Last updated on 2025-09-13 13:50:27 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| clustur | 2 | 11 | |
| mpactr | 6 | 2 | 5 |
| phylotypr | 3 | 10 |
Current CRAN status: NOTE: 2, OK: 11
Version: 0.1.3
Check: installed package size
Result: NOTE
installed size is 19.5Mb
sub-directories of 1Mb or more:
libs 19.1Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Current CRAN status: ERROR: 6, NOTE: 2, OK: 5
Version: 0.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [130s/129s]
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(mpactr)
>
> test_check("mpactr")
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1303 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 796 ions failed the Blanks filter, 507 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method .
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1289 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 65 ions failed the mispicked filter, 1224 ions remain.
i Parsing 1224 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 698 ions failed the Blanks filter, 526 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1233 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 0 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 451 peaks for insource ions.
v 25 ions failed the insource filter, 426 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks for replicability across technical replicates.
v 279 ions failed the cv_filter filter, 954 ions remain.
i Parsing 954 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 384 ions failed the Blanks filter, 570 ions remain.
i Parsing 570 peaks for insource ions.
v 26 ions failed the insource filter, 544 ions remain.
Found duplicate compound values, will add a suffix to unique the value.
Found duplicate compound values, will add a suffix to unique the value.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 354 ions failed the Coculture filter, 879 ions remain.
Rows: 1306 Columns: 21
-- Column specification --------------------------------------------------------
Delimiter: ","
dbl (21): Compound, mz, rt, 102623_UM1848B_JC1_69_1_5004, 102623_UM1846B_Med...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 293 ions failed the Coculture filter, 191 ions remain.
i Parsing 191 peaks for insource ions.
v 15 ions failed the insource filter, 176 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-peak_table_formatter.R:32:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-qc_graph_pactr-class.R:32:3'): plot_QC_Tree generates the correct plot ──
class(plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
`actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
`expected[2:2]`: "ggplot"
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [109s/162s]
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(mpactr)
>
> test_check("mpactr")
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1303 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 796 ions failed the Blanks filter, 507 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method .
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1289 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 65 ions failed the mispicked filter, 1224 ions remain.
i Parsing 1224 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 698 ions failed the Blanks filter, 526 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1233 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 0 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 451 peaks for insource ions.
v 25 ions failed the insource filter, 426 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks for replicability across technical replicates.
v 279 ions failed the cv_filter filter, 954 ions remain.
i Parsing 954 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 384 ions failed the Blanks filter, 570 ions remain.
i Parsing 570 peaks for insource ions.
v 26 ions failed the insource filter, 544 ions remain.
Found duplicate compound values, will add a suffix to unique the value.
Found duplicate compound values, will add a suffix to unique the value.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 354 ions failed the Coculture filter, 879 ions remain.
Rows: 1306 Columns: 21
-- Column specification --------------------------------------------------------
Delimiter: ","
dbl (21): Compound, mz, rt, 102623_UM1848B_JC1_69_1_5004, 102623_UM1846B_Med...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 293 ions failed the Coculture filter, 191 ions remain.
i Parsing 191 peaks for insource ions.
v 15 ions failed the insource filter, 176 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-peak_table_formatter.R:32:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-qc_graph_pactr-class.R:32:3'): plot_QC_Tree generates the correct plot ──
class(plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
`actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
`expected[2:2]`: "ggplot"
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [118s/121s]
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(mpactr)
>
> test_check("mpactr")
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1303 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 796 ions failed the Blanks filter, 507 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method .
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1289 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 65 ions failed the mispicked filter, 1224 ions remain.
i Parsing 1224 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 698 ions failed the Blanks filter, 526 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1233 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 0 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 451 peaks for insource ions.
v 25 ions failed the insource filter, 426 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks for replicability across technical replicates.
v 279 ions failed the cv_filter filter, 954 ions remain.
i Parsing 954 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 384 ions failed the Blanks filter, 570 ions remain.
i Parsing 570 peaks for insource ions.
v 26 ions failed the insource filter, 544 ions remain.
Found duplicate compound values, will add a suffix to unique the value.
Found duplicate compound values, will add a suffix to unique the value.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 354 ions failed the Coculture filter, 879 ions remain.
Rows: 1306 Columns: 21
-- Column specification --------------------------------------------------------
Delimiter: ","
dbl (21): Compound, mz, rt, 102623_UM1848B_JC1_69_1_5004, 102623_UM1846B_Med...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 293 ions failed the Coculture filter, 191 ions remain.
i Parsing 191 peaks for insource ions.
v 15 ions failed the insource filter, 176 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-peak_table_formatter.R:32:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-qc_graph_pactr-class.R:32:3'): plot_QC_Tree generates the correct plot ──
class(plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
`actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
`expected[2:2]`: "ggplot"
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [109s/134s]
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(mpactr)
>
> test_check("mpactr")
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1303 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 796 ions failed the Blanks filter, 507 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method .
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1289 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 65 ions failed the mispicked filter, 1224 ions remain.
i Parsing 1224 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 698 ions failed the Blanks filter, 526 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1233 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 0 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 451 peaks for insource ions.
v 25 ions failed the insource filter, 426 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks for replicability across technical replicates.
v 279 ions failed the cv_filter filter, 954 ions remain.
i Parsing 954 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 384 ions failed the Blanks filter, 570 ions remain.
i Parsing 570 peaks for insource ions.
v 26 ions failed the insource filter, 544 ions remain.
Found duplicate compound values, will add a suffix to unique the value.
Found duplicate compound values, will add a suffix to unique the value.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 354 ions failed the Coculture filter, 879 ions remain.
Rows: 1306 Columns: 21
-- Column specification --------------------------------------------------------
Delimiter: ","
dbl (21): Compound, mz, rt, 102623_UM1848B_JC1_69_1_5004, 102623_UM1846B_Med...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 293 ions failed the Coculture filter, 191 ions remain.
i Parsing 191 peaks for insource ions.
v 15 ions failed the insource filter, 176 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-peak_table_formatter.R:32:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-qc_graph_pactr-class.R:32:3'): plot_QC_Tree generates the correct plot ──
class(plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
`actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
`expected[2:2]`: "ggplot"
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.3.0
Check: tests
Result: ERROR
Running 'testthat.R' [59s]
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(mpactr)
>
> test_check("mpactr")
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1303 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 796 ions failed the Blanks filter, 507 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method .
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1289 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 65 ions failed the mispicked filter, 1224 ions remain.
i Parsing 1224 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 698 ions failed the Blanks filter, 526 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1233 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 0 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 451 peaks for insource ions.
v 25 ions failed the insource filter, 426 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks for replicability across technical replicates.
v 279 ions failed the cv_filter filter, 954 ions remain.
i Parsing 954 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 384 ions failed the Blanks filter, 570 ions remain.
i Parsing 570 peaks for insource ions.
v 26 ions failed the insource filter, 544 ions remain.
Found duplicate compound values, will add a suffix to unique the value.
Found duplicate compound values, will add a suffix to unique the value.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 354 ions failed the Coculture filter, 879 ions remain.
Rows: 1306 Columns: 21
-- Column specification --------------------------------------------------------
Delimiter: ","
dbl (21): Compound, mz, rt, 102623_UM1848B_JC1_69_1_5004, 102623_UM1846B_Med...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 293 ions failed the Coculture filter, 191 ions remain.
i Parsing 191 peaks for insource ions.
v 15 ions failed the insource filter, 176 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-peak_table_formatter.R:32:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-qc_graph_pactr-class.R:32:3'): plot_QC_Tree generates the correct plot ──
class(plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
`actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
`expected[2:2]`: "ggplot"
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.3.0
Check: installed package size
Result: NOTE
installed size is 9.4Mb
sub-directories of 1Mb or more:
doc 4.8Mb
extdata 1.9Mb
libs 2.0Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.3.0
Check: tests
Result: ERROR
Running 'testthat.R' [68s]
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(mpactr)
>
> test_check("mpactr")
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1303 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 796 ions failed the Blanks filter, 507 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method .
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1289 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 65 ions failed the mispicked filter, 1224 ions remain.
i Parsing 1224 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 698 ions failed the Blanks filter, 526 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Checking 1233 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 0 ions failed the mispicked filter, 1233 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
! Argument merge_peaks is: FALSE. Mispicked peaks will not be merged.
v 70 ions failed the mispicked filter, 1303 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
! Argument remove_ions is FALSE. Peaks from Blanks will not be removed.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for replicability across technical replicates.
v 33 ions failed the cv_filter filter, 451 ions remain.
i Parsing 451 peaks for insource ions.
v 25 ions failed the insource filter, 426 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks for replicability across technical replicates.
v 279 ions failed the cv_filter filter, 954 ions remain.
i Parsing 954 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 384 ions failed the Blanks filter, 570 ions remain.
i Parsing 570 peaks for insource ions.
v 26 ions failed the insource filter, 544 ions remain.
Found duplicate compound values, will add a suffix to unique the value.
Found duplicate compound values, will add a suffix to unique the value.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 354 ions failed the Coculture filter, 879 ions remain.
Rows: 1306 Columns: 21
-- Column specification --------------------------------------------------------
Delimiter: ","
dbl (21): Compound, mz, rt, 102623_UM1848B_JC1_69_1_5004, 102623_UM1846B_Med...
i Use `spec()` to retrieve the full column specification for this data.
i Specify the column types or set `show_col_types = FALSE` to quiet this message.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks based on the sample group: Coculture.
i Argument remove_ions is: TRUE.Removing peaks from Coculture.
v 293 ions failed the Coculture filter, 191 ions remain.
i Parsing 191 peaks for insource ions.
v 15 ions failed the insource filter, 176 ions remain.
i Checking 1303 peaks for mispicked peaks.
i Argument merge_peaks is: TRUE. Merging mispicked peaks with method sum.
v 70 ions failed the mispicked filter, 1233 ions remain.
i Parsing 1233 peaks based on the sample group: Blanks.
i Argument remove_ions is: TRUE.Removing peaks from Blanks.
v 749 ions failed the Blanks filter, 484 ions remain.
i Parsing 484 peaks for insource ions.
v 27 ions failed the insource filter, 457 ions remain.
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• empty test (1): 'test-peak_table_formatter.R:32:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-qc_graph_pactr-class.R:32:3'): plot_QC_Tree generates the correct plot ──
class(plot) (`actual`) not equal to c("gg", "ggplot") (`expected`).
`actual`: "ggplot2::ggplot" "ggplot" "ggplot2::gg" "S7_object" "gg"
`expected[2:2]`: "ggplot"
[ FAIL 1 | WARN 0 | SKIP 1 | PASS 171 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64
Current CRAN status: NOTE: 3, OK: 10
Version: 0.1.1
Check: installed package size
Result: NOTE
installed size is 5.3Mb
sub-directories of 1Mb or more:
data 1.6Mb
doc 2.1Mb
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64