#7FFFD4"
.. ..$ TEST : chr "#0000CD"
.. ..$ NEG : chr "#EE3B3B"
.. ..$ NEUTRAL: chr "#BF3EFF"
$ dataset_name: chr "dat_1"
$ data_summary: chr "36 Wells Used"
- attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:5"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: remove_outliers"
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
"gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
`actual`: "gg"
`expected`: "ggplot2::ggplot"
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 2.0.0
Check: tests
Result: ERROR
Running 'testthat.R' [40s]
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(normfluodbf)
== Welcome to normfluodbf - Developed by Tingwei Adeck and Tesla Adeck (Jesus Followers) ===========================================================================
If you find this package useful, please leave a star:
https://github.com/AlphaPrime7/normfluodbf
If you want to support me in my learning and development journey:
https://www.buymeacoffee.com/tingweiadeck
If you encounter a bug or want to request an enhancement please file an issue at:
https://github.com/AlphaPrime7/normfluodbf/issues
Thank you for using normfluodbf!
Attaching package: 'normfluodbf'
The following object is masked from 'package:stats':
step
The following object is masked from 'package:utils':
demo
The following object is masked from 'package:base':
subset
>
> test_check("normfluodbf")
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "27"
Crikee, some values in your original data violate thresholds 🐷 🐫
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "A01"
[[2]]
[1] "A02"
[[3]]
[1] "A03"
[[4]]
[1] "B01"
[[5]]
[1] "B02"
[[6]]
[1] "B03"
[[7]]
[1] "C01"
[[8]]
[1] "C02"
[[9]]
[1] "C03"
Data Initialized step DONE...
DONE (0 seconds)
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
List of 9
$ plate_meta : tibble [96 x 5] (S3: tbl_df/tbl/data.frame)
..$ well : chr [1:96] "A1" "A2" "A3" "A4" ...
..$ sample : logi [1:96] NA NA NA NA NA NA ...
..$ well_row: Factor w/ 8 levels "A","B","C","D",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ well_col: Factor w/ 12 levels "1","2","3","4",..: 1 2 3 4 5 6 7 8 9 10 ...
..$ used : logi [1:96] FALSE FALSE FALSE FALSE FALSE FALSE ...
$ plate_data : md_nrmf_ [1,500 x 8] (S3: mod_normfluodbf_data/tbl_df/tbl/data.frame)
..$ well : chr [1:1500] "A1" "A1" "A1" "A1" ...
..$ well_row : chr [1:1500] "A" "A" "A" "A" ...
..$ well_col : Factor w/ 12 levels "1","10","11",..: 1 1 1 1 1 1 1 1 1 1 ...
..$ used : logi [1:1500] TRUE TRUE TRUE TRUE TRUE TRUE ...
..$ Cycle_Number : num [1:1500] 1 2 3 4 5 6 7 8 9 10 ...
..$ fluor_values : num [1:1500] 1 0.872 0.788 0.715 0.731 ...
..$ outlier : logi [1:1500] FALSE FALSE FALSE FALSE FALSE FALSE ...
..$ outlier_color: chr [1:1500] "#EE3B3B" "#EE3B3B" "#EE3B3B" "#EE3B3B" ...
$ steps : num 0
$ status : num 5
$ dirty : logi TRUE
$ version : chr "2.0.0"
$ params :List of 3
..$ GENERAL :List of 5
.. ..$ X_VAR_ONE : chr "Time"
.. ..$ X_VAR_TWO : chr "Cycle_Number"
.. ..$ Y_VAR : chr "FLUORESCENCE"
.. ..$ X_VAR_ONE_LABEL: chr "TIME"
.. ..$ X_VAR_TWO_LABEL: chr "CYCLE NUMBER"
..$ THRESHOLDS:List of 4
.. ..$ MAX_FLUOR : num 65536
.. ..$ MIN_FLUOR : num 128
.. ..$ CUTOFF_UPPER_LIMIT: num 32768
.. ..$ CUTOFF_LOWER_LIMIT: num 4096
..$ COLORS :List of 4
.. ..$ POS : chr "#7FFFD4"
.. ..$ TEST : chr "#0000CD"
.. ..$ NEG : chr "#EE3B3B"
.. ..$ NEUTRAL: chr "#BF3EFF"
$ dataset_name: chr "dat_1"
$ data_summary: chr "36 Wells Used"
- attr(*, "class")= chr [1:3] "96well_plate" "normfluodbf_plate" "list"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (2 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:4"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
Crikee, some values in your original data violate thresholds 🐷 🐫
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
The upload_data step needs to be completed
Initializing Data ...
[1] "Outlier wells (Mixtures might be problematic and should be investigated with mixtools)"
[[1]]
[1] "C9"
Data Initialized step DONE...
DONE (1 seconds)
[1] "Steps left:5"
[1] "Next step function: format_plate_data"
Formating Plate Data ...
Data Formatted step DONE...
DONE (0 seconds)
[1] "Next step function: remove_outliers"
[1] "Next step function: normalize_by_well"
Normalizing Data ...
Data Normalized step DONE...
DONE (0 seconds)
[1] "Next step function: modify_plate_data"
[1] "Next step function: analyze_ready"
Process complete
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_plot.R:21:3'): test normfluodbf plot ─────────────────────────
"gg" (`actual`) not equal to class(plt.obj)[1] (`expected`).
`actual`: "gg"
`expected`: "ggplot2::ggplot"
[ FAIL 1 | WARN 617 | SKIP 0 | PASS 23 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.