Last updated on 2025-09-28 11:54:52 CEST.
| Package | ERROR | OK |
|---|---|---|
| normfluodbf | 9 | 4 |
| tidyDenovix | 13 |
Current CRAN status: ERROR: 9, OK: 4
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
Current CRAN status: OK: 13
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.
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