Remove aes_string() and Fix CI

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

@@ -1,14 +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
+    branches: [main, master]
   pull_request:
-    branches:
-      - main
-      - master
+    branches: [main, master]
 
 name: R-CMD-check
 
@@ -22,65 +18,32 @@ 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: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
 
-      - uses: r-lib/actions/setup-pandoc@v1
-
-      - 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-dependencies@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
-        if: runner.os == 'Linux'
-        run: |
-          while read -r cmd
-          do
-            eval sudo $cmd
-          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
-
-      - name: Install dependencies
-        run: |
-          remotes::install_deps(dependencies = TRUE)
-          remotes::install_cran("rcmdcheck")
-          install.packages("BiocManager")
-          BiocManager::install(c("VariantAnnotation", "GenomicRanges", "S4Vectors", "IRanges"))
-        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}
+          extra-packages: any::rcmdcheck
+          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

DESCRIPTION

@@ -26,7 +26,7 @@ BugReports: https://github.com/dcgerard/updog/issues
 URL: https://github.com/dcgerard/updog/
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
 LinkingTo: Rcpp,
     RcppArmadillo
 Imports: 

R/multidog.R

@@ -741,7 +741,7 @@ export_vcf <- function(obj, filename) {
         strand=NULL,
         seqinfo = NULL,
         names = obj$snpdf$snp),
-      colData = DataFrame(row.names = indvec),
+      colData = S4Vectors::DataFrame(row.names = indvec),
       exptData = list(
         header = VariantAnnotation::VCFHeader(
           reference = character(),

R/oracle.R

@@ -269,6 +269,7 @@ oracle_mis_vec_from_joint <- function(jd) {
 #' print(pl)
 #'
 oracle_plot <- function(jd) {
+  .data <- NULL ## stupid work around for ggplot2 and R CMD check
   mat_text <- format(round(jd, digits = 2), digits = 2)
   probability_text <- c(sub("0\\.", "\\.", sub("0.00", "0", mat_text)))
 
@@ -279,9 +280,9 @@ oracle_plot <- function(jd) {
   omiss <- oracle_mis_from_joint(jd = jd)
   ocorr <- oracle_cor_from_joint(jd = jd)
 
-  ggplot2::ggplot(data = dfdat, mapping = ggplot2::aes_string(x = "x", y = "y", fill = "Probability")) +
+  ggplot2::ggplot(data = dfdat, mapping = ggplot2::aes(x = .data[["x"]], y = .data[["y"]], fill = .data[["Probability"]])) +
     ggplot2::geom_tile() +
-    ggplot2::geom_text(ggplot2::aes_string(label = "probability_text")) +
+    ggplot2::geom_text(ggplot2::aes(label = .data[["probability_text"]])) +
     ggplot2::xlab("Estimated Genotype") +
     ggplot2::ylab("True Genotype") +
     ggplot2::ggtitle(paste0("Misclassification Error Rate: ",

R/plot_geno.R

@@ -79,6 +79,7 @@ plot_geno <- function(refvec,
     use_colorblind <- FALSE
   }
 
+  .data <- NULL ## stupid work around for ggplot2 and R CMD check
   assertthat::assert_that(all(refvec >= 0, na.rm = TRUE))
   assertthat::assert_that(all(sizevec >= refvec, na.rm = TRUE))
   assertthat::assert_that(ploidy >= 1)
@@ -108,14 +109,14 @@ plot_geno <- function(refvec,
 
   ## Plot children
   if (is.null(maxpostprob)) {
-    pl <- ggplot2::ggplot(data = dfdat, mapping = ggplot2::aes_string(y = "A", x = "a"))
+    pl <- ggplot2::ggplot(data = dfdat, mapping = ggplot2::aes(y = .data[["A"]], x = .data[["a"]]))
   } else {
-    pl <- ggplot2::ggplot(data = dfdat, mapping = ggplot2::aes_string(y = "A", x = "a", alpha = "maxpostprob"))
+    pl <- ggplot2::ggplot(data = dfdat, mapping = ggplot2::aes(y = .data[["A"]], x = .data[["a"]], alpha = .data[["maxpostprob"]]))
   }
 
   ## add offspring genotypes ------------------------------------------------
   if (!is.null(geno)) {
-    pl <- pl + ggplot2::geom_point(ggplot2::aes_string(color = "genotype"))
+    pl <- pl + ggplot2::geom_point(ggplot2::aes(color = .data[["genotype"]]))
   } else {
     pl <- pl + ggplot2::geom_point()
   }
@@ -125,7 +126,7 @@ plot_geno <- function(refvec,
     ggplot2::ylim(0, maxcount) +
     ggplot2::ylab("Counts A") +
     ggplot2::xlab("Counts a")  +
-    ggplot2::geom_segment(data = df_lines, mapping = ggplot2::aes_string(x = "x", y = "y", xend = "xend", yend = "yend"),
+    ggplot2::geom_segment(data = df_lines, mapping = ggplot2::aes(x = .data[["x"]], y = .data[["y"]], xend = .data[["xend"]], yend = .data[["yend"]]),
                           lty = 2, alpha = 1/2, color = "black", size = 0.5)
 
   ## add parents if we have them
@@ -143,7 +144,7 @@ plot_geno <- function(refvec,
     p1dat <- data.frame(A = p1ref, a = p1size - p1ref)
     if (!is.null(p1geno)) {
       p1dat$genotype <- factor(p1geno, levels = 0:ploidy)
-      pl <- pl + ggplot2::geom_point(data = p1dat, mapping = ggplot2::aes_string(color = "genotype"),
+      pl <- pl + ggplot2::geom_point(data = p1dat, mapping = ggplot2::aes(color = .data[["genotype"]]),
                                      size = 3, pch = 3, alpha = 1, show.legend = FALSE)
       pl <- pl + ggplot2::geom_point(data = p1dat, size = 1, color = "black", pch = 16, alpha = 1)
     } else {
@@ -164,7 +165,7 @@ plot_geno <- function(refvec,
     p2dat <- data.frame(A = p2ref, a = p2size - p2ref)
     if (!is.null(p2geno)) {
       p2dat$genotype <- factor(p2geno, levels = 0:ploidy)
-      pl <- pl + ggplot2::geom_point(data = p2dat, mapping = ggplot2::aes_string(color = "genotype"),
+      pl <- pl + ggplot2::geom_point(data = p2dat, mapping = ggplot2::aes(color = .data[["genotype"]]),
                                      size = 3, pch = 4, alpha = 1, show.legend = FALSE)
       pl <- pl + ggplot2::geom_point(data = p2dat, size = 1, color = "black", pch = 16, alpha = 1)
     } else {

README.Rmd

@@ -14,7 +14,7 @@ knitr::opts_chunk$set(
 
 # updog <img src="man/figures/logo.png" align="right" height="139" />
 
-[![R-CMD-check](https://github.com/dcgerard/updog/workflows/R-CMD-check/badge.svg)](https://github.com/dcgerard/updog/actions)
+[![R-CMD-check](https://github.com/dcgerard/updog/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dcgerard/updog/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/dcgerard/updog/branch/master/graph/badge.svg?token=zjDBKZWjCs)](https://app.codecov.io/gh/dcgerard/updog)
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/updog)](https://cran.r-project.org/package=updog)

README.md

@@ -3,7 +3,7 @@
 
 # updog <img src="man/figures/logo.png" align="right" height="139" />
 
-[![R-CMD-check](https://github.com/dcgerard/updog/workflows/R-CMD-check/badge.svg)](https://github.com/dcgerard/updog/actions)
+[![R-CMD-check](https://github.com/dcgerard/updog/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/dcgerard/updog/actions/workflows/R-CMD-check.yaml)
 [![codecov](https://codecov.io/gh/dcgerard/updog/branch/master/graph/badge.svg?token=zjDBKZWjCs)](https://app.codecov.io/gh/dcgerard/updog)
 [![License: GPL
 v3](https://img.shields.io/badge/License-GPL%20v3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
@@ -32,22 +32,21 @@ the data.
 
 Also provided are:
 
--   `filter_snp()`: filter out SNPs based on the output of `multidog()`.
--   `format_multidog()`: format the output of `multidog()` in terms of a
-    multidimensional array.
--   Plot methods. Both `flexdog()` and `multidog()` have plot methods.
-    See the help files of `plot.flexdog()` and `plot.multidog()` for
-    details.
--   Functions to simulate genotypes (`rgeno()`) and read-counts
-    (`rflexdog()`). These support all of the models available in
-    `flexdog()`.
--   Functions to evaluate oracle genotyping performance:
-    `oracle_joint()`, `oracle_mis()`, `oracle_mis_vec()`, and
-    `oracle_cor()`. We mean “oracle” in the sense that we assume that
-    the entire data generation process is known (i.e. the genotype
-    distribution, sequencing error rate, allele bias, and overdispersion
-    are all known). These are good approximations when there are a lot
-    of individuals (but not necessarily large read-depth).
+- `filter_snp()`: filter out SNPs based on the output of `multidog()`.
+- `format_multidog()`: format the output of `multidog()` in terms of a
+  multidimensional array.
+- Plot methods. Both `flexdog()` and `multidog()` have plot methods. See
+  the help files of `plot.flexdog()` and `plot.multidog()` for details.
+- Functions to simulate genotypes (`rgeno()`) and read-counts
+  (`rflexdog()`). These support all of the models available in
+  `flexdog()`.
+- Functions to evaluate oracle genotyping performance: `oracle_joint()`,
+  `oracle_mis()`, `oracle_mis_vec()`, and `oracle_cor()`. We mean
+  “oracle” in the sense that we assume that the entire data generation
+  process is known (i.e. the genotype distribution, sequencing error
+  rate, allele bias, and overdispersion are all known). These are good
+  approximations when there are a lot of individuals (but not
+  necessarily large read-depth).
 
 The original `updog` package is now named `updogAlpha` and may be found
 [here](https://github.com/dcgerard/updogAlpha).

src/Makevars

@@ -1,6 +1,2 @@
-
-## optional
-CXX_STD = CXX11
-
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
-PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

src/Makevars.win

@@ -1,6 +1,2 @@
-
-## optional
-CXX_STD = CXX11
-
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
-PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
+PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)