Merge pull request #34 from jasenfinch/devel

v0.5.6

.Rbuildignore

@@ -6,5 +6,4 @@
 ^codecov\.yml$
 ^_pkgdown\.yml$
 ^docs$
-^pkgdown$
-^iris\.csv$
+^pkgdown$

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

@@ -1,13 +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
+    branches: [main, master]
   schedule:
     - cron: '0 0 * * *'
 
@@ -23,70 +20,47 @@ 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: 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
+      - name: System 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
+          sudo apt-get install -y libopenbabel-dev libnetcdf-dev libglpk-dev libgit2-dev libsodium-dev
+          
+      - 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-
+          extra-packages: |
+            rcmdcheck
 
-      - 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 install libopenbabel-dev libnetcdf-dev libglpk-dev libgit2-dev libsodium-dev
+      - uses: r-lib/actions/check-r-package@v1
 
-      - name: Install dependencies
-        run: |
-          install.packages('http://fgcz-ms.uzh.ch/~cpanse/rawrr_0.1.8.tar.gz',repos = NULL)
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran(c("rcmdcheck","goodpractice"))
-          metaboData::downloadDataSet('FIE-HRMS','BdistachyonEcotypes',ask = FALSE)
-        shell: Rscript {0}
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
 
-      - 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()
-        shell: Rscript {0}
-
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0}
-
+      
       - name: Upload check results
         if: failure()
         uses: actions/upload-artifact@main

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: metaboMisc
 Title: Miscellaneous Functions for Metabolomics Analyses
-Version: 0.5.5
+Version: 0.5.6
 Authors@R: person("Jasen", "Finch", email = "jsf9@aber.ac.uk", role = c("aut", "cre"))
 Description: Miscellaneous helper functions for metabolomics analyses that do not yet have a permanent home.
-URL:  https://jasenfinch.github.io/metaboMisc
+URL: https://jasenfinch.github.io/metaboMisc
 BugReports: https://github.com/jasenfinch/metaboMisc/issues
 biocViews: Metabolomics
 Depends: R (>= 3.4)
@@ -28,9 +28,8 @@ Imports: binneR,
     ggplot2
 License: GPL (>= 3)
 Encoding: UTF-8
-LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Suggests: 
     testthat (>= 3.0.0),
     metaboData,

NEWS.md

@@ -1,3 +1,7 @@
+# metaboMisc 0.5.6
+
+* Fixed missing argument error in `detectPretreatmentParameters()` when miss injections are detected.
+
 # metaboMisc 0.5.5
 
 * Added `gzip_ext` argument to `convertSampleInfo()` to enable the addition of the `.gz` file extension to file names in the `fileNames` column.

R/detect.R

@@ -307,7 +307,7 @@ detectPretreatment <- function(x){
                 remove = list(
                     samples = list(idx = miss_injections$idx,samples = miss_injections$missInjections)
                 )),
-            parameters(pre_treat_params)
+            parameters(pre_treat_params,'pre-treatment')
         )
     }
 

README.md

@@ -2,7 +2,7 @@
 
 <!-- badges: start -->
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://www.tidyverse.org/lifecycle/#experimental)
-[![R build status](https://github.com/jasenfinch/metaboMisc/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/metaboMisc/actions)
+[![R-CMD-check](https://github.com/jasenfinch/metaboMisc/workflows/R-CMD-check/badge.svg)](https://github.com/jasenfinch/metaboMisc/actions)
 [![Codecov test coverage](https://codecov.io/gh/jasenfinch/metaboMisc/branch/master/graph/badge.svg)](https://codecov.io/gh/jasenfinch/metaboMisc?branch=master)
 [![license](https://img.shields.io/badge/license-GNU%20GPL%20v3.0-blue.svg)](https://github.com/jasenfinch/metaboMisc/blob/master/DESCRIPTION)
 <!-- badges: end -->

docs/pkgdown.yml

@@ -1,8 +1,8 @@
-pandoc: 2.11.2
+pandoc: 2.11.4
 pkgdown: 1.6.1
 pkgdown_sha: ~
 articles: {}
-last_built: 2021-05-10T14:01Z
+last_built: 2021-09-21T08:03Z
 urls:
   reference: https://jasenfinch.github.io/metaboMisc//reference
   article: https://jasenfinch.github.io/metaboMisc//articles