Merge pull request #45 from Cristianetaniguti/update_checks

Update checks

.Rbuildignore

@@ -1,14 +1,15 @@
-^Meta$
-^doc$
-todo
-copying
-^\.travis\.yml$
-^.*\.Rproj$
-^NEWS\.md$
-^vignettes_highres$
-^\.Rproj\.user$
-
-^README.md
-^vignettes_highres
-Dockerfile
-
+^Meta$
+^doc$
+todo
+copying
+^\.travis\.yml$
+^.*\.Rproj$
+^NEWS\.md$
+^vignettes_highres$
+^\.Rproj\.user$
+
+^README.md
+^vignettes_highres
+Dockerfile
+
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/check-standard.yaml

@@ -0,0 +1,92 @@
+# 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
+on:
+  push:
+    branches:
+      - main
+      - master
+      - update_checks
+  pull_request:
+    branches:
+      - main
+      - master
+      - update_checks
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      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", http-user-agent: "R/4.1.0 (ubuntu-20.04) R (4.1.0 x86_64-pc-linux-gnu x86_64 linux-gnu) on GitHub Actions" }
+
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@v1
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Restore R package cache
+        uses: actions/cache@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")
+          remotes::install_cran("covr")
+        shell: Rscript {0}
+
+      - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: |
+          options(crayon.enabled = TRUE)
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "error", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@main
+        with:
+          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
+          path: check
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}

.gitignore

@@ -1,14 +1,16 @@
-.Rhistory
-*~
-.Rproj.user
-.RData
-onemap.Rproj
-.Rd
-*.o
-*.so
-*.cro
-*.map
-*.bak
-*.Rproj
-Meta
-new_find_bins
+.Rhistory
+*~
+.Rproj.user
+.RData
+onemap.Rproj
+.Rd
+*.o
+*.so
+*.cro
+*.map
+*.bak
+*.Rproj
+Meta
+/doc/
+/Meta/
+/src/onemap.dll

.travis.yml

@@ -1,26 +1,32 @@
-language: r
-cache: packages
-
-r_build_args: --no-build-vignettes
-r_check_args: --no-vignettes
-
-notifications:
-  email:
-    on_success: change
-    on_failure: change
-
-services:
-    - xvfb
-
-before_install:
-    - export DISPLAY=:99.0
-    - export RGL_USE_NULL=TRUE
-    - tlmgr install index
-
-apt_packages:
-    - libssl-dev 
-    - libftgl2 
-    - libglu1-mesa-dev 
-    - libftgl2 
-    - libfreetype6-dev  
-    - libxml2-dev
+language: r
+cache: packages
+
+r_build_args: --no-build-vignettes
+r_check_args: --no-vignettes
+
+notifications:
+  email:
+    on_success: change
+    on_failure: change
+
+services:
+    - xvfb
+
+before_install:
+    - export DISPLAY=:99.0
+    - export RGL_USE_NULL=FALSE
+    - tlmgr install index
+
+apt_packages:
+    - libssl-dev 
+    - libftgl2 
+    - libglu1-mesa-dev 
+    - libftgl2 
+    - libfreetype6-dev  
+    - libxml2-dev
+
+r_packages:
+ - covr
+
+after_success:
+  - Rscript -e 'library(covr); codecov()'

DESCRIPTION

@@ -1,59 +1,62 @@
-Package: onemap
-Title: Construction of Genetic Maps in Experimental Crosses: Full-Sib,
-        RILs, F2 and Backcrosses
-Version: 2.2.0
-Description: Analysis of molecular marker data from model (backcrosses,
-    F2 and recombinant inbred lines) and non-model systems (i. e.
-    outcrossing species). For the later, it allows statistical
-    analysis by simultaneously estimating linkage and linkage
-    phases (genetic map construction) according to Wu et al. (2002)
-    <doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint 
-    approaches using hidden Markov models.
-Date: 2020-02-14
-Authors@R: c(person("Gabriel", "Margarido", role = "aut", email =
-        "gramarga@usp.br"), person("Marcelo", "Mollinari", role =
-        "aut", email = "mmollina@usp.br"), person("Karl",
-        "Broman", role = "ctb", email = "kbroman@biostat.wisc.edu"),
-        person("Getulio", "Ferreira", role="ctb", email="getulio.caifer@usp.br"),
-        person("Rodrigo", "Amadeu", role = "ctb", email = "rodrigo.amadeu@usp.br"),
-        person("Cristiane", "Taniguti", role=c("ctb", "cre"), email="chtaniguti@usp.br"),
-        person("Augusto", "Garcia", role = c("aut", "ctb"), email =
-        "augusto.garcia@usp.br"))
-Author: Gabriel Margarido [aut], Marcelo Mollinari [aut], Karl
-        Broman [ctb], Getulio Ferreira [ctb], Rodrigo Amadeu [ctb], Cristiane Taniguti [ctb, cre], Augusto Garcia [aut, ctb]
-LinkingTo: Rcpp (>= 0.10.5)
-Depends: R (>= 3.6.0)
-Imports: ggplot2 (>= 2.2.1), 
-        plotly (>= 4.7.1),
-        reshape2 (>= 1.4.1), 
-        Rcpp (>= 0.10.5),
-        graphics, 
-        methods, 
-        stats, 
-        utils,
-        grDevices,
-        MDSMap,
-        parallel,
-        updog,
-        dplyr,
-        tidyr,
-        stringr,
-        htmlwidgets,
-        ggpubr,
-        RColorBrewer
-Suggests: qtl (>= 1.36-6), 
-          knitr (>= 1.10), 
-          rmarkdown, 
-          vcfR (>= 1.6.0),
-VignetteBuilder: knitr
-Encoding: UTF-8
-License: GPL-3
-URL: https://github.com/augusto-garcia/onemap
-BugReports: https://github.com/augusto-garcia/onemap/wiki
-Maintainer: Cristiane Taniguti <chtaniguti@usp.br>
-Repository: CRAN
-Packaged: 2019-09-22 22:25:43 UTC; cris
-NeedsCompilation: yes
-Date/Publication: 2019-09-22 22:48:07 UTC
-RoxygenNote: 7.1.1
-biocViews:
+Package: onemap
+Title: Construction of Genetic Maps in Experimental Crosses: Full-Sib,
+        RILs, F2 and Backcrosses
+Version: 2.8.0
+Description: Analysis of molecular marker data from model (backcrosses,
+    F2 and recombinant inbred lines) and non-model systems (i. e.
+    outcrossing species). For the later, it allows statistical
+    analysis by simultaneously estimating linkage and linkage
+    phases (genetic map construction) according to Wu et al. (2002)
+    <doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint 
+    approaches using hidden Markov models.
+Date: 2021-08-19
+Authors@R: c(person("Gabriel", "Margarido", role = "aut", email =
+        "gramarga@usp.br"), person("Marcelo", "Mollinari", role =
+        "aut", email = "mmollina@usp.br"), person("Karl",
+        "Broman", role = "ctb", email = "kbroman@biostat.wisc.edu"),
+        person("Getulio", "Ferreira", role="ctb", email="getulio.caifer@usp.br"),
+        person("Rodrigo", "Amadeu", role = "ctb", email = "rodrigo.amadeu@usp.br"),
+        person("Cristiane", "Taniguti", role=c("ctb", "cre"), email="chtaniguti@usp.br"),
+        person("Augusto", "Garcia", role = c("aut", "ctb"), email =
+        "augusto.garcia@usp.br"))
+Author: Gabriel Margarido [aut], Marcelo Mollinari [aut], Karl
+        Broman [ctb], Getulio Ferreira [ctb], Rodrigo Amadeu [ctb], Cristiane Taniguti [ctb, cre], Augusto Garcia [aut, ctb]
+LinkingTo: Rcpp (>= 0.10.5)
+Depends: R (>= 3.6.0)
+Imports: ggplot2 (>= 2.2.1), 
+        plotly (>= 4.7.1),
+        reshape2 (>= 1.4.1), 
+        Rcpp (>= 0.10.5),
+        graphics, 
+        methods, 
+        stats, 
+        utils,
+        grDevices,
+        smacof,
+        princurve,
+        parallel,
+        dplyr,
+        tidyr,
+        htmlwidgets,
+        ggpubr,
+        RColorBrewer,
+        dendextend,
+        rebus,
+        vcfR (>= 1.6.0)
+Suggests: 
+    knitr (>= 1.10),
+    rmarkdown,
+    testthat,
+    stringr
+VignetteBuilder: knitr
+Encoding: UTF-8
+License: GPL-3
+URL: https://github.com/augusto-garcia/onemap
+BugReports: https://github.com/augusto-garcia/onemap/wiki
+Maintainer: Cristiane Taniguti <chtaniguti@usp.br>
+Repository: CRAN
+Packaged: 2019-09-22 22:25:43 UTC; cris
+NeedsCompilation: yes
+Date/Publication: 2019-09-22 22:48:07 UTC
+RoxygenNote: 7.1.1.9001
+biocViews: