Merge pull request #80 from jasenfinch/devel

v0.14.3

.github/workflows/R-CMD-check.yaml

@@ -1,15 +1,10 @@
-# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
-# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - master
-      - devel
+    branches: [main, master, devel]
   pull_request:
-    branches:
-      - master
-  schedule:
-    - cron: '0 0 * * *'
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -23,63 +18,43 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: macOS-latest, r: 'release'}
-          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          - {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel/1'}
 
     env:
-      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - uses: r-lib/actions/setup-r@v1
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v1
+      - uses: r-lib/actions/setup-r-dependencies@v1
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
-
-      - name: Install system dependencies
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-          sudo apt-get install -y libgit2-dev
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran(c("rcmdcheck","goodpractice"))
-        shell: Rscript {0}
+          extra-packages: rcmdcheck
 
       - name: Check
         env:
-          _R_CHECK_CRAN_INCOMING_REMOTE_: false
-        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
-        shell: Rscript {0}
-
-      - name: Goodpractice
-        run: goodpractice::goodpractice()
+          _R_CHECK_CRAN_INCOMING_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
       - name: Test coverage
         run: covr::codecov()

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: metabolyseR
 Title: Methods for Pre-Treatment, Data Mining and Correlation Analyses of Metabolomics Data
-Version: 0.14.2
+Version: 0.14.3
 Authors@R: person("Jasen", "Finch", email = "[email protected]", role = c("aut", "cre"))
 Description: A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data.
-URL:  https://jasenfinch.github.io/metabolyseR
+URL: https://jasenfinch.github.io/metabolyseR
 BugReports: https://github.com/jasenfinch/metabolyseR/issues
 biocViews: Metabolomics
 Depends: R (>= 3.4.0)
@@ -37,9 +37,8 @@ Imports: Hmisc,
          future
 License: GPL (>= 3)
 Encoding: UTF-8
-LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Suggests: knitr,
     rmarkdown,
     readr,
@@ -87,4 +86,4 @@ Collate: allClasses.R
     univariate.R
     modelling-accessors.R
 VignetteBuilder: knitr
-Remotes: aberHRML/metaboData
+Remotes: jasenfinch/missForest

NEWS.md

@@ -1,3 +1,21 @@
+# metabolyseR 0.14.3
+
+* Temporarily added [jasenfinch/missForest](https://github.com/jasenfinch/missForest) as a remote until [stekhoven/missForest](https://github.com/stekhoven/missForest) pull request [#25](https://github.com/stekhoven/missForest/pull/25) is resolved.
+
+* The limit of the number of plotted features in [`plotExplanatoryHeatmap`](https://jasenfinch.github.io/metabolyseR/reference/plotExplanatoryHeatmap.html) can now be specified using the `featureLimit` argument. 
+
+* [`plotExplanatoryHeatmap()`](https://jasenfinch.github.io/metabolyseR/reference/plotExplanatoryHeatmap.html) now returns NULL and returns a message when no explanatory features are found.
+
+* Fixed the alignment of the dendrogram branches with heat map rows in [`plotExplanatoryHeatmap()`](https://jasenfinch.github.io/metabolyseR/reference/plotExplanatoryHeatmap.html).
+
+* Fixed `ggplot2::guides()` warning in [`plotFeature()`](https://jasenfinch.github.io/metabolyseR/reference/plotFeature.html) and [`plotTIC()`](https://jasenfinch.github.io/metabolyseR/reference/plotTIC.html).
+
+* Fixed bug in [`explanatoryFeatures()`](https://jasenfinch.github.io/metabolyseR/reference/modelling-accessors.html) methods for [`Analysis`](https://jasenfinch.github.io/metabolyseR/reference/Analysis-class.html) class and lists where the threshold was not applied.
+
+* Fixed the error in [`plotRSD()`](https://jasenfinch.github.io/metabolyseR/reference/plotRSD.html) method for the [`Analysis`](https://jasenfinch.github.io/metabolyseR/reference/Analysis-class.html) class.
+
+* Corrected the text in the [modelling vignette](https://jasenfinch.github.io/metabolyseR/articles/modelling.html) concerning the results of using unsupervised random forest for outlier detection.
+
 # metabolyseR 0.14.2
 
 * Package version, creation date and verbose argument added to prototype of `Analysis` class.

R/modelling-accessors.R

@@ -218,7 +218,7 @@ setGeneric('explanatoryFeatures', function(x,...)
 #' @importFrom dplyr arrange
 
 setMethod('explanatoryFeatures',signature = 'Univariate',
-          function(x,threshold = 0.05,...){
+          function(x,threshold = 0.05){
             importance(x) %>%
               filter(adjusted.p.value < threshold) %>% 
               arrange(adjusted.p.value)
@@ -247,7 +247,7 @@ setMethod('explanatoryFeatures',signature = 'RandomForest',
 #' @rdname modelling-accessors
 
 setMethod('explanatoryFeatures',signature = 'list',
-          function(x,threshold = 0.05, ...){
+          function(x,...){
             object_classes <- x %>%
               map_chr(class)
 
@@ -266,7 +266,7 @@ setMethod('explanatoryFeatures',signature = 'list',
 #' @rdname modelling-accessors
 
 setMethod('explanatoryFeatures',signature = 'Analysis',
-          function(x,threshold = 0.05, ...){
+          function(x,...){
             x %>% 
               analysisResults(element = 'modelling') %>% 
               explanatoryFeatures(...)