From 77221b253429c695e05b4d0284b864cf1f692a55 Mon Sep 17 00:00:00 2001 From: andrie Date: Thu, 25 Jan 2024 19:33:48 +0000 Subject: [PATCH] Add revdep results --- revdep/README.md | 102 ++++---- revdep/cran.md | 2 +- revdep/failures.md | 14 +- revdep/problems.md | 611 +-------------------------------------------- 4 files changed, 60 insertions(+), 669 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index b919984..2c401b6 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -1,47 +1,47 @@ # Platform -|field |value | -|:--------|:-----------------------------------------------------| -|version |R version 4.3.1 (2023-06-16 ucrt) | -|os |Windows 11 x64 (build 22621) | -|system |x86_64, mingw32 | -|ui |RStudio | -|language |(EN) | -|collate |English_United Kingdom.utf8 | -|ctype |English_United Kingdom.utf8 | -|tz |GMT | -|date |2023-10-01 | -|rstudio |2023.09.0+463 Desert Sunflower (desktop) | -|pandoc |3.1.6.2 @ C:/Users/apdev/scoop/shims/ (via rmarkdown) | +|field |value | +|:--------|:-----------------------------------------------| +|version |R version 4.3.2 (2023-10-31 ucrt) | +|os |Windows 11 x64 (build 22631) | +|system |x86_64, mingw32 | +|ui |RStudio | +|language |(EN) | +|collate |English_United Kingdom.utf8 | +|ctype |English_United Kingdom.utf8 | +|tz |GMT | +|date |2024-01-25 | +|rstudio |2023.12.1+371 Ocean Storm (desktop) | +|pandoc |3.1.6.2 @ C:\Users\apdev\scoop\shims\pandoc.exe | # Dependencies -|package |old |new |Δ | -|:------------|:------|:-----------|:--| -|ggdendro |0.1.23 |0.1.23.9000 |* | -|cli |3.6.1 |3.6.1 | | -|colorspace |2.1-0 |2.1-0 | | -|fansi |1.0.4 |1.0.4 | | -|farver |2.1.1 |2.1.1 | | -|ggplot2 |3.4.3 |3.4.3 | | -|glue |1.6.2 |1.6.2 | | -|gtable |0.3.4 |0.3.4 | | -|isoband |0.2.7 |0.2.7 | | -|labeling |0.4.3 |0.4.3 | | -|lifecycle |1.0.3 |1.0.3 | | -|magrittr |2.0.3 |2.0.3 | | -|munsell |0.5.0 |0.5.0 | | -|pillar |1.9.0 |1.9.0 | | -|pkgconfig |2.0.3 |2.0.3 | | -|R6 |2.5.1 |2.5.1 | | -|RColorBrewer |1.1-3 |1.1-3 | | -|rlang |1.1.1 |1.1.1 | | -|scales |1.2.1 |1.2.1 | | -|tibble |3.2.1 |3.2.1 | | -|utf8 |1.2.3 |1.2.3 | | -|vctrs |0.6.3 |0.6.3 | | -|viridisLite |0.4.2 |0.4.2 | | -|withr |2.5.1 |2.5.1 | | +|package |old |new |Δ | +|:------------|:------|:------|:--| +|ggdendro |0.1.23 |0.1.24 |* | +|cli |3.6.2 |3.6.2 | | +|colorspace |2.1-0 |2.1-0 | | +|fansi |1.0.6 |1.0.6 | | +|farver |2.1.1 |2.1.1 | | +|ggplot2 |3.4.4 |3.4.4 | | +|glue |1.7.0 |1.7.0 | | +|gtable |0.3.4 |0.3.4 | | +|isoband |0.2.7 |0.2.7 | | +|labeling |0.4.3 |0.4.3 | | +|lifecycle |1.0.4 |1.0.4 | | +|magrittr |2.0.3 |2.0.3 | | +|munsell |0.5.0 |0.5.0 | | +|pillar |1.9.0 |1.9.0 | | +|pkgconfig |2.0.3 |2.0.3 | | +|R6 |2.5.1 |2.5.1 | | +|RColorBrewer |1.1-3 |1.1-3 | | +|rlang |1.1.3 |1.1.3 | | +|scales |1.3.0 |1.3.0 | | +|tibble |3.2.1 |3.2.1 | | +|utf8 |1.2.4 |1.2.4 | | +|vctrs |0.6.5 |0.6.5 | | +|viridisLite |0.4.2 |0.4.2 | | +|withr |3.0.0 |3.0.0 | | # Revdeps @@ -49,24 +49,14 @@ |package |version |error |warning |note | |:-----------|:-------|:-----|:-------|:----| -|netZooR |1.4.0 |1 | | | -|scRNAseqApp |1.0.1 |1 | |1 | +|netZooR |1.6.0 |1 | | | +|scRNAseqApp |1.2.2 |1 | |1 | |SensMap |0.7 |1 | | | -## New problems (12) +## New problems (2) -|package |version |error |warning |note | -|:-------------|:-------|:--------|:-------|:----| -|[chemodiv](problems.md#chemodiv)|0.3.0 |__+2__ | | | -|[fairmodels](problems.md#fairmodels)|1.2.1 |__+2__ | | | -|[forestmangr](problems.md#forestmangr)|0.9.5 |__+1__ | | | -|[ggh4x](problems.md#ggh4x)|0.2.6 |__+2__ | | | -|[iheatmapr](problems.md#iheatmapr)|0.7.0 |__+1__ | | | -|[Linnorm](problems.md#linnorm)|2.24.1 |1 __+1__ | |2 | -|[microeco](problems.md#microeco)|1.1.0 |__+1__ | | | -|[mosaic](problems.md#mosaic)|1.8.4.2 |__+1__ | |2 | -|[qPLEXanalyzer](problems.md#qplexanalyzer)|1.18.0 |__+1__ | |2 | -|[SPARTAAS](problems.md#spartaas)|1.2.1 |__+1__ | | | -|[statVisual](problems.md#statvisual)|1.2.1 |__+1__ | |1 | -|[triplot](problems.md#triplot)|1.3.0 |__+2__ | |1 | +|package |version |error |warning |note | +|:---------|:-------|:------|:-------|:----| +|[iheatmapr](problems.md#iheatmapr)|0.7.0 |__+1__ | | | +|[mosaic](problems.md#mosaic)|1.9.0 |__+1__ | |2 | diff --git a/revdep/cran.md b/revdep/cran.md index a32aaba..cab75ed 100644 --- a/revdep/cran.md +++ b/revdep/cran.md @@ -1,6 +1,6 @@ ## revdepcheck results -We checked 62 reverse dependencies (0 from CRAN + 62 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. +We checked 61 reverse dependencies (12 from CRAN + 49 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. * We saw 0 new problems * We failed to check 0 packages diff --git a/revdep/failures.md b/revdep/failures.md index b84188c..11a1212 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -2,11 +2,11 @@
-* Version: 1.4.0 +* Version: 1.6.0 * GitHub: https://github.com/netZoo/netZooR * Source code: https://github.com/cran/netZooR -* Date/Publication: 2023-04-25 -* Number of recursive dependencies: 227 +* Date/Publication: 2023-10-24 +* Number of recursive dependencies: 228 Run `revdepcheck::revdep_details(, "netZooR")` for more info @@ -60,11 +60,11 @@ ERROR: lazy loading failed for package 'netZooR'
-* Version: 1.0.1 +* Version: 1.2.2 * GitHub: https://github.com/jianhong/scRNAseqApp * Source code: https://github.com/cran/scRNAseqApp -* Date/Publication: 2023-04-26 -* Number of recursive dependencies: 225 +* Date/Publication: 2023-11-02 +* Number of recursive dependencies: 235 Run `revdepcheck::revdep_details(, "scRNAseqApp")` for more info @@ -128,7 +128,7 @@ ERROR: lazy loading failed for package 'scRNAseqApp' * GitHub: https://github.com/IbtihelRebhi/SensMap * Source code: https://github.com/cran/SensMap * Date/Publication: 2022-07-04 19:00:02 UTC -* Number of recursive dependencies: 146 +* Number of recursive dependencies: 145 Run `revdepcheck::revdep_details(, "SensMap")` for more info diff --git a/revdep/problems.md b/revdep/problems.md index a8f285c..656e5e2 100644 --- a/revdep/problems.md +++ b/revdep/problems.md @@ -1,236 +1,3 @@ -# chemodiv - -
- -* Version: 0.3.0 -* GitHub: https://github.com/hpetren/chemodiv -* Source code: https://github.com/cran/chemodiv -* Date/Publication: 2023-08-17 17:52:33 UTC -* Number of recursive dependencies: 172 - -Run `revdepcheck::revdep_details(, "chemodiv")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in 'chemodiv-Ex.R' failed - The error most likely occurred in: - - > ### Name: chemoDivPlot - > ### Title: Plot chemodiversity - > ### Aliases: chemoDivPlot - > - > ### ** Examples - > - > minimalDiv <- calcDiv(minimalSampData, minimalCompDis, type = "FuncHillDiv") - ... - 20. │ └─ggplot2 (local) compute_aesthetics(..., self = self) - 21. │ └─ggplot2:::scales_add_defaults(...) - 22. │ └─base::lapply(aesthetics[new_aesthetics], eval_tidy, data = data) - 23. │ └─rlang (local) FUN(X[[i]], ...) - 24. ├─label - 25. ├─rlang:::`$.rlang_data_pronoun`(.data, label) - 26. │ └─rlang:::data_pronoun_get(...) - 27. └─rlang:::abort_data_pronoun(x, call = y) - 28. └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call) - Execution halted - ``` - -* checking tests ... - ``` - Running 'testthat.R' - ERROR - Running the tests in 'tests/testthat.R' failed. - Last 13 lines of output: - ══ Skipped tests (3) ═══════════════════════════════════════════════════════════ - • On CRAN (3): 'test-NPCTable.R:16:3', 'test-NPCTable.R:24:3', - 'test-compDis.R:28:3' - - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Error ('test-chemoDivPlot.R:17:1'): (code run outside of `test_that()`) ───── - Error in `ggplot2::geom_text(data = compDisMatClustDendData$labels, ggplot2::aes(x = .data$x, - y = .data$y, label = .data$label), hjust = -0.1, angle = 0)`: Problem while computing aesthetics. - ℹ Error occurred in the 2nd layer. - Caused by error in `.data$label`: - ! Column `label` not found in `.data`. - - [ FAIL 1 | WARN 48 | SKIP 3 | PASS 81 ] - Error: Test failures - Execution halted - ``` - -# fairmodels - -
- -* Version: 1.2.1 -* GitHub: https://github.com/ModelOriented/fairmodels -* Source code: https://github.com/cran/fairmodels -* Date/Publication: 2022-08-23 19:50:06 UTC -* Number of recursive dependencies: 91 - -Run `revdepcheck::revdep_details(, "fairmodels")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in 'fairmodels-Ex.R' failed - The error most likely occurred in: - - > ### Name: fairness_heatmap - > ### Title: Fairness heatmap - > ### Aliases: fairness_heatmap - > - > ### ** Examples - > - > - ... -  Fairness object created succesfully  - > - > - > fh <- fairness_heatmap(fobject) - > - > plot(fh) - Error in `[.data.frame`(dendro_data1$labels, "label") : - undefined columns selected - Calls: plot ... plot.fairness_heatmap -> unlist -> [ -> [.data.frame - Execution halted - ``` - -* checking tests ... - ``` - Running 'testthat.R' - ERROR - Running the tests in 'tests/testthat.R' failed. - Last 13 lines of output: - 2. │ └─base::withCallingHandlers(...) - 3. ├─fairmodels:::expect_s3_class(...) - 4. │ ├─testthat::expect(...) at C:\Users\apdev\Documents\github\R-packages\maintainer\ggdendro\ggdendro\revdep\checks\fairmodels\new\fairmodels.Rcheck\tests\testthat\helper_objects.R:70:19 - 5. │ └─base::class(object) %in% class - 6. ├─fairmodels::plot_fairmodels(fc, type = "fairness_heatmap") - 7. └─fairmodels:::plot_fairmodels.fairness_object(fc, type = "fairness_heatmap") - 8. └─fairmodels:::plot_fairmodels.default(x, type, ...) - 9. └─fairmodels:::plot.fairness_heatmap(fairness_heatmap(x, ...)) - 10. ├─base::unlist(dendro_data1$labels["label"]) - 11. ├─dendro_data1$labels["label"] - 12. └─base::`[.data.frame`(dendro_data1$labels, "label") - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 300 ] - Error: Test failures - Execution halted - ``` - -# forestmangr - -
- -* Version: 0.9.5 -* GitHub: https://github.com/sollano/forestmangr -* Source code: https://github.com/cran/forestmangr -* Date/Publication: 2023-02-15 22:20:02 UTC -* Number of recursive dependencies: 128 - -Run `revdepcheck::revdep_details(, "forestmangr")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in 'forestmangr-Ex.R' failed - The error most likely occurred in: - - > ### Name: similarity_matrix - > ### Title: Get the similarity matrix of an area - > ### Aliases: similarity_matrix - > - > ### ** Examples - > - > library(forestmangr) - ... - 15. │ └─forestmangr (local) .f(.x[[i]], ...) - 16. │ ├─base::merge(dendr[["labels"]], clust.df, by = "label") - 17. │ └─base::merge.data.frame(dendr[["labels"]], clust.df, by = "label") - 18. │ └─base (local) fix.by(by.x, x) - 19. │ └─base::stop(...) - 20. └─base::.handleSimpleError(...) - 21. └─purrr (local) h(simpleError(msg, call)) - 22. └─cli::cli_abort(...) - 23. └─rlang::abort(...) - Execution halted - ``` - -# ggh4x - -
- -* Version: 0.2.6 -* GitHub: https://github.com/teunbrand/ggh4x -* Source code: https://github.com/cran/ggh4x -* Date/Publication: 2023-08-30 19:10:06 UTC -* Number of recursive dependencies: 81 - -Run `revdepcheck::revdep_details(, "ggh4x")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in 'ggh4x-Ex.R' failed - The error most likely occurred in: - - > ### Name: guide_dendro - > ### Title: Dendrogram guide - > ### Aliases: guide_dendro - > - > ### ** Examples - > - > clust <- hclust(dist(USArrests), "ave") - ... - + geom_raster() + - + scale_y_dendrogram(hclust = clust, - + guide = guide_dendro(n.dodge = 2)) - > - > # The looks of the dendrogram are controlled through ticks - > g + theme(axis.ticks = element_line(colour = "red")) - Error in `$<-.data.frame`(`*tmp*`, "label", value = character(0)) : - replacement has 0 rows, data has 50 - Calls: ... guide_train -> guide_train.dendroguide -> $<- -> $<-.data.frame - Execution halted - ``` - -* checking tests ... - ``` - Running 'testthat.R' - ERROR - Running the tests in 'tests/testthat.R' failed. - Last 13 lines of output: - 6. └─base::lapply(...) - 7. └─ggplot2 (local) FUN(X[[i]], ...) - 8. └─ggplot2 (local) train_panel_guides(..., self = self) - 9. └─base::lapply(...) - 10. └─ggplot2 (local) FUN(X[[i]], ...) - 11. ├─ggplot2::guide_train(guide, panel_params[[aesthetic]]) - 12. └─ggh4x:::guide_train.dendroguide(guide, panel_params[[aesthetic]]) - 13. ├─base::`$<-`(`*tmp*`, "label", value = ``) - 14. └─base::`$<-.data.frame`(`*tmp*`, "label", value = ``) - - [ FAIL 4 | WARN 0 | SKIP 21 | PASS 774 ] - Deleting unused snapshots: - • facet_manual/removable-whitespace.svg - Error: Test failures - Execution halted - ``` - # iheatmapr
@@ -239,7 +6,7 @@ Run `revdepcheck::revdep_details(, "ggh4x")` for more info * GitHub: https://github.com/ropensci/iheatmapr * Source code: https://github.com/cran/iheatmapr * Date/Publication: 2023-08-30 17:00:17 UTC -* Number of recursive dependencies: 94 +* Number of recursive dependencies: 93 Run `revdepcheck::revdep_details(, "iheatmapr")` for more info @@ -262,154 +29,23 @@ Run `revdepcheck::revdep_details(, "iheatmapr")` for more info ... Backtrace: ▆ - 1. └─iheatmapr:::expect_iheatmap(...) at test_dendro.R:22:2 - 2. └─iheatmapr:::expect_ihm_equal_to_reference(...) at C:\Users\apdev\Documents\github\R-packages\maintainer\ggdendro\ggdendro\revdep\checks\iheatmapr\new\iheatmapr.Rcheck\tests\testthat\helper_expectation.R:56:2 + 1. └─iheatmapr:::expect_iheatmap(...) at test_dendro.R:22:3 + 2. └─iheatmapr:::expect_ihm_equal_to_reference(...) at C:\Users\apdev\Documents\github\R-packages\maintainer\ggdendro\ggdendro\revdep\checks\iheatmapr\new\iheatmapr.Rcheck\tests\testthat\helper_expectation.R:56:3 [ FAIL 14 | WARN 0 | SKIP 0 | PASS 348 ] Error: Test failures Execution halted ``` -# Linnorm - -
- -* Version: 2.24.1 -* GitHub: NA -* Source code: https://github.com/cran/Linnorm -* Date/Publication: 2023-05-02 -* Number of recursive dependencies: 107 - -Run `revdepcheck::revdep_details(, "Linnorm")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in 'Linnorm-Ex.R' failed - The error most likely occurred in: - - > ### Name: Linnorm.HClust - > ### Title: Linnorm-hierarchical clustering analysis. - > ### Aliases: Linnorm.HClust - > ### Keywords: CPM Clustering Count Expression FPKM Linnorm Parametric - > ### RNA-seq RPKM Raw TPM hierarchical normalization transformation - > - > ### ** Examples - ... - > - > #Obtain example matrix: - > data(Islam2011) - > #Example: - > HClust.results <- Linnorm.HClust(Islam2011, Group=c(rep("ESC",48), rep("EF",44), rep("NegCtrl",4))) - Warning in Linnorm.HClust(Islam2011, Group = c(rep("ESC", 48), rep("EF", : - NAs introduced by coercion - Error in fix.by(by.x, x) : 'by' must specify a uniquely valid column - Calls: Linnorm.HClust -> merge -> merge.data.frame -> fix.by - Execution halted - ``` - -## In both - -* checking tests ... - ``` - Running 'testthat.R' - ERROR - Running the tests in 'tests/testthat.R' failed. - Last 13 lines of output: - - Error in `library(matrixStats)`: there is no package called 'matrixStats' - Backtrace: - ▆ - 1. └─base::library(matrixStats) at test_Misc_Stats.R:3:0 - ── Error ('test_SkewVar.R:3:1'): (code run outside of `test_that()`) ─────────── - - Error in `library(matrixStats)`: there is no package called 'matrixStats' - Backtrace: - ▆ - 1. └─base::library(matrixStats) at test_SkewVar.R:3:0 - - [ FAIL 2 | WARN 0 | SKIP 0 | PASS 6 ] - Error: Test failures - Execution halted - ``` - -* checking installed package size ... NOTE - ``` - installed size is 5.5Mb - sub-directories of 1Mb or more: - data 2.3Mb - doc 1.9Mb - libs 1.0Mb - ``` - -* checking R code for possible problems ... NOTE - ``` - Linnorm.HClust: no visible binding for global variable 'x' - Linnorm.HClust: no visible binding for global variable 'y' - Linnorm.HClust: no visible binding for global variable 'xend' - Linnorm.HClust: no visible binding for global variable 'yend' - Linnorm.HClust: no visible binding for global variable 'cluster' - Linnorm.HClust: no visible binding for global variable 'X1' - Linnorm.HClust: no visible binding for global variable 'X2' - Linnorm.HVar: no visible binding for global variable 'SD' - Linnorm.HVar: no visible binding for global variable 'group' - Undefined global functions or variables: - SD X1 X2 cluster group x xend y yend - ``` - -# microeco - -
- -* Version: 1.1.0 -* GitHub: https://github.com/ChiLiubio/microeco -* Source code: https://github.com/cran/microeco -* Date/Publication: 2023-09-13 23:00:02 UTC -* Number of recursive dependencies: 176 - -Run `revdepcheck::revdep_details(, "microeco")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in 'microeco-Ex.R' failed - The error most likely occurred in: - - > ### Name: trans_beta - > ### Title: Create 'trans_beta' object for beta-diversity analysis based on - > ### the distance matrix - > ### Aliases: trans_beta - > - > ### ** Examples - > - ... - 1. └─t1$plot_clustering(...) - 2. ├─base::suppressWarnings(...) - 3. │ └─base::withCallingHandlers(...) - 4. ├─dplyr::left_join(...) - 5. └─dplyr:::left_join.data.frame(...) - 6. └─dplyr:::join_mutate(...) - 7. └─dplyr:::join_cols(...) - 8. └─dplyr:::check_join_vars(by$x, x_names, by$condition, "x", error_call = error_call) - 9. └─rlang::abort(bullets, call = error_call) - Execution halted - ``` - # mosaic
-* Version: 1.8.4.2 +* Version: 1.9.0 * GitHub: https://github.com/ProjectMOSAIC/mosaic * Source code: https://github.com/cran/mosaic -* Date/Publication: 2022-09-20 18:10:02 UTC -* Number of recursive dependencies: 139 +* Date/Publication: 2023-11-10 00:10:13 UTC +* Number of recursive dependencies: 133 Run `revdepcheck::revdep_details(, "mosaic")` for more info @@ -452,238 +88,3 @@ Run `revdepcheck::revdep_details(, "mosaic")` for more info Package unavailable to check Rd xrefs: 'cubature' ``` -# qPLEXanalyzer - -
- -* Version: 1.18.0 -* GitHub: https://github.com/crukci-bioinformatics/qPLEXanalyzer -* Source code: https://github.com/cran/qPLEXanalyzer -* Date/Publication: 2023-04-25 -* Number of recursive dependencies: 150 - -Run `revdepcheck::revdep_details(, "qPLEXanalyzer")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in 'qPLEXanalyzer-Ex.R' failed - The error most likely occurred in: - - > ### Name: hierarchicalPlot - > ### Title: Hierarchical clustering plot - > ### Aliases: hierarchicalPlot - > - > ### ** Examples - > - > - ... - 6. ├─dplyr:::mutate.data.frame(., SampleName = as.character(label)) - 7. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by) - 8. │ ├─base::withCallingHandlers(...) - 9. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns) - 10. │ └─mask$eval_all_mutate(quo) - 11. │ └─dplyr (local) eval() - 12. └─base::.handleSimpleError(...) - 13. └─dplyr (local) h(simpleError(msg, call)) - 14. └─rlang::abort(message, class = error_class, parent = parent, call = error_call) - Execution halted - ``` - -## In both - -* checking package dependencies ... NOTE - ``` - Package suggested but not available for checking: 'qPLEXdata' - ``` - -* checking R code for possible problems ... NOTE - ``` - convertToMSnset: no visible binding for global variable 'SampleName' - corrPlot: no visible binding for global variable 'X' - corrPlot: no visible binding for global variable 'AddValues' - corrPlot: no visible binding for global variable 'Cor' - corrPlot: no visible binding for global variable 'Y' - corrPlot: no visible binding for global variable 'CorTxt' - coveragePlot: no visible binding for global variable 'Accessions' - coveragePlot: no visible binding for global variable 'Sequences' - getContrastResults: no visible binding for global variable 'B' - getContrastResults: no visible binding for global variable 'AveExpr' - ... - summarizeIntensities: no visible binding for global variable - 'Sequences' - summarizeIntensities: no visible global function definition for 'where' - summarizeIntensities: no visible binding for global variable 'Count' - Undefined global functions or variables: - Accessions AddValues AveExpr B Cor CorTxt Count GeneSymbol Intensity - Mean Modifications PeptideID RLI RowID SampleName Seq_Acc Sequences - Sites Sites_Acc SymbolLab Type Variance X Y adj.P.Val group logFC - logInt logIntensity meanscaledIntensity medianLogInt sInt where x - xend y yend - ``` - -# SPARTAAS - -
- -* Version: 1.2.1 -* GitHub: NA -* Source code: https://github.com/cran/SPARTAAS -* Date/Publication: 2023-06-06 13:10:09 UTC -* Number of recursive dependencies: 191 - -Run `revdepcheck::revdep_details(, "SPARTAAS")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in 'SPARTAAS-Ex.R' failed - The error most likely occurred in: - - > ### Name: hclustcompro - > ### Title: hclustcompro - > ### Aliases: hclustcompro perioclust - > - > ### ** Examples - > - > library(SPARTAAS) - ... - 9. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) - 10. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) - 11. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) - 12. │ └─base::withCallingHandlers(...) - 13. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) - 14. └─l$compute_aesthetics(d, plot) - 15. └─ggplot2 (local) compute_aesthetics(..., self = self) - 16. └─cli::cli_abort(...) - 17. └─rlang::abort(...) - Execution halted - ``` - -# statVisual - -
- -* Version: 1.2.1 -* GitHub: NA -* Source code: https://github.com/cran/statVisual -* Date/Publication: 2020-02-20 19:30:02 UTC -* Number of recursive dependencies: 190 - -Run `revdepcheck::revdep_details(, "statVisual")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in 'statVisual-Ex.R' failed - The error most likely occurred in: - - > ### Name: Dendro - > ### Title: Compare Groups Based on Dendrogram - > ### Aliases: Dendro - > ### Keywords: method - > - > ### ** Examples - > - ... - > - > pDat$grp = factor(pDat$grp) - > - > statVisual(type = 'Dendro', - + x = pDat[, c(3:8)], - + group = pDat$grp) - Error in `$<-.data.frame`(`*tmp*`, "group", value = integer(0)) : - replacement has 0 rows, data has 20 - Calls: statVisual -> Dendro -> $<- -> $<-.data.frame - Execution halted - ``` - -## In both - -* checking dependencies in R code ... NOTE - ``` - Namespaces in Imports field not imported from: - 'gbm' 'ggfortify' 'tibble' 'tidyverse' - All declared Imports should be used. - ``` - -# triplot - -
- -* Version: 1.3.0 -* GitHub: https://github.com/ModelOriented/triplot -* Source code: https://github.com/cran/triplot -* Date/Publication: 2020-07-13 17:00:03 UTC -* Number of recursive dependencies: 79 - -Run `revdepcheck::revdep_details(, "triplot")` for more info - -
- -## Newly broken - -* checking examples ... ERROR - ``` - Running examples in 'triplot-Ex.R' failed - The error most likely occurred in: - - > ### Name: hierarchical_importance - > ### Title: Calculates importance of hierarchically grouped aspects - > ### Aliases: hierarchical_importance plot.hierarchical_importance - > - > ### ** Examples - > - > library(DALEX) - ... - 8. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers) - 9. │ │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]]) - 10. │ │ └─base (local) doTryCatch(return(expr), name, parentenv, handler) - 11. │ └─base::withCallingHandlers(...) - 12. └─ggplot2 (local) f(l = layers[[i]], d = data[[i]]) - 13. └─l$compute_aesthetics(d, plot) - 14. └─ggplot2 (local) compute_aesthetics(..., self = self) - 15. └─cli::cli_abort(...) - 16. └─rlang::abort(...) - Execution halted - ``` - -* checking tests ... - ``` - Running 'testthat.R' - ERROR - Running the tests in 'tests/testthat.R' failed. - Last 13 lines of output: - ══ Failed tests ════════════════════════════════════════════════════════════════ - ── Failure ('test_group_variables.R:23:3'): check plot.cluster_variables function ── - `plot(p)` threw an error. - Message: Problem while computing aesthetics. - ℹ Error occurred in the 3rd layer. - Caused by error in `compute_aesthetics()`: - ! Aesthetics are not valid data columns. - ✖ The following aesthetics are invalid: - ✖ `label = label` - ℹ Did you mistype the name of a data column or forget to add `after_stat()`? - Class: rlang_error/error/condition - - [ FAIL 1 | WARN 1 | SKIP 0 | PASS 83 ] - Error: Test failures - Execution halted - ``` - -## In both - -* checking LazyData ... NOTE - ``` - 'LazyData' is specified without a 'data' directory - ``` -