(v1.6.0.9028) new unit test flow

.github/workflows/check.yaml

@@ -78,8 +78,8 @@ jobs:
           - {os: ubuntu-16.04,   r: '3.5',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           - {os: ubuntu-16.04,   r: '3.4',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           - {os: ubuntu-16.04,   r: '3.3',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          # - {os: ubuntu-16.04,   r: '3.2',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.2',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
-          # - {os: ubuntu-16.04,   r: '3.1',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
+          - {os: ubuntu-16.04,   r: '3.1',     allowfail: true,  rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           - {os: ubuntu-16.04,   r: '3.0',     allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
           
     env:
@@ -161,14 +161,12 @@ jobs:
         run: |
           tar -xf data-raw/AMR_latest.tar.gz
           rm -rf AMR/vignettes
-          Rscript -e "utils::installed.packages()"
+          R CMD check AMR --no-manual --as-cran --no-vignettes --library='/Users/runner/work/_temp/Library'
-          R CMD check AMR --no-manual --as-cran
         shell: bash
 
       - name: Show testthat output
         if: always()
         run: |
-          ls -lh
           find . -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
@@ -177,4 +175,4 @@ jobs:
         uses: actions/upload-artifact@master
         with:
           name: ${{ matrix.config.os }}-r${{ matrix.config.r }}-results
-          path: check
+          path: *.Rcheck

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: AMR
-Version: 1.6.0.9027
+Version: 1.6.0.9028
 Date: 2021-05-13
 Title: Antimicrobial Resistance Data Analysis
 Authors@R: c(

NEWS.md

@@ -1,4 +1,4 @@
-# `AMR` 1.6.0.9027
+# `AMR` 1.6.0.9028
 ## <small>Last updated: 13 May 2021</small>
 
 ### New

docs/404.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9028</span>
       </span>
     </div>
 

docs/LICENSE-text.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9028</span>
       </span>
     </div>
 

docs/articles/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9028</span>
       </span>
     </div>
 

docs/authors.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9028</span>
       </span>
     </div>
 

docs/index.html

@@ -42,7 +42,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9028</span>
       </span>
     </div>
 

docs/news/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9028</span>
       </span>
     </div>
 
@@ -236,9 +236,9 @@
       <small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
     </div>
 
-    <div id="amr-1609027" class="section level1">
+    <div id="amr-1609028" class="section level1">
-<h1 class="page-header" data-toc-text="1.6.0.9027">
+<h1 class="page-header" data-toc-text="1.6.0.9028">
-<a href="#amr-1609027" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9027</h1>
+<a href="#amr-1609028" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9028</h1>
 <div id="last-updated-13-may-2021" class="section level2">
 <h2 class="hasAnchor">
 <a href="#last-updated-13-may-2021" class="anchor"></a><small>Last updated: 13 May 2021</small>

docs/pkgdown.yml

@@ -12,7 +12,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-13T19:35Z
+last_built: 2021-05-13T20:43Z
 urls:
   reference: https://msberends.github.io/AMR//reference
   article: https://msberends.github.io/AMR//articles

docs/reference/index.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9028</span>
       </span>
     </div>
 

docs/survey.html

@@ -81,7 +81,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9027</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9028</span>
       </span>
     </div>
 

tests/testthat/test-_misc.R

@@ -51,15 +51,17 @@ test_that("looking up ab columns works", {
   expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
   expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))
   expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS"))
-  expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
+  if (suppressWarnings(require("dplyr"))) {
-  expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
+    expect_warning(get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
+    expect_warning(get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
+  }
 })
 
 test_that("looking up ab columns works", {
   skip_on_cran()
-
+  
   # we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_true(is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
   }
 

tests/testthat/test-ab_class_selectors.R

@@ -28,19 +28,20 @@ context("ab_class_selectors.R")
 test_that("Antibiotic class selectors work", {
   skip_on_cran()
   
-  expect_lt(example_isolates %>% dplyr::select(aminoglycosides()) %>% ncol(), ncol(example_isolates))
+  if (suppressWarnings(require("dplyr"))) {
-  expect_lt(example_isolates %>% dplyr::select(carbapenems()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(aminoglycosides()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(cephalosporins()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(carbapenems()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(cephalosporins_1st()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(cephalosporins()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(cephalosporins_2nd()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(cephalosporins_1st()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(cephalosporins_3rd()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(cephalosporins_2nd()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(cephalosporins_4th()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(cephalosporins_3rd()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(cephalosporins_5th()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(cephalosporins_4th()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(fluoroquinolones()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(cephalosporins_5th()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(glycopeptides()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(fluoroquinolones()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(macrolides()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(glycopeptides()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(oxazolidinones()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(macrolides()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(penicillins()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(oxazolidinones()) %>% ncol(), ncol(example_isolates))
-  expect_lt(example_isolates %>% dplyr::select(tetracyclines()) %>% ncol(), ncol(example_isolates))
+    expect_lt(example_isolates %>% select(penicillins()) %>% ncol(), ncol(example_isolates))
-  
+    expect_lt(example_isolates %>% select(tetracyclines()) %>% ncol(), ncol(example_isolates))
+  }
 })

tests/testthat/test-count.R

@@ -58,7 +58,7 @@ test_that("counts work", {
   expect_error(count_df(c("A", "B", "C")))
   expect_error(count_df(example_isolates[, "date"]))
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
     expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
     expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)

tests/testthat/test-disk.R

@@ -47,14 +47,14 @@ test_that("disk works", {
   expect_silent(plot(as.disk(c(10, 20, 40))))
   expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
   expect_silent(plot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"))
-  if (require("ggplot2")) {
+  if (suppressWarnings(require("ggplot2"))) {
     expect_s3_class(ggplot(as.disk(c(10, 20, 40))), "gg")
     expect_s3_class(ggplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
     expect_s3_class(ggplot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"), "gg")
   }
   expect_output(print(as.disk(12)))
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_output(print(tibble(d = as.disk(12))))
   }
 

tests/testthat/test-episode.R

@@ -41,7 +41,7 @@ test_that("episodes work", {
   expect_equal(get_episode(test_df$date, 365),
                c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3))
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_identical(test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date, 365)) %>% pull(f),
                      c(TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE))
     

tests/testthat/test-eucast_rules.R

@@ -77,7 +77,7 @@ test_that("EUCAST rules work", {
   expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
   
   # piperacillin must be R in Enterobacteriaceae when tica is R
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_equal(suppressWarnings(
       example_isolates %>%
         filter(mo_family(mo) == "Enterobacteriaceae") %>%
@@ -115,7 +115,7 @@ test_that("EUCAST rules work", {
     "S")
   
   # also test norf
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
   }
   

tests/testthat/test-filter_ab_class.R

@@ -28,7 +28,7 @@ context("filter_ab_class.R")
 test_that("ATC-group filtering works", {
   skip_on_cran()
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_gt(example_isolates %>% filter_ab_class("carbapenem") %>% nrow(), 0)
     expect_gt(example_isolates %>% filter_aminoglycosides() %>% ncol(), 0)
     expect_gt(example_isolates %>% filter_carbapenems() %>% ncol(), 0)

tests/testthat/test-first_isolate.R

@@ -121,28 +121,34 @@ test_that("first isolates work", {
                              col_date = "non-existing col",
                              col_mo = "mo"))
 
-  require("dplyr")
+  if (suppressWarnings(require("dplyr"))) {
-  
+    # if mo is not an mo class, result should be the same
-  # if mo is not an mo class, result should be the same
+    expect_identical(example_isolates %>%
-  expect_identical(example_isolates %>%
+                       mutate(mo = as.character(mo)) %>%
-                     mutate(mo = as.character(mo)) %>%
+                       first_isolate(col_date = "date",
-                     first_isolate(col_date = "date",
+                                     col_mo = "mo",
-                                   col_mo = "mo",
+                                     col_patient_id = "patient_id",
-                                   col_patient_id = "patient_id",
+                                     info = FALSE),
-                                   info = FALSE),
+                     example_isolates %>%
-                   example_isolates %>%
+                       first_isolate(col_date = "date",
-                     first_isolate(col_date = "date",
+                                     col_mo = "mo",
-                                   col_mo = "mo",
+                                     col_patient_id = "patient_id",
-                                   col_patient_id = "patient_id",
+                                     info = FALSE))
-                                   info = FALSE))
+    
-  
+    # support for WHONET
-  # support for WHONET
+    expect_message(example_isolates %>%
-  expect_message(example_isolates %>%
+                     select(-patient_id) %>%
-                   select(-patient_id) %>%
+                     mutate(`First name` = "test",
-                   mutate(`First name` = "test",
+                            `Last name` = "test", 
-                          `Last name` = "test", 
+                            Sex = "Female") %>% 
-                          Sex = "Female") %>% 
+                     first_isolate(info = TRUE))
-                   first_isolate(info = TRUE))
+    
+    # groups
+    x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate())
+    y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.))
+    expect_identical(x, y)
+    
+  }
 
   # missing dates should be no problem
   df <- example_isolates
@@ -185,10 +191,4 @@ test_that("first isolates work", {
   
   # only one isolate, so return fast
   expect_true(first_isolate(data.frame(mo = "Escherichia coli", date = Sys.Date(), patient = "patient"), info = TRUE))
-
-  # groups
-  x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate())
-  y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.))
-  expect_identical(x, y)
-  
 })

tests/testthat/test-ggplot_rsi.R

@@ -32,7 +32,7 @@ test_that("ggplot_rsi works", {
   skip_if_not_installed("ggplot2")
   skip_if_not_installed("dplyr")
   
-  if (require("dplyr") & require("ggplot2")) {
+  if (suppressWarnings(require("dplyr")) & suppressWarnings(require("ggplot2"))) {
     
     pdf(NULL) # prevent Rplots.pdf being created
     

tests/testthat/test-mdro.R

@@ -244,7 +244,7 @@ test_that("mdro works", {
                       info = FALSE))
   
   # print groups
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE))
     expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE))
   }

tests/testthat/test-mic.R

@@ -53,7 +53,7 @@ test_that("mic works", {
   expect_silent(plot(as.mic(c(1, 2, 4, 8))))
   expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
   expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "esco", ab = "cipr"))
-  if (require("ggplot2")) {
+  if (suppressWarnings(require("ggplot2"))) {
     expect_s3_class(ggplot(as.mic(c(1, 2, 4, 8))), "gg")
     expect_s3_class(ggplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
     expect_s3_class(ggplot(as.mic(c(1, 2, 4, 8, 32)), mo = "esco", ab = "cipr"), "gg")
@@ -62,7 +62,7 @@ test_that("mic works", {
   
   expect_s3_class(summary(as.mic(c(2, 8))), c("summaryDefault", "table"))
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_output(print(tibble(m = as.mic(2:4))))
   }
 })

tests/testthat/test-mo.R

@@ -150,7 +150,7 @@ test_that("as.mo works", {
   expect_identical(as.character(as.mo("S. salivarius",  Lancefield = FALSE)), "B_STRPT_SLVR")
   expect_identical(as.character(as.mo("S. salivarius",  Lancefield = TRUE)),  "B_STRPT_GRPK") # group K
 
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     # select with one column
     expect_identical(
       example_isolates[1:10, ] %>%
@@ -282,8 +282,10 @@ test_that("as.mo works", {
   expect_equal(suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))), 
                c("F_YEAST", "F_FUNGUS"))
   
-  # print tibble
+  if (suppressWarnings(require("dplyr"))) {
-  expect_output(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
+    # print tibble
+    expect_output(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
+  }
   
   # assigning and subsetting
   x <- example_isolates$mo
@@ -299,7 +301,7 @@ test_that("as.mo works", {
                c("B_ESCHR_COLI", NA))
   
   # frequency tables
-  if (require("cleaner")) {
+  if (suppressWarnings(require("cleaner"))) {
     expect_s3_class(cleaner::freq(example_isolates$mo), "freq")
   }
   

tests/testthat/test-mo_property.R

@@ -131,7 +131,7 @@ test_that("mo_property works", {
   expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")), 
                "Escherichia coli")
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
                  730)
     expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(),

tests/testthat/test-pca.R

@@ -49,10 +49,12 @@ test_that("PCA works", {
   expect_s3_class(pca_model, "pca")
   
   pdf(NULL) # prevent Rplots.pdf being created
-  ggplot_pca(pca_model, ellipse = TRUE)
+  if (suppressWarnings(require("ggplot2"))) {
-  ggplot_pca(pca_model, arrows_textangled = FALSE)
+    ggplot_pca(pca_model, ellipse = TRUE)
+    ggplot_pca(pca_model, arrows_textangled = FALSE)
+  }
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     resistance_data <- example_isolates %>% 
       group_by(order = mo_order(mo),
                genus = mo_genus(mo)) %>%
@@ -60,7 +62,9 @@ test_that("PCA works", {
     pca_result <- resistance_data %>%         
       pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, "SXT") 
     expect_s3_class(pca_result, "prcomp")
-    ggplot_pca(pca_result, ellipse = TRUE)
+    if (suppressWarnings(require("ggplot2"))) {
-    ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
+      ggplot_pca(pca_result, ellipse = TRUE)
+      ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
+    }
   }
 })

tests/testthat/test-proportion.R

@@ -52,7 +52,7 @@ test_that("proportions works", {
                0.9382647,
                tolerance = 0.0001)
 
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     # percentages
     expect_equal(example_isolates %>%
                    group_by(hospital_id) %>%

tests/testthat/test-resistance_predict.R

@@ -28,7 +28,7 @@ context("resistance_predict.R")
 test_that("prediction of rsi works", {
   skip_on_cran()
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_output(AMX_R <- example_isolates %>%
                     filter(mo == "B_ESCHR_COLI") %>%
                     rsi_predict(col_ab = "AMX",

tests/testthat/test-rsi.R

@@ -42,7 +42,7 @@ test_that("rsi works", {
   pdf(NULL) # prevent Rplots.pdf being created
   expect_silent(barplot(as.rsi(c("S", "I", "R"))))
   expect_silent(plot(as.rsi(c("S", "I", "R"))))
-  if (require("ggplot2")) expect_s3_class(ggplot(as.rsi(c("S", "I", "R"))), "gg")
+  if (suppressWarnings(require("ggplot2"))) expect_s3_class(ggplot(as.rsi(c("S", "I", "R"))), "gg")
   expect_output(print(as.rsi(c("S", "I", "R"))))
   
   expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
@@ -64,7 +64,7 @@ test_that("rsi works", {
   
   expect_error(get_guideline("this one does not exist"))
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     # 40 rsi columns
     expect_equal(example_isolates %>%
                    mutate_at(vars(PEN:RIF), as.character) %>%
@@ -77,10 +77,10 @@ test_that("rsi works", {
     expect_output(print(tibble(ab = as.rsi("S"))))
   }
   
-   if (require("skimr")) {
+   if (suppressWarnings(require("skimr"))) {
     expect_s3_class(skim(example_isolates),
                     "data.frame")
-    if (require("dplyr")) {
+    if (suppressWarnings(require("dplyr"))) {
       expect_s3_class(example_isolates %>%
                         mutate(m = as.mic(2),
                                d = as.disk(20)) %>% 
@@ -116,7 +116,7 @@ test_that("mic2rsi works", {
   expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
                as.rsi("R"))
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_true(suppressWarnings(example_isolates %>%
                                    mutate(amox_mic = as.mic(2)) %>%
                                    select(mo, amox_mic) %>%
@@ -149,7 +149,7 @@ test_that("disk2rsi works", {
            guideline = "CLSI")),
     "R")
   
-  if (require("dplyr")) {
+  if (suppressWarnings(require("dplyr"))) {
     expect_true(example_isolates %>%
                   mutate(amox_disk = as.disk(15)) %>%
                   select(mo, amox_disk) %>%
@@ -159,7 +159,7 @@ test_that("disk2rsi works", {
   }
   
   # frequency tables
-  if (require("cleaner")) {
+  if (suppressWarnings(require("cleaner"))) {
     expect_s3_class(cleaner::freq(example_isolates$AMX), "freq")
   }
 })

tests/testthat/test-zzz.R

@@ -109,7 +109,9 @@ test_that("imports work", {
     fn <- names(import_functions)[i]
     pkg <- unname(import_functions[i])
     # function should exist in foreign pkg namespace
-    expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
+    if (pkg %in% rownames(installed.packages())) {
-           failure_message = paste0("Function ", pkg, "::", fn, "() does not exist anymore"))
+      expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
+             failure_message = paste0("Function ", pkg, "::", fn, "() does not exist anymore"))
+    }
   }
 })