Running ‘testthat.R’ [19s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(AMR)
  > 
  > test_check("AMR")
  ── 1. Error: atc_property works (@test-atc.R#10)  ──────────────────────────────
  Timeout was reached: Resolving timed out after 10000 milliseconds
  1: expect_equal(atc_property("J01CA04", property = "unit"), "g") at testthat/test-atc.R:10
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: atc_property("J01CA04", property = "unit")
  5: xml2::read_html(atc_url) %>% rvest::html_nodes("table") %>% rvest::html_table(header = TRUE) %>% 
         as.data.frame(stringsAsFactors = FALSE)
  6: eval(lhs, parent, parent)
  7: eval(lhs, parent, parent)
  8: xml2::read_html(atc_url)
  9: read_html.default(atc_url)
  10: suppressWarnings(read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options))
  11: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  12: read_xml(x, encoding = encoding, ..., as_html = TRUE, options = options)
  13: read_xml.character(x, encoding = encoding, ..., as_html = TRUE, options = options)
  14: read_xml.connection(con, encoding = encoding, ..., as_html = as_html, base_url = x, 
         options = options)
  15: open(x, "rb")
  16: open.connection(x, "rb")
  
  Class 'rsi'
  [1] S I R
  Class 'mic'
  [1] 1 2 4 8
  
  Applying rules to 2,000 rows according to "EUCAST Expert Rules Version 3.1"
  - Table 1:  Intrinsic resistance in Enterobacteriaceae
  - Table 2:  Intrinsic resistance in non-fermentative Gram-negative bacteria
  - Table 3:  Intrinsic resistance in other Gram-negative bacteria
  - Table 4:  Intrinsic resistance in Gram-positive bacteria
  - Table 8:  Interpretive rules for B-lactam agents and Gram-positive cocci
  - Table 9:  Interpretive rules for B-lactam agents and Gram-negative rods
  - Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria
  - Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins
  - Table 12: Interpretive rules for aminoglycosides
  - Table 13: Interpretive rules for quinolones
  - Non-EUCAST: trim = R where trsu = R and ampi = R where amcl = R
  - Non-EUCAST: trsu = S where trim = S and amcl = S where ampi = S
  Done.
  
  EUCAST Expert rules applied to 1,954 different rows; overwritten a total of 13,112 test results.
  
  
  Applying rules to 3 rows according to "EUCAST Expert Rules Version 3.1"
  - Table 1:  Intrinsic resistance in Enterobacteriaceae
  - Table 2:  Intrinsic resistance in non-fermentative Gram-negative bacteria
  - Table 3:  Intrinsic resistance in other Gram-negative bacteria
  - Table 4:  Intrinsic resistance in Gram-positive bacteria
  - Table 8:  Interpretive rules for B-lactam agents and Gram-positive cocci
  - Table 9:  Interpretive rules for B-lactam agents and Gram-negative rods
  - Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria
  - Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins
  - Table 12: Interpretive rules for aminoglycosides
  - Table 13: Interpretive rules for quinolones
  - Non-EUCAST: trim = R where trsu = R and ampi = R where amcl = R
  - Non-EUCAST: trsu = S where trim = S and amcl = S where ampi = S
  Done.
  
  EUCAST Expert rules applied to 3 different rows; overwritten a total of 3 test results.
  
  [Criteria] Inclusion based on key antibiotics, ignoring I.
  [Criteria] Inclusion based on key antibiotics, using points threshold of 2.
  
  [Criteria] Excluded isolates from ICU.
  [Criteria] Excluded other than specimen group 'Urine'
  [Criteria] Excluded other than specimen group 'Urine'
  [Criteria] Excluded isolates from ICU.
  
  Logistic regression model (logit) with binomial distribution
  ------------------------------------------------------------
  
  Call:
  glm(formula = cbind(R, S) ~ year, family = binomial)
  
  Deviance Residuals: 
      Min       1Q   Median       3Q      Max  
  -3.2291  -0.8564   0.0665   1.3996   3.0724  
  
  Coefficients:
               Estimate Std. Error z value Pr(>|z|)  
  (Intercept) -90.46722   49.47800  -1.828   0.0675 .
  year          0.04498    0.02460   1.828   0.0675 .
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 41.868  on 13  degrees of freedom
  Residual deviance: 38.501  on 12  degrees of freedom
  AIC: 93.075
  
  Number of Fisher Scoring iterations: 3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 206 SKIPPED: 1 FAILED: 1
  1. Error: atc_property works (@test-atc.R#10) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In tryCatchOne(expr, names, parentenv, handlers[[1L]]) :
    closing unused connection 4 (https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no)
  Execution halted