Merge pull request #18 from bitarellolab/bbita-dev

Bbita dev

..Rcheck/00check.log

@@ -0,0 +1,13 @@
+* using log directory ‘/Users/dudutchy/Documents/GitHub/balselr/..Rcheck’
+* using R version 4.3.3 (2024-02-29)
+* using platform: aarch64-apple-darwin20 (64-bit)
+* R was compiled by
+ Apple clang version 14.0.0 (clang-1400.0.29.202)
+ GNU Fortran (GCC) 12.2.0
+* running under: macOS Sonoma 14.4.1
+* using session charset: UTF-8
+* checking for file ‘./DESCRIPTION’ ... ERROR
+Required fields missing or empty:
+ ‘Author’ ‘Maintainer’
+* DONE
+Status: 1 ERROR

.Rbuildignore

@@ -6,3 +6,5 @@
 ^LICENSE\.md$
 ^BalSelTools\.Rproj$
 ^README\.Rmd$
+^\.github$
+^\.library$

.Renviron

@@ -1,2 +1 @@
 RENV_CONFIG_WATCHDOG_ENABLED = FALSE
-R_BUILD_TAR=tar

.Rprofile

@@ -1,4 +1,4 @@
-source("renv/activate.R")
+# source("renv/activate.R")
 if (interactive()) {
  suppressMessages(require(devtools))
 }

.github/.gitignore

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

.github/workflows/R-CMD-check.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: 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: 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:
+ GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+ R_KEEP_PKG_SOURCE: yes
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - 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-r-dependencies@v2
+ with:
+ extra-packages: any::rcmdcheck
+ needs: check
+
+ - uses: r-lib/actions/check-r-package@v2
+ with:
+ upload-snapshots: true
+ build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.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: ${{ secrets.GITHUB_TOKEN }}
+
+ steps:
+ - uses: actions/checkout@v4
+
+ - uses: r-lib/actions/setup-r@v2
+ with:
+ use-public-rspm: true
+
+ - uses: r-lib/actions/setup-r-dependencies@v2
+ with:
+ extra-packages: any::covr
+ needs: coverage
+
+ - name: Test coverage
+ run: |
+ covr::codecov(
+ quiet = FALSE,
+ clean = FALSE,
+ install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+ )
+ shell: Rscript {0}
+
+ - name: Show testthat output
+ if: always()
+ run: |
+ ## --------------------------------------------------------------------
+ find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+ shell: bash
+
+ - name: Upload test results
+ if: failure()
+ uses: actions/upload-artifact@v4
+ with:
+ name: coverage-test-failures
+ path: ${{ runner.temp }}/package

.gitignore

@@ -7,3 +7,4 @@
 .DS_Store
 local_only/
 inst/doc
+.quarto

.library/DT/DESCRIPTION

@@ -0,0 +1,60 @@
+Package: DT
+Type: Package
+Title: A Wrapper of the JavaScript Library 'DataTables'
+Version: 0.33
+Authors@R: c(
+ person("Yihui", "Xie", role = "aut"),
+ person("Joe", "Cheng", email = "[email protected]", role = c("aut", "cre")),
+ person("Xianying", "Tan", role = "aut"),
+ person("JJ", "Allaire", role = "ctb"),
+ person("Maximilian", "Girlich", role = "ctb"),
+ person("Greg", "Freedman Ellis", role = "ctb"),
+ person("Johannes", "Rauh", role = "ctb"),
+ person("SpryMedia Limited", role = c("ctb", "cph"), comment = "DataTables in htmlwidgets/lib"),
+ person("Brian", "Reavis", role = c("ctb", "cph"), comment = "selectize.js in htmlwidgets/lib"),
+ person("Leon", "Gersen", role = c("ctb", "cph"), comment = "noUiSlider in htmlwidgets/lib"),
+ person("Bartek", "Szopka", role = c("ctb", "cph"), comment = "jquery.highlight.js in htmlwidgets/lib"),
+ person("Alex", "Pickering", role = c("ctb")),
+ person("William", "Holmes", role = c("ctb")),
+ person("Mikko", "Marttila", role = c("ctb")),
+ person("Andres", "Quintero", role = c("ctb")),
+ person("Stéphane", "Laurent", role = c("ctb")),
+ person(given = "Posit Software, PBC", role = c("cph", "fnd"))
+ )
+Description: Data objects in R can be rendered as HTML tables using the
+ JavaScript library 'DataTables' (typically via R Markdown or Shiny). The
+ 'DataTables' library has been included in this R package. The package name
+ 'DT' is an abbreviation of 'DataTables'.
+URL: https://github.com/rstudio/DT
+BugReports: https://github.com/rstudio/DT/issues
+License: GPL-3 | file LICENSE
+Imports: htmltools (>= 0.3.6), htmlwidgets (>= 1.3), httpuv, jsonlite
+ (>= 0.9.16), magrittr, crosstalk, jquerylib, promises
+Suggests: knitr (>= 1.8), rmarkdown, shiny (>= 1.6), bslib, future,
+ testit, tibble
+VignetteBuilder: knitr
+RoxygenNote: 7.3.1
+Encoding: UTF-8
+NeedsCompilation: no
+Packaged: 2024-04-03 14:36:50 UTC; yihui
+Author: Yihui Xie [aut],
+ Joe Cheng [aut, cre],
+ Xianying Tan [aut],
+ JJ Allaire [ctb],
+ Maximilian Girlich [ctb],
+ Greg Freedman Ellis [ctb],
+ Johannes Rauh [ctb],
+ SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib),
+ Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib),
+ Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib),
+ Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib),
+ Alex Pickering [ctb],
+ William Holmes [ctb],
+ Mikko Marttila [ctb],
+ Andres Quintero [ctb],
+ Stéphane Laurent [ctb],
+ Posit Software, PBC [cph, fnd]
+Maintainer: Joe Cheng <[email protected]>
+Repository: CRAN
+Date/Publication: 2024-04-04 05:03:17 UTC
+Built: R 4.3.1; ; 2024-04-04 06:14:53 UTC; unix

.library/DT/INDEX

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+JS Objects imported from other packages
+coerceValue Coerce a character string to the same type as a
+ target value
+dataTableAjax Register a data object in a shiny session for
+ DataTables
+dataTableOutput Helper functions for using DT in Shiny
+dataTableProxy Manipulate an existing DataTables instance in a
+ Shiny app
+datatable Create an HTML table widget using the
+ DataTables library
+doColumnSearch Server-side searching
+editData Edit a data object using the information from
+ the editor in a DataTable
+formatCurrency Format table columns
+replaceData Replace data in an existing table
+styleInterval Conditional CSS styles
+tableHeader Generate a table header or footer from column
+ names