Merge pull request #257 from grunwaldlab/fix-cran-bug-256

Fix cran bug 256

.Rbuildignore

@@ -24,3 +24,4 @@ vignettes/poppr_manual.Rmd
 ^pkgdown$
 ^\.github$
 ^docs$
+^CRAN-SUBMISSION$

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

@@ -1,14 +1,14 @@
-# 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]
+  release:
+    types: [published]
+  schedule:
+    - cron: '0 4 * * 2'
 
 name: R-CMD-check
 
@@ -22,70 +22,42 @@ 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
+      TINYTEX_INSTALLER: TinyTex
 
     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: ${{ matrix.config.r }}
-
-      - uses: r-lib/actions/setup-pandoc@v1
-      - uses: r-lib/actions/setup-tinytex@v1
-      - name: Install LaTeX packages
-        run: |
-          tlmgr install colortbl
-          tlmgr install mathtools
-          tlmgr install preprint
-          tlmgr install natbib
-
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Cache R packages
-        if: runner.os != 'Windows'
-        uses: actions/cache@v2
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-tinytex@v2
+      # - name: Install LaTeX packages
+      #   run: |
+      #     tlmgr install colortbl
+      #     tlmgr install mathtools
+      #     tlmgr install preprint
+      #     tlmgr install natbib
+
+      - 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")
-        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, local::.
+          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/test-coverage.yaml

@@ -0,0 +1,50 @@
+# 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
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, local::.
+          needs: check
+
+      - 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

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 2.9.4
+Date: 2023-03-23 00:53:20 UTC
+SHA: b43ac8e7096d534fab19e3a7834a42215b6e9081

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: poppr
 Type: Package
 Title: Genetic Analysis of Populations with Mixed Reproduction
-Version: 2.9.3
+Version: 2.9.4
 Authors@R: c(person(c("Zhian", "N."), "Kamvar", role = c("cre", "aut"),
     email = "zkamvar@gmail.com", comment = c(ORCID = "0000-0003-1458-7108")),
     person(c("Javier", "F."), "Tabima", role = "aut",
@@ -33,7 +33,7 @@ Description: Population genetic analyses for hierarchical analysis of partially
     clonal populations built upon the architecture of the 'adegenet' package. 
     Originally described in Kamvar, Tabima, and Grünwald (2014) 
     <doi:10.7717/peerj.281> with version 2.0 described in Kamvar, Brooks, and 
-    Grünwald (2015) <doi:10.3389/fgene.2015.00208>.
+    Grünwald (2015) <doi:10.3389/fgene.2015.00208>. 
 MailingList: https://groups.google.com/d/forum/poppr
 BugReports: https://github.com/grunwaldlab/poppr/issues/
 Depends:
@@ -63,8 +63,8 @@ Suggests:
     knitr,
     rmarkdown,
     poweRlaw,
-    cowplot,
-    RClone
+    cowplot
+Config/Needs/check: dbailleul/RClone
 License: GPL-2 | GPL-3
 VignetteBuilder: knitr
-RoxygenNote: 7.1.1
+RoxygenNote: 7.2.3

NEWS.md

@@ -1,3 +1,19 @@
+poppr 2.9.4
+===========
+
+CRAN MAINTENANCE
+----------------
+
+* a function declaration was added for `SEXP omp_test()`
+* failing tests were fixed.
+* code where object classes were compared with `==` was fixed to use `inherits()`
+
+DEPENDENCIES
+------------
+
+* {RClone} has been removed as a suggested package as it was archived on CRAN
+  some time ago.
+
 poppr 2.9.3
 ===========
 

R/bootstraping.R

@@ -588,7 +588,7 @@ diversity_boot <- function(tab, n, n.boot = 1L, n.rare = NULL, H = TRUE,
 #'   one clear method for calculating confidence intervals. A suggestion for
 #'   correction in Shannon's index is to center the CI around the observed
 #'   statistic (Marcon, 2012), but there are theoretical limitations to this.
-#'   For details, see <http://stats.stackexchange.com/q/156235/49413>.
+#'   For details, see <https://stats.stackexchange.com/q/156235/49413>.
 #'   }
 #' 
 #'   \subsection{User-defined functions}{ 
@@ -604,6 +604,7 @@ diversity_boot <- function(tab, n, n.boot = 1L, n.rare = NULL, H = TRUE,
 #'   vegan::rarefy(t(as.matrix(x)), 10)`).
 #'   }
 #' @export
+#' @md
 #' @seealso [diversity_boot()] [diversity_stats()]
 #'   [poppr()] [boot::boot()] [boot::norm.ci()]
 #'   [boot::boot.ci()]

R/data_subset.r

@@ -296,9 +296,9 @@ popsub <- function(gid, sublist="ALL", exclude=NULL, blacklist=NULL, mat=NULL, d
   if (!is.null(exclude)){
 
     # If both the sublist and exclude are numeric or character.
-    if (is.numeric(sublist) & is.numeric(exclude) | class(sublist) == class(exclude)){
+    if (is.numeric(sublist) && is.numeric(exclude) || identical(class(sublist), class(exclude))){
       sublist <- sublist[!sublist %in% exclude]
-    } else if (is.numeric(sublist) & class(exclude) == "character"){
+    } else if (is.numeric(sublist) && inherits(exclude, "character")){
       # if the sublist is numeric and exclude is a character. eg s=1:10, b="USA"
       sublist <- sublist[sublist %in% which(!popnames %in% exclude)]
     } else {

R/distances.r

@@ -205,7 +205,7 @@ diss.dist <- function(x, percent=FALSE, mat=FALSE){
 #' Prevosti A. (1974) La distancia genetica entre poblaciones. Miscellanea
 #' Alcobe, 68, 109-118. 
 #' 
-#' Prevosti A., Oca\~na J. and Alonso G. (1975) Distances
+#' Prevosti A., Ocana J. and Alonso G. (1975) Distances
 #' between populations of Drosophila subobscura, based on chromosome
 #' arrangements frequencies. Theoretical and Applied Genetics, 45, 231-241. 
 #' 

R/internal.r

@@ -197,9 +197,9 @@ sub_index <- function(pop, sublist="ALL", exclude=NULL){
   # Treating anything present in exclude.
   if (!is.null(exclude)){
     # If both the sublist and exclude are numeric or character.
-    if (is.numeric(sublist) & is.numeric(exclude) | class(sublist) == class(exclude)){
+    if (is.numeric(sublist) && is.numeric(exclude) || identical(class(sublist), class(exclude))) {
       sublist <- sublist[!sublist %in% exclude]
-    } else if (is.numeric(sublist) & class(exclude) == "character"){
+    } else if (is.numeric(sublist) && inherits(exclude, "character")){
     # if the sublist is numeric and exclude is a character. eg s=1:10, b="USA"
       sublist <- sublist[sublist %in% which(!popNames(pop) %in% exclude)]
     } else {

R/poppr.R

@@ -84,7 +84,7 @@
 #'
 #'   Examples of analyses are available in a primer written by Niklaus J.
 #'   Grünwald, Zhian N. Kamvar, and Sydney E.  Everhart at
-#'   <http://grunwaldlab.github.io/Population_Genetics_in_R/>.}
+#'   <https://grunwaldlab.github.io/Population_Genetics_in_R/>.}
 #'   
 #'   \subsection{Getting help}{ If you have a specific question or issue with 
 #'   \pkg{poppr}, feel free to contribute to the google group at 

README.md

@@ -1,7 +1,7 @@
 # Poppr version 2 <img src="man/figures/small_logo.png" align="right" height="98"/>
 
 <!-- badges: start -->
-[![R-CMD-check](https://github.com/grunwaldlab/poppr/workflows/R-CMD-check/badge.svg)](https://github.com/grunwaldlab/poppr/actions)
+[![R-CMD-check](https://github.com/grunwaldlab/poppr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/grunwaldlab/poppr/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 ## What is *poppr*?
@@ -98,7 +98,7 @@ New features are occasionally added to {poppr}, but it can take time for it to
 get to CRAN. If you know that you want the latest version of {poppr}, (which
 will contain bug fixes and new features to be included in future releases), then
 you can use the custom R-Universe repository, which is updated hourly: 
-<https://zkamvar.r-universe.dev/ui#builds>
+<https://zkamvar.r-universe.dev/builds>
 
 To install poppr from the R-Universe, you can use the following code:
 

cran-comments.md

@@ -1,23 +1,5 @@
-# Poppr version 2.9.3
+# Poppr version 2.9.4
 
-This update rearranges the C files to declare all non-R headers before R headers to address the openmp failures in clang13 as pointed out by Prof. Ripley. 
-
-## Test environments
-
-* local macOS install, R 4.1.1
-* local ubuntu 20.04 install, R 4.1.1, R devel
-* windows R Under development (unstable) 
-
-## R CMD check results
-
-Ubuntu Linux: OK
-macOS:        OK
-Windows:      OK
-
-
-## Downstream dependencies
-
-- popprxl:  OK
-- vcfR:     OK
-- adegenet: OK
+This fixes broken tests, provides a declaration for an exported C function, and fixes object class comparison to use identical()
+This also removes RClone from Suggests. There is no user-facing code that contains RClone and it is an archived package on CRAN.
 

inst/CITATION

@@ -3,9 +3,9 @@ umlaut <- iconv("\x9f", from = "MAC", to = "UTF-8") # paste0("u", "\u0308")
 header <- paste("To cite poppr in publications or presentations, please specify poppr version", meta$Version, "and with the following citation:")
 citHeader(header)
 
-citEntry(entry = 'article',
+bibentry(bibtype = 'article',
  title = "\\textit{Poppr}: an {R} package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction.",
- author = personList(as.person("Zhian N. Kamvar"),
+ author = c(as.person("Zhian N. Kamvar"),
                      as.person("Javier F. Tabima"),
                      as.person(paste0("Niklaus J. Gr", umlaut, "nwald"))
           ),
@@ -22,9 +22,9 @@ citEntry(entry = 'article',
  textVersion = paste0("Kamvar ZN, Tabima JF, Grünwald NJ. (2014) Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction. PeerJ 2:e281. doi: 10.7717/peerj.281")
 )
 
-citEntry(entry = 'article',
+bibentry(bibtype = 'article',
  title = "{Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality}",
- author = personList(as.person("Zhian N. Kamvar"),
+ author = c(as.person("Zhian N. Kamvar"),
                      as.person("Jonah C. Brooks"),
                      as.person(paste0("Niklaus J. Gr", umlaut, "nwald"))
           ),