Added changes for v2.3.1

royfrancis · Dec 27, 2020 · 6c2e83e · 6c2e83e
1 parent 3ad0dba
commit 6c2e83e
Show file tree

Hide file tree

Showing 289 changed files with 253,254 additions and 2,860 deletions.
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -10,3 +10,4 @@ NEWS.md
 .git/
 vignettes/
 vignettes/*
+..Rcheck/
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,16 +1,23 @@
+## GITHUB ACTION FOR R PACKAGE
+## Build, check, test, code coverage
+## Required secrets
+## CODECOV_TOKEN
+## TOKEN
+
 name: build
 on:
+  pull_request:
   push:
     branches:
       - master
 jobs:
   linux:
     name: ubuntu
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     strategy:
       fail-fast: false
       matrix:
-        r: [3.5]
+        r: [3.5.3,3.6.3,4.0.0]
     steps:
       - uses: actions/checkout@v1
       - uses: r-lib/actions/setup-r@master
@@ -21,20 +28,20 @@ jobs:
       - name: Install linux dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install -y libfreetype6-dev libcurl4-openssl-dev libssl-dev libxml2-dev
+          sudo apt-get install -y libfreetype6-dev libcurl4-openssl-dev libssl-dev libxml2-dev libnlopt-dev
 
       - name: Check R installation
         run: Rscript -e "print('R installation works!')"
 
       - name: Cache R packages
-        id: cache-rp
-        uses: actions/cache@v1
+        id: cache-r-packages
+        uses: actions/cache@v2
         with:
           path: "/home/runner/work/_temp/Library"
-          key: ${{ runner.os }}-cache-rp-$(ls /home/runner/work/_temp/Library/ | sha256sum)
+          key: ${{runner.os}}-${{matrix.r}}-$(ls /home/runner/work/_temp/Library/ | sha256sum)
 
       - name: Install R dependencies
-        if: steps.cache-rp.outputs.cache-hit != 'true'
+        if: steps.cache-r-packages.outputs.cache-hit != 'true'
         run: |
           Rscript -e "install.packages(c('remotes','covr','rcmdcheck'))"
           Rscript -e "remotes::install_deps(pkgdir='.',dependencies=TRUE,repos='https://cran.rstudio.com/')"
@@ -44,93 +51,34 @@ jobs:
           R CMD INSTALL .
 
       - name: Code coverage
+        if: matrix.r == '4.0.0'
         run: Rscript -e 'covr::codecov(token="${{ secrets.CODECOV_TOKEN }}",quiet=FALSE)'
 
   windows:
     runs-on: windows-latest
     strategy:
       fail-fast: false
       matrix:
-        r: [3.5,3.6]
+        r: [3.5.3,3.6.3,4.0.0]
     steps:
       - uses: actions/checkout@v1
       - uses: r-lib/actions/setup-r@master
         with:
           r-version: ${{matrix.r}}
 
       - name: Cache R packages
-        id: cache-rp
-        uses: actions/cache@v1
+        id: cache-r-packages
+        uses: actions/cache@v2
         with:
           path: "C:/R/library"
-          key: ${{ runner.os }}-cache-rp
+          key: ${{runner.os}}-${{matrix.r}}
 
       - name: Install R dependencies
-        if: steps.cache-rp.outputs.cache-hit != 'true'
+        if: steps.cache-r-packages.outputs.cache-hit != 'true'
         run: |
           Rscript -e "install.packages(c('remotes','rcmdcheck','stringi'),lib='C:/R/library')"
           Rscript -e "remotes::install_deps(pkgdir='.',dependencies=TRUE,repos='https://cran.rstudio.com/',lib='C:/R/library')"
           Rscript -e "(print(.libPaths()))"
       - name: RMD check and install package
         run: |
           Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'warning', check_dir = 'check')"
-          R CMD INSTALL .
-  pkgdown:
-    needs: [mac, linux, windows]
-    runs-on: ubuntu-18.04
-    steps:
-      - uses: actions/checkout@v1
-      - uses: r-lib/actions/setup-r@master
-        with:
-          r-version: 3.6.2
-      - uses: r-lib/actions/setup-pandoc@master
-
-      - name: Install linux dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libfreetype6-dev libcurl4-openssl-dev libssl-dev libxml2-dev
-
-      - name: Check R installation
-        run: Rscript -e "print('R installation works!')"
-
-      - name: Cache R packages
-        id: cache-rp
-        uses: actions/cache@v1
-        with:
-          path: "/home/runner/work/_temp/Library"
-          key: ${{ runner.os }}-cache-rp-$(ls /home/runner/work/_temp/Library/ | sha256sum)
-
-      - name: Install R dependencies
-        if: steps.cache-rp.outputs.cache-hit != 'true'
-        run: |
-          Rscript -e "install.packages(c('remotes','rcmdcheck','pkgdown'))"
-          Rscript -e "remotes::install_deps(pkgdir='.',dependencies=TRUE,repos='https://cran.rstudio.com/')"
-
-      - name: RMD check and install package
-        run: |
-          Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'warning', check_dir = 'check')"
-          R CMD INSTALL .
-
-      - name: Render site, pull repo, copy folder, push repo
-        run: |
-          # Add git info
-          git config --global user.email "do_not_email@example.com"
-          git config --global user.name "gh_action"
-
-          # Render website
-          Rscript -e "pkgdown::build_site()"
-
-          # Clone gh-pages branch
-          git clone --single-branch --branch gh-pages "https://${{ secrets.TOKEN }}@github.com/${GITHUB_REPOSITORY}.git" tmprepo
-          cd tmprepo
-          rm -rf *
-          git add .
-          git commit -m "Old contents deleted."
-          cp -r ../docs/* .
-          echo "Folder contents at $(pwd):"
-          ls -lh
-
-          # Push changes back
-          git add .
-          git commit -m "Updated contents at $(date +%Y%m%d-%H%M%S)"
-          git push origin
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,37 +1,30 @@
 Package: pophelper
 Type: Package
-Title: Tabulate, analyse and visualise admixture proportions from STRUCTURE, TESS, BAPS, ADMIXTURE and tab-delimited q-matrices
-    files
-Version: 2.3.0
-Date: 2019-08-15
+Title: Tabulate, Analyse and Visualise Admixture Proportions
+Version: 2.3.1
+Date: 2020-12-28
 Author: Roy Mathew Francis
-Authors@R: person("Roy", "Francis", email = "roy.m.francis@outlook.com",role = c("aut", "cre"))
 Maintainer: Roy Mathew Francis <roy.m.francis@outlook.com>
-Description: A set of useful functions for processing admixture proportion files from the
-    population structure analysis softwares STRUCTURE, TESS, ADMIXTURE, BAPS, fastSTRUCTURE etc. The
-    package contains functions to read runs, tabulate runs, summarise runs, plot runs, estimate
-    K using Evanno method, export clumpp files, export distruct files and generate barplots.
+Description: Process admixture proportion files from the population structure analysis tools such as 'STRUCTURE', 'TESS', 'ADMIXTURE', 'BAPS', 'fastSTRUCTURE' etc. The package contains functions to read runs, tabulate runs, summarise runs, plot runs, estimate K using 'EVANNO' method, export 'CLUMPP' files, export 'DISTRUCT' files and generate barplots.
 URL: https://github.com/royfrancis/pophelper
 Depends:
-    R(>= 3.5.0),
-    ggplot2
+    R(>= 3.5)
 Imports:
+    ggplot2,
+    grDevices,
     grid,
     gridExtra,
-    gtable,
     label.switching,
-    tidyr
+    stats,
+    tidyr,
+    utils
 Suggests:
-    bookdown,
-    curl,
     captioner,
-    showtext,
-    ggpubr,
     knitr,
     rmarkdown,
+    showtext,
     testthat
 License: GPL-3
 Encoding: UTF-8
 BugReports: https://github.com/royfrancis/pophelper/issues
-VignetteBuilder: knitr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -26,8 +26,57 @@ export(splitQ)
 export(summariseQ)
 export(tabulateQ)
 export(verifyGrplab)
-import(grid)
-import(gridExtra)
-import(gtable)
-import(label.switching)
-import(tidyr)
+importFrom(ggplot2,aes)
+importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_line)
+importFrom(ggplot2,element_rect)
+importFrom(ggplot2,element_text)
+importFrom(ggplot2,facet_grid)
+importFrom(ggplot2,facet_wrap)
+importFrom(ggplot2,geom_bar)
+importFrom(ggplot2,geom_blank)
+importFrom(ggplot2,geom_errorbar)
+importFrom(ggplot2,geom_line)
+importFrom(ggplot2,geom_path)
+importFrom(ggplot2,geom_point)
+importFrom(ggplot2,geom_text)
+importFrom(ggplot2,geom_vline)
+importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggplotGrob)
+importFrom(ggplot2,guide_legend)
+importFrom(ggplot2,guides)
+importFrom(ggplot2,labeller)
+importFrom(ggplot2,labs)
+importFrom(ggplot2,margin)
+importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_x_discrete)
+importFrom(ggplot2,scale_y_continuous)
+importFrom(ggplot2,theme)
+importFrom(ggplot2,theme_bw)
+importFrom(ggplot2,theme_grey)
+importFrom(ggplot2,unit)
+importFrom(ggplot2,waiver)
+importFrom(grDevices,colorRampPalette)
+importFrom(grDevices,dev.off)
+importFrom(grDevices,jpeg)
+importFrom(grDevices,pdf)
+importFrom(grDevices,png)
+importFrom(grDevices,tiff)
+importFrom(grid,unit.pmax)
+importFrom(gridExtra,arrangeGrob)
+importFrom(gridExtra,grid.arrange)
+importFrom(label.switching,stephens)
+importFrom(stats,aggregate)
+importFrom(stats,as.formula)
+importFrom(stats,ave)
+importFrom(stats,sd)
+importFrom(tidyr,pivot_longer)
+importFrom(tidyr,pivot_wider)
+importFrom(utils,packageDescription)
+importFrom(utils,read.delim)
+importFrom(utils,read.table)
+importFrom(utils,setTxtProgressBar)
+importFrom(utils,str)
+importFrom(utils,txtProgressBar)
+importFrom(utils,write.table)
diff --git a/NEWS b/NEWS
@@ -1,7 +1,21 @@
+pophelper 2.3.1
+=================
+* 28-Dec-2020
+* Min req R-3.5.
+* Error bars in first plot of Evanno method showed max/min rather than SD. Fixed to show SD.
+* Input and output directories are to be specified explicitly by user as per CRAN guidelines
+* cat and print statements replaced with message or warning
+* Argument 'quiet' removed in all functions
+* Fixed dependency issues
+* Automatic CI testing added
+* Fixed an issue where runs merged using mergeQ() produced a warning about missing attributes.
+* In function clumppExport() and distructExport(), argument 'path' changed to 'exportpath' to be consistent with other functions.
+* Fixed minor errors in documentation.
+
 pophelper 2.3.0
 =================
 * 11-Aug-2019
-* Built on R-3.6.0. Min req R-3.5.0.
+* Min req R-3.5.0.
 * Removed CLUMPP and DISTRUCT executables
 * 'useexe' argument in ClumppExport() deprecated.
 * Added alignK() function for label switching within and between K