Merge pull request #28 from jasenfinch/devel

v0.9.2

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

@@ -1,17 +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/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches:
-      - main
-      - master
-      - devel
+    branches: [main, master, devel]
   pull_request:
-    branches:
-      - main
-      - master
-  schedule:
-    - cron: '0 0 * * *'
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -25,71 +18,40 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          #- {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: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {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: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
-        with:
-          r-version: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - 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@v2
+      - uses: r-lib/actions/setup-r@v2
         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
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+          
+      - name: Install Linux 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 libopenbabel-dev libnetcdf-dev libglpk-dev texlive-base libsodium-dev
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran(c("rcmdcheck","goodpractice"))
-        shell: Rscript {0}
-
-      - 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: Good practice
-        run: goodpractice::goodpractice()
-        shell: Rscript {0}
-
-      - name: Test coverage
-        run: covr::codecov()
-        shell: Rscript {0}
+          sudo apt install libnetcdf-dev libglpk-dev texlive-base libsodium-dev libopenbabel-dev libeigen3-dev
+          
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::rcmdcheck
+            bioc::BiocParallel
+            bioc::MSnbase
+          needs: check
 
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
+      - uses: r-lib/actions/check-r-package@v2
         with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check
+          upload-snapshots: true

.github/workflows/pkgdown.yaml

@@ -0,0 +1,55 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt install libnetcdf-dev libglpk-dev texlive-base libsodium-dev libopenbabel-dev libeigen3-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::pkgdown 
+            local::.
+            bioc::BiocParallel
+            bioc::MSnbase
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -0,0 +1,58 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install Linux system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt install libnetcdf-dev libglpk-dev texlive-base libsodium-dev libopenbabel-dev libeigen3-dev
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: | 
+            any::covr 
+            bioc::BiocParallel
+            bioc::MSnbase
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+docs

DESCRIPTION

@@ -1,14 +1,13 @@
 Package: hrm
 Title: Install, Load and Update R Packages for High Resolution Metabolomics Analyses
-Version: 0.9.1
+Version: 0.9.2
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: Easily install, load and update R packages for high resolution metabolomics analyses.
-URL: jasenfinch.github.io/hrm/
+URL: https://jasenfinch.github.io/hrm/
 BugReports: https://github.com/jasenfinch/hrm/issues
 Depends: R (>= 3.5.0)
 Imports: BiocManager,
         cli,
-        composition,
         construction,
         crayon,
         dplyr,
@@ -26,11 +25,10 @@ Imports: BiocManager,
         tidyverse
 License: GPL (>= 3)
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.3
 Suggests: testthat,
     covr
-Remotes: jasenfinch/composition,
-        jasenfinch/construction,
+Remotes: jasenfinch/construction,
         jasenfinch/grover,
         jasenfinch/metaboMisc,
         jasenfinch/metaboWorkflows,

NAMESPACE

@@ -6,7 +6,6 @@ export(hrmUpdate)
 importFrom(BiocManager,install)
 importFrom(cli,rule)
 importFrom(cli,symbol)
-importFrom(composition,keggPathways)
 importFrom(construction,construction)
 importFrom(crayon,black)
 importFrom(crayon,blue)
@@ -23,7 +22,7 @@ importFrom(metaboMisc,preTreatModes)
 importFrom(metaboWorkflows,defineWorkflow)
 importFrom(purrr,map_chr)
 importFrom(remotes,install_github)
-importFrom(riches,enrichmentParameters)
+importFrom(riches,functionalEnrichment)
 importFrom(rstudioapi,getThemeInfo)
 importFrom(rstudioapi,hasFun)
 importFrom(rstudioapi,isAvailable)

NEWS.md

@@ -1,3 +1,9 @@
+# hrm 0.9.2
+
+* Remove the {composition} package.
+
+* Updated {MFassign} to [{assignments}](https://aberhrml.github.io/assignments/) with package name change
+
 # hrm 0.9.1
 
 * Added the [`grover`](https://jasenfinch.github.io/grover) package.

R/hrm.R

@@ -3,8 +3,7 @@ globalVariables('.')
 ## Suppress imports check notes
 #' @importFrom metaboData availableDataSets
 #' @importFrom construction construction
-#' @importFrom composition keggPathways
-#' @importFrom riches enrichmentParameters
+#' @importFrom riches functionalEnrichment
 #' @importFrom metaboMisc preTreatModes
 #' @importFrom metaboWorkflows defineWorkflow
 #' @importFrom tidyverse tidyverse_packages

README.Rmd

@@ -17,23 +17,23 @@ knitr::opts_chunk$set(
 
 <!-- badges: start -->
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
-[![R build status](https://github.com/jasenfinch/hrm/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/hrm/actions)
-[![Coverage Status](https://img.shields.io/codecov/c/github/jasenfinch/hrm/master.svg)](https://codecov.io/github/jasenfinch/hrm?branch=master)
+[![R-CMD-check](https://github.com/jasenfinch/hrm/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jasenfinch/hrm/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/jasenfinch/hrm/branch/master/graph/badge.svg)](https://app.codecov.io/gh/jasenfinch/hrm?branch=master)
+[![GitHub release](https://img.shields.io/github/release/jasenfinch/hrm.svg)](https://GitHub.com/jasenfinch/hrm/releases/)
 <!-- badges: end -->
 
 Easily install, load and update an R package ecosystem for performing analyses of high resolution metabolomics data.
 
 `hrm` packages include:
 
-* [metaboData](https://aberHRML.github.io/metaboData) - Example data sets for metabolomics analyses
+* [metaboData](https://aberhrml.github.io/metaboData) - Example data sets for metabolomics analyses
 * [grover](https://jasenfinch.github.io/grover) - Web API Framework for Mass Spectrometry Data Transfer
-* [binneR](https://aberHRML.github.io/binneR) - Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
+* [binneR](https://aberhrml.github.io/binneR) - Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
 * [metabolyseR](https://jasenfinch.github.io/metabolyseR) - A tool kit for pre-treatment, modelling, feature selection and correlation analyses of metabolomics data
 * [profilePro](https://jasenfinch.github.io/profilePro) - Unified Input and Output for Processing of Metabolomic Profiling Experiments
-* [mzAnnotation](https://jasenfinch.github.io/mzAnnotation) -  Tools for putative annotation of accurate m/z from electrospray ionisation mass spectrometry data
-* [MFassign](https://github.com/jasenfinch/MFassign) - Molecular formula assignment for high resolution ESI metabolomics
-* [construction](https://github.com/jasenfinch/construction) - Consensus structural classifications for putative molecular formula assignments
-* [composition](https://github.com/jasenfinch/composition) - Compositional analyses for metabolomics data
+* [mzAnnotation](https://aberhrml.github.io/mzAnnotation) -  Tools for putative annotation of accurate m/z from electrospray ionisation mass spectrometry data
+* [assignments](https://aberhrml.github.io/assignments) - Molecular formula assignment for high resolution ESI metabolomics
+* [construction](https://jasenfinch.github.io/construction) - Consensus structural classifications for putative molecular formula assignments
 * [riches](https://jasenfinch.github.io/riches) - Structural and functional enrichment for metabolomics data
 * [metaboMisc](https://jasenfinch.github.io/metaboMisc) - A collection of miscellaneous helper and linker functions for metabolomics analyses
 * [metaboWorkflows](https://jasenfinch.github.io/metaboWorkflows) - Workflow Project Templates for Metabolomics Analyses