diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index a3ac618..74d8c97 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -29,7 +29,7 @@ jobs: R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index ed7650c..a7276e8 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -22,7 +22,7 @@ jobs: permissions: contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -41,7 +41,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/.github/workflows/style.yaml b/.github/workflows/style.yaml index bee3e48..66958a4 100644 --- a/.github/workflows/style.yaml +++ b/.github/workflows/style.yaml @@ -13,7 +13,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - name: Checkout repo - uses: actions/checkout@v3 + uses: actions/checkout@v4 with: fetch-depth: 0 @@ -46,7 +46,7 @@ jobs: shell: Rscript {0} - name: Cache styler - uses: actions/cache@v3 + uses: actions/cache@v4 with: path: ${{ steps.styler-location.outputs.location }} key: ${{ runner.os }}-styler-${{ github.sha }} diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml index 2c5bb50..960234c 100644 --- a/.github/workflows/test-coverage.yaml +++ b/.github/workflows/test-coverage.yaml @@ -15,7 +15,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: @@ -31,7 +31,7 @@ jobs: covr::codecov( quiet = FALSE, clean = FALSE, - install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") + install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") ) shell: Rscript {0} @@ -44,7 +44,7 @@ jobs: - name: Upload test results if: failure() - uses: actions/upload-artifact@v3 + uses: actions/upload-artifact@v4 with: name: coverage-test-failures path: ${{ runner.temp }}/package diff --git a/tests/testthat.R b/tests/testthat.R index 1c0e5ea..ae5107a 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,6 +1,4 @@ library(testthat) -library(dplyr) library(r2rtf) -library(ggplot2) test_check("r2rtf") diff --git a/tests/testthat/test-independent-testing-as_rtf_pageby.R b/tests/testthat/test-independent-testing-as_rtf_pageby.R index 009752c..16f7bb1 100644 --- a/tests/testthat/test-independent-testing-as_rtf_pageby.R +++ b/tests/testthat/test-independent-testing-as_rtf_pageby.R @@ -1,5 +1,3 @@ -library(dplyr) -svg(tempfile("tmp.svg")) test_that("Test for case when output has title, footnote and source", { x <- iris[1:2, ] |> rtf_title("Title") |> @@ -21,13 +19,13 @@ test_that("Test the pageby rows are the last rows of a page", { rtf_pageby(page_by = "Species", new_page = TRUE, pageby_header = FALSE) y <- as.data.frame(attributes(as_rtf_pageby(x))) |> - group_by(info.id) |> - summarise_all(last) |> - mutate(row = substr(as.character(info.page), 1, 1)) + dplyr::group_by(info.id) |> + dplyr::summarise_all(dplyr::last) |> + dplyr::mutate(row = substr(as.character(info.page), 1, 1)) z <- as.data.frame(table(x$Species)) |> - mutate(cu = cumsum(Freq)) - z <- z |> mutate(cum = cu + as.numeric(rownames(z))) + dplyr::mutate(cu = cumsum(Freq)) + z <- z |> dplyr::mutate(cum = cu + as.numeric(rownames(z))) expect_equal(y$row, rownames(y)) expect_equal(y$info.index, z$cum) @@ -66,8 +64,8 @@ test_that("Test if page_dict attribute is created for tbl", { test_that("Test for more than one page_by var", { x <- iris |> - mutate(cat = rep(1:5, 30)) |> - arrange(Species, cat) |> + dplyr::mutate(cat = rep(1:5, 30)) |> + dplyr::arrange(Species, cat) |> rtf_page(nrow = 5) |> rtf_body() |> rtf_pageby(page_by = c("Species", "cat"), new_page = TRUE, pageby_header = TRUE) @@ -92,8 +90,8 @@ test_that("Test if new_page is FALSE and group_by is NOT NULL", { }) test_that("Test whether lines with '-----' were removed correctly", { - x <- distinct(iris |> subset(Species != "virginica"), Species, .keep_all = T) |> - mutate(Species = ifelse(Species == "setosa", "-----", Species)) |> + x <- dplyr::distinct(iris |> subset(Species != "virginica"), Species, .keep_all = TRUE) |> + dplyr::mutate(Species = ifelse(Species == "setosa", "-----", Species)) |> rtf_colheader("Sepal.Length | Sepal.Width | Petal.Length | Petal.Width", col_rel_width = rep(1, 4) ) |> @@ -111,8 +109,8 @@ test_that("Test whether lines with '-----' were removed correctly", { test_that("Test when using subline_by and page_by together in rtf_body", { tbl1 <- iris[c(1:4, 51:54), 3:5] |> - mutate(s2 = paste0(Species, 1:2), s3 = s2) |> - arrange(Species, s2) |> + dplyr::mutate(s2 = paste0(Species, 1:2), s3 = s2) |> + dplyr::arrange(Species, s2) |> rtf_body( subline_by = "s2", page_by = "Species" @@ -125,8 +123,8 @@ test_that("Test when using subline_by and page_by together in rtf_body", { test_that("Test when using subline_by and page_by with pageby_row = 'first_row' in rtf_body", { tbl2 <- iris[c(1:4, 51:54), 3:5] |> - mutate(s2 = paste0(Species, 1:2), s3 = s2) |> - arrange(Species, s2) |> + dplyr::mutate(s2 = paste0(Species, 1:2), s3 = s2) |> + dplyr::arrange(Species, s2) |> rtf_body( subline_by = "s2", page_by = "Species", @@ -136,5 +134,3 @@ test_that("Test when using subline_by and page_by with pageby_row = 'first_row' expect_snapshot_output(tbl2$body) }) - -dev.off() diff --git a/tests/testthat/test-independent-testing-as_rtf_table.R b/tests/testthat/test-independent-testing-as_rtf_table.R index 295b128..63c9588 100644 --- a/tests/testthat/test-independent-testing-as_rtf_table.R +++ b/tests/testthat/test-independent-testing-as_rtf_table.R @@ -31,8 +31,8 @@ test_that("Case for having group_by without page_by", { # add additional test to increase coverage and for new feature test_that("Test case when subline is not NULL", { x <- iris[c(1:4, 51:54), 3:5] |> - mutate(s2 = paste0(Species, 1:2), s3 = s2) |> - arrange(Species, s2) |> + dplyr::mutate(s2 = paste0(Species, 1:2), s3 = s2) |> + dplyr::arrange(Species, s2) |> rtf_body( subline_by = "Species", page_by = "s2", @@ -45,18 +45,18 @@ test_that("Test case when subline is not NULL", { data(r2rtf_adae) ae <- r2rtf_adae[200:260, ] |> - arrange(SITEID, TRTA, USUBJID, ASTDY) + dplyr::arrange(SITEID, TRTA, USUBJID, ASTDY) ae <- ae |> - mutate( + dplyr::mutate( AEDECODNUM = as.character(rownames(ae)), SUBLINEBY = paste0( "Trial Number: ", STUDYID, ", Site Number: ", SITEID ), ) |> - select(USUBJID, ASTDY, AEDECODNUM, TRTA, SUBLINEBY) |> - arrange(SUBLINEBY, TRTA, USUBJID, ASTDY) |> + dplyr::select(USUBJID, ASTDY, AEDECODNUM, TRTA, SUBLINEBY) |> + dplyr::arrange(SUBLINEBY, TRTA, USUBJID, ASTDY) |> rtf_colheader("Subject| Rel Day | Adverse Code|") |> rtf_body( subline_by = "SUBLINEBY", diff --git a/tests/testthat/test-independent-testing-assemble.R b/tests/testthat/test-independent-testing-assemble.R index c29ab5a..7142bbc 100644 --- a/tests/testthat/test-independent-testing-assemble.R +++ b/tests/testthat/test-independent-testing-assemble.R @@ -46,28 +46,28 @@ test_that("rtf_assemble: output without using officer", { }) # test functionality with officer -if (requireNamespace("officer")) { - test_that("rtf_assemble: output with using officer", { - file_tmp <- tempfile(fileext = ".docx") - rtf_path <- assemble_docx( - input = file, - output = file_tmp, - landscape = c(FALSE, TRUE) - ) +test_that("rtf_assemble: output with using officer", { + skip_if_not_installed("officer") - expect_equal(rtf_path, file_tmp) + file_tmp <- tempfile(fileext = ".docx") + rtf_path <- assemble_docx( + input = file, + output = file_tmp, + landscape = c(FALSE, TRUE) + ) + + expect_equal(rtf_path, file_tmp) - # Need to read in and expose document text for our test - docx <- officer::read_docx(rtf_path) - tmp_docx <- officer::docx_summary(docx) - body_docx <- officer::docx_body_xml(docx) + # Need to read in and expose document text for our test + docx <- officer::read_docx(rtf_path) + tmp_docx <- officer::docx_summary(docx) + body_docx <- officer::docx_body_xml(docx) - # Need to check if both "table seq table" texts are in the docx file. - expect_true(grepl("Table SEQ Table", tmp_docx$text[1])) + # Need to check if both "table seq table" texts are in the docx file. + expect_true(grepl("Table SEQ Table", tmp_docx$text[1])) - expect_equal( - unlist(lapply(xml2::as_list(xml2::xml_find_all(body_docx, "//w:pgSz")), FUN = function(x) attr(x, "orient"))), - c("portrait", "landscape") - ) - }) -} + expect_equal( + unlist(lapply(xml2::as_list(xml2::xml_find_all(body_docx, "//w:pgSz")), FUN = function(x) attr(x, "orient"))), + c("portrait", "landscape") + ) +}) diff --git a/tests/testthat/test-independent-testing-rtf_body.R b/tests/testthat/test-independent-testing-rtf_body.R index c75a842..acef933 100644 --- a/tests/testthat/test-independent-testing-rtf_body.R +++ b/tests/testthat/test-independent-testing-rtf_body.R @@ -352,8 +352,8 @@ test_that("Case for page_by", { test_that("Case for using subline_by and page_by together", { tbl1 <- iris[c(1:4, 51:54), 3:5] |> - mutate(s2 = paste0(Species, 1:2), s3 = s2) |> - arrange(Species, s2) |> + dplyr::mutate(s2 = paste0(Species, 1:2), s3 = s2) |> + dplyr::arrange(Species, s2) |> rtf_body( subline_by = "Species", page_by = "s2" @@ -382,8 +382,8 @@ test_that("Case for using subline_by and page_by together", { test_that("Case for using subline_by and page_by with pageby_row = 'first_row'", { tbl2 <- iris[c(1:4, 51:54), 3:5] |> - mutate(s2 = paste0(Species, 1:2), s3 = s2) |> - arrange(Species, s2) |> + dplyr::mutate(s2 = paste0(Species, 1:2), s3 = s2) |> + dplyr::arrange(Species, s2) |> rtf_body( subline_by = "Species", page_by = "s2", diff --git a/tests/testthat/test-independent-testing-rtf_encode_table.R b/tests/testthat/test-independent-testing-rtf_encode_table.R index b04bf0f..da4d75f 100644 --- a/tests/testthat/test-independent-testing-rtf_encode_table.R +++ b/tests/testthat/test-independent-testing-rtf_encode_table.R @@ -231,8 +231,8 @@ test_that("Test case when pageby$border_color_last is not NULL", { test_that("Test case when subline is not NULL", { ir3 <- iris[c(1:4, 51:54), 3:5] |> - mutate(s2 = paste0(Species, 1:2)) |> - arrange(Species, s2) |> + dplyr::mutate(s2 = paste0(Species, 1:2)) |> + dplyr::arrange(Species, s2) |> rtf_colheader("patelLength|patelWidth|s2") |> rtf_body(subline_by = "Species") @@ -243,8 +243,8 @@ test_that("Test case when subline is not NULL", { test_that("Test case when subline is not NULL and verbose equals to TRUE", { ir3 <- iris[c(1:4, 51:54), 3:5] |> - mutate(s2 = paste0(Species, 1:2)) |> - arrange(Species, s2) |> + dplyr::mutate(s2 = paste0(Species, 1:2)) |> + dplyr::arrange(Species, s2) |> rtf_colheader("patelLength|patelWidth|s2") |> rtf_body(subline_by = "Species") @@ -256,14 +256,14 @@ test_that("Test case when subline is not NULL and verbose equals to TRUE", { test_that("Test case when using subline_by, page_by, group_by simultaneously in rtf_body", { data(r2rtf_adae) ae_t1 <- r2rtf_adae[200:260, ] |> - mutate( + dplyr::mutate( SUBLINEBY = paste0( "Trial Number: ", STUDYID, ", Site Number: ", SITEID ), ) |> - select(USUBJID, ASTDY, AEDECOD, TRTA, SUBLINEBY) |> - arrange(SUBLINEBY, TRTA, USUBJID, ASTDY) |> + dplyr::select(USUBJID, ASTDY, AEDECOD, TRTA, SUBLINEBY) |> + dplyr::arrange(SUBLINEBY, TRTA, USUBJID, ASTDY) |> rtf_colheader("Subject| Rel Day | Adverse |") |> rtf_body( subline_by = "SUBLINEBY", @@ -281,14 +281,14 @@ test_that("Test case when using subline_by, page_by, group_by simultaneously wit data(r2rtf_adae) ae_t2 <- r2rtf_adae[200:260, ] |> subset(USUBJID != "01-701-1442") |> - mutate( + dplyr::mutate( SUBLINEBY = paste0( "Trial Number: ", STUDYID, ", Site Number: ", SITEID ), ) |> - select(USUBJID, ASTDY, AEDECOD, TRTA, SUBLINEBY) |> - arrange(SUBLINEBY, TRTA, USUBJID, ASTDY) |> + dplyr::select(USUBJID, ASTDY, AEDECOD, TRTA, SUBLINEBY) |> + dplyr::arrange(SUBLINEBY, TRTA, USUBJID, ASTDY) |> rtf_colheader("Subject| Rel Day | Adverse |", border_bottom = "single" ) |> @@ -309,14 +309,14 @@ test_that("Test case when using subline_by, page_by, group_by simultaneously wit data(r2rtf_adae) ae_t3 <- r2rtf_adae[200:260, ] |> subset(USUBJID != "01-701-1442") |> - mutate( + dplyr::mutate( SUBLINEBY = paste0( "Trial Number: ", STUDYID, ", Site Number: ", SITEID ), ) |> - select(USUBJID, ASTDY, AEDECOD, TRTA, SUBLINEBY) |> - arrange(SUBLINEBY, TRTA, USUBJID, ASTDY) |> + dplyr::select(USUBJID, ASTDY, AEDECOD, TRTA, SUBLINEBY) |> + dplyr::arrange(SUBLINEBY, TRTA, USUBJID, ASTDY) |> rtf_colheader("Subject| Rel Day | Adverse |", border_bottom = "single" ) |> diff --git a/tests/testthat/test-independent-testing-rtf_nrow.R b/tests/testthat/test-independent-testing-rtf_nrow.R index f0779f0..46dd7e3 100644 --- a/tests/testthat/test-independent-testing-rtf_nrow.R +++ b/tests/testthat/test-independent-testing-rtf_nrow.R @@ -1,5 +1,4 @@ # create testing example -svg(tempfile("tmp.svg")) font <- 2:3 format <- matrix(c("", "i", "b", "ib"), nrow = 4, ncol = 2, byrow = FALSE) @@ -174,5 +173,3 @@ test_that("test for rtf-nrow() if 'rtf-nrow' attributes are added correctly for test_that("test for rtf-nrow() if 'rtf-nrow' attributes are added correctly for pageby_row table", { expect_equal(irspagebyrows[1], 1) }) - -dev.off() diff --git a/tests/testthat/test-independent-testing-rtf_pageby.R b/tests/testthat/test-independent-testing-rtf_pageby.R index 0e1e9b6..dfbda83 100644 --- a/tests/testthat/test-independent-testing-rtf_pageby.R +++ b/tests/testthat/test-independent-testing-rtf_pageby.R @@ -1,5 +1,3 @@ -library(dplyr) - test_that("Test case when page_by is NULL and new_page is TRUE", { expect_error(iris[1:2, ] |> rtf_body() |> @@ -8,7 +6,7 @@ test_that("Test case when page_by is NULL and new_page is TRUE", { test_that("Test case when page_by is not NULL and data is sorted by the page_by variable", { expect_output(str(iris[1:2, ] |> - arrange(Petal.Length) |> + dplyr::arrange(Petal.Length) |> rtf_body() |> rtf_pageby( page_by = c("Petal.Length"), new_page = TRUE, @@ -16,7 +14,7 @@ test_that("Test case when page_by is not NULL and data is sorted by the page_by )), "2 obs") a <- iris[1:2, ] |> - arrange(Sepal.Width) |> + dplyr::arrange(Sepal.Width) |> rtf_body() |> rtf_pageby( page_by = c("Sepal.Width"), new_page = TRUE, @@ -60,8 +58,8 @@ test_that("Test if there are more than one page_by variables", { # add tests for new features test_that("Test case when pageby_row='first_row'", { x <- iris[c(1:4, 51:54), 3:5] |> - mutate(s2 = paste0(Species, 1:2), s3 = s2) |> - arrange(Species, s2) |> + dplyr::mutate(s2 = paste0(Species, 1:2), s3 = s2) |> + dplyr::arrange(Species, s2) |> rtf_colheader("patelLength|patelWidth|s3") |> rtf_body(subline_by = "Species") |> rtf_pageby( @@ -78,8 +76,8 @@ test_that("Test case when pageby_row='first_row'", { test_that("Test case when subline is not NULL", { x <- iris[c(1:4, 51:54), 3:5] |> - mutate(s2 = paste0(Species, 1:2), s3 = s2) |> - arrange(Species, s2) |> + dplyr::mutate(s2 = paste0(Species, 1:2), s3 = s2) |> + dplyr::arrange(Species, s2) |> rtf_colheader("patelLength|patelWidth|s3") |> rtf_body(subline_by = "Species") |> rtf_pageby( diff --git a/tests/testthat/test-independent-testing-rtf_read_figure.R b/tests/testthat/test-independent-testing-rtf_read_figure.R index 8bb157f..b70cd26 100644 --- a/tests/testthat/test-independent-testing-rtf_read_figure.R +++ b/tests/testthat/test-independent-testing-rtf_read_figure.R @@ -1,4 +1,3 @@ -library(dplyr) test_that("Test fig_format attribute", { a <- rtf_read_figure(c("fig/fig3.jpeg", "fig/fig2.png", "fig/fig4.emf"))