Last updated on 2025-12-19 21:49:42 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.3.1 | 25.35 | 185.75 | 211.10 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.3.1 | 18.86 | 108.20 | 127.06 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.3.1 | 52.00 | 258.81 | 310.81 | ERROR | |
| r-devel-linux-x86_64-fedora-gcc | 0.3.1 | 49.00 | 261.89 | 310.89 | ERROR | |
| r-devel-windows-x86_64 | 0.3.1 | 34.00 | 203.00 | 237.00 | OK | |
| r-patched-linux-x86_64 | 0.3.1 | 28.07 | 171.05 | 199.12 | OK | |
| r-release-linux-x86_64 | 0.3.1 | 27.07 | 170.06 | 197.13 | OK | |
| r-release-macos-arm64 | 0.3.1 | OK | ||||
| r-release-macos-x86_64 | 0.3.1 | 21.00 | 389.00 | 410.00 | OK | |
| r-release-windows-x86_64 | 0.3.1 | 33.00 | 200.00 | 233.00 | OK | |
| r-oldrel-macos-arm64 | 0.3.1 | NOTE | ||||
| r-oldrel-macos-x86_64 | 0.3.1 | 22.00 | 367.00 | 389.00 | NOTE | |
| r-oldrel-windows-x86_64 | 0.3.1 | 44.00 | 260.00 | 304.00 | NOTE |
Version: 0.3.1
Check: compiled code
Result: NOTE
File ‘mpactr/libs/mpactr.so’:
Found non-API call to R: ‘ATTRIB’
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual,
and section ‘Moving into C API compliance’ for issues with the use of
non-API entry points.
Flavors: r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3.1
Check: examples
Result: ERROR
Running examples in ‘mpactr-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: filter_insource_ions
> ### Title: Filter Insource ions
> ### Aliases: filter_insource_ions
>
> ### ** Examples
>
> ## Don't show:
> limit_cores()
> ## End(Don't show)
> data <- import_data(
+ example_path("coculture_peak_table.csv"),
+ example_path("metadata.csv"),
+ format = "Progenesis"
+ )
>
> data_filter <- filter_insource_ions(data,
+ cluster_threshold = 0.95
+ )
ℹ Parsing 1303 peaks for insource ions.
Error in `[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, :
attempt access index 22/22 in VECTOR_ELT
Calls: filter_insource_ions -> <Anonymous> -> <Anonymous> -> [ -> [.data.table
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [26s/33s]
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)
>
> limit_cores()
> 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.
Saving _problems/test-filter_pactr-methods-371.R
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.
Saving _problems/test-filters-176.R
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.
Saving _problems/test-filters-217.R
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.
Saving _problems/test-import_data-53.R
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.
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.
Saving _problems/test-qc_graph_pactr-class-25.R
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.
Saving _problems/test-quality_control-18.R
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.
Saving _problems/test-quality_control-44.R
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 154 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-filter_pactr-methods.R:371:3'): filter_inscource_ions filters out data properly ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─filter_class$filter_insource_ions(cluster_threshold = 0.95) at test-filter_pactr-methods.R:371:3
2. ├─self$mpactr_data$set_peak_table(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-filters.R:174:3'): filter insource ions wrapper works as expected ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(...) at test-filters.R:174:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-filters.R:217:3'): filters abort if the filter has already been run ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(data_mpactr, cluster_threshold = 0.95) at test-filters.R:217:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-import_data.R:45:3'): We can use a data.frame as input our peak table in import_data ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(...) at test-import_data.R:45:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-qc_graph_pactr-class.R:25:3'): plot_QC_Tree generates the correct plot ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─filter_class$filter_insource_ions(cluster_threshold = 0.95) at test-qc_graph_pactr-class.R:25:3
2. ├─self$mpactr_data$set_peak_table(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-quality_control.R:18:3'): qc_summary returns a summary data.table ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(data, cluster_threshold = 0.95) at test-quality_control.R:18:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-quality_control.R:44:3'): qc plot returns a generates a plot ───
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(data, cluster_threshold = 0.95) at test-quality_control.R:44:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 154 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
...
--- re-building ‘downstream_analyses.Rmd’ using rmarkdown
Warning: Duplicated chunk option(s) 'warning' in both chunk header and pipe comments of the chunk 'unnamed-chunk-19'.
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘downstream_analyses.Rmd’
--- re-building ‘mpactr.Rmd’ using rmarkdown
Quitting from mpactr.Rmd:296-301 [unnamed-chunk-23]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 34/34 in VECTOR_ELT
---
Backtrace:
▆
1. ├─mpactr::filter_insource_ions(...)
2. │ └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. │ ├─self$mpactr_data$set_peak_table(...)
4. │ ├─...[]
5. │ └─data.table:::`[.data.table`(...)
6. └─private$deconvolute_correlation(.SD, cluster_threshold)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'mpactr.Rmd' failed with diagnostics:
attempt access index 34/34 in VECTOR_ELT
--- failed re-building ‘mpactr.Rmd’
--- re-building ‘reference_semantics.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘reference_semantics.Rmd’
SUMMARY: processing the following file failed:
‘mpactr.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.3.1
Check: examples
Result: ERROR
Running examples in ‘mpactr-Ex.R’ failed
The error most likely occurred in:
> ### Name: filter_insource_ions
> ### Title: Filter Insource ions
> ### Aliases: filter_insource_ions
>
> ### ** Examples
>
> ## Don't show:
> limit_cores()
> ## End(Don't show)
> data <- import_data(
+ example_path("coculture_peak_table.csv"),
+ example_path("metadata.csv"),
+ format = "Progenesis"
+ )
>
> data_filter <- filter_insource_ions(data,
+ cluster_threshold = 0.95
+ )
ℹ Parsing 1303 peaks for insource ions.
Error in `[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, :
attempt access index 22/22 in VECTOR_ELT
Calls: filter_insource_ions -> <Anonymous> -> <Anonymous> -> [ -> [.data.table
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [73s/116s]
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)
>
> limit_cores()
> 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.
Saving _problems/test-filter_pactr-methods-371.R
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.
Saving _problems/test-filters-176.R
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.
Saving _problems/test-filters-217.R
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.
Saving _problems/test-import_data-53.R
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.
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.
Saving _problems/test-qc_graph_pactr-class-25.R
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.
Saving _problems/test-quality_control-18.R
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.
Saving _problems/test-quality_control-44.R
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 154 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-filter_pactr-methods.R:371:3'): filter_inscource_ions filters out data properly ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─filter_class$filter_insource_ions(cluster_threshold = 0.95) at test-filter_pactr-methods.R:371:3
2. ├─self$mpactr_data$set_peak_table(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-filters.R:174:3'): filter insource ions wrapper works as expected ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(...) at test-filters.R:174:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-filters.R:217:3'): filters abort if the filter has already been run ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(data_mpactr, cluster_threshold = 0.95) at test-filters.R:217:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-import_data.R:45:3'): We can use a data.frame as input our peak table in import_data ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(...) at test-import_data.R:45:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-qc_graph_pactr-class.R:25:3'): plot_QC_Tree generates the correct plot ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─filter_class$filter_insource_ions(cluster_threshold = 0.95) at test-qc_graph_pactr-class.R:25:3
2. ├─self$mpactr_data$set_peak_table(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-quality_control.R:18:3'): qc_summary returns a summary data.table ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(data, cluster_threshold = 0.95) at test-quality_control.R:18:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-quality_control.R:44:3'): qc plot returns a generates a plot ───
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(data, cluster_threshold = 0.95) at test-quality_control.R:44:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 154 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.3.1
Check: re-building of vignette outputs
Result: ERROR
Error(s) in re-building vignettes:
--- re-building ‘downstream_analyses.Rmd’ using rmarkdown
Warning: Duplicated chunk option(s) 'warning' in both chunk header and pipe comments of the chunk 'unnamed-chunk-19'.
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘downstream_analyses.Rmd’
--- re-building ‘mpactr.Rmd’ using rmarkdown
Quitting from mpactr.Rmd:296-301 [unnamed-chunk-23]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `[.data.table`:
! attempt access index 34/34 in VECTOR_ELT
---
Backtrace:
▆
1. ├─mpactr::filter_insource_ions(...)
2. │ └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. │ ├─self$mpactr_data$set_peak_table(...)
4. │ ├─...[]
5. │ └─data.table:::`[.data.table`(...)
6. └─private$deconvolute_correlation(.SD, cluster_threshold)
7. ├─...[]
8. └─data.table:::`[.data.table`(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'mpactr.Rmd' failed with diagnostics:
attempt access index 34/34 in VECTOR_ELT
--- failed re-building ‘mpactr.Rmd’
--- re-building ‘reference_semantics.Rmd’ using rmarkdown
[WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead.
--- finished re-building ‘reference_semantics.Rmd’
SUMMARY: processing the following file failed:
‘mpactr.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.3.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [71s/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)
>
> limit_cores()
> 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.
Saving _problems/test-filter_pactr-methods-371.R
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.
Saving _problems/test-filters-176.R
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.
Saving _problems/test-filters-217.R
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.
Saving _problems/test-import_data-53.R
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.
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.
Saving _problems/test-qc_graph_pactr-class-25.R
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.
Saving _problems/test-quality_control-18.R
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.
Saving _problems/test-quality_control-44.R
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 154 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-filter_pactr-methods.R:371:3'): filter_inscource_ions filters out data properly ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─filter_class$filter_insource_ions(cluster_threshold = 0.95) at test-filter_pactr-methods.R:371:3
2. ├─self$mpactr_data$set_peak_table(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-filters.R:174:3'): filter insource ions wrapper works as expected ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(...) at test-filters.R:174:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-filters.R:217:3'): filters abort if the filter has already been run ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(data_mpactr, cluster_threshold = 0.95) at test-filters.R:217:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-import_data.R:45:3'): We can use a data.frame as input our peak table in import_data ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(...) at test-import_data.R:45:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-qc_graph_pactr-class.R:25:3'): plot_QC_Tree generates the correct plot ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─filter_class$filter_insource_ions(cluster_threshold = 0.95) at test-qc_graph_pactr-class.R:25:3
2. ├─self$mpactr_data$set_peak_table(...)
3. ├─...[]
4. └─data.table:::`[.data.table`(...)
── Error ('test-quality_control.R:18:3'): qc_summary returns a summary data.table ──
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(data, cluster_threshold = 0.95) at test-quality_control.R:18:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
── Error ('test-quality_control.R:44:3'): qc plot returns a generates a plot ───
Error in ``[.data.table`(self$mpactr_data$get_peak_table(), , `:=`(cor, private$deconvolute_correlation(.SD, cluster_threshold)), by = .(rt))`: attempt access index 22/22 in VECTOR_ELT
Backtrace:
▆
1. └─mpactr::filter_insource_ions(data, cluster_threshold = 0.95) at test-quality_control.R:44:3
2. └─mpactr_object$filter_insource_ions(cluster_threshold = cluster_threshold)
3. ├─self$mpactr_data$set_peak_table(...)
4. ├─...[]
5. └─data.table:::`[.data.table`(...)
[ FAIL 7 | WARN 0 | SKIP 0 | PASS 154 ]
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.3.1
Check: installed package size
Result: NOTE
installed size is 9.3Mb
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