Running 'testthat.R' [120s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # ==================================================================== #
  > # TITLE                                                                #
  > # Antimicrobial Resistance (AMR) Analysis                              #
  > #                                                                      #
  > # SOURCE                                                               #
  > # https://gitlab.com/msberends/AMR                                     #
  > #                                                                      #
  > # LICENCE                                                              #
  > # (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl)  #
  > #                                                                      #
  > # This R package is free software; you can freely use and distribute   #
  > # it for both personal and commercial purposes under the terms of the  #
  > # GNU General Public License version 2.0 (GNU GPL-2), as published by  #
  > # the Free Software Foundation.                                        #
  > #                                                                      #
  > # This R package was created for academic research and was publicly    #
  > # released in the hope that it will be useful, but it comes WITHOUT    #
  > # ANY WARRANTY OR LIABILITY.                                           #
  > # Visit our website for more info: https://msberends.gitab.io/AMR.     #
  > # ==================================================================== #
  > 
  > library(testthat)
  > library(AMR)
  > 
  > test_check("AMR")
  
  Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
  
  EUCAST Clinical Breakpoints (v9.0, 2019)
  Enterobacteriales (Order) (no changes)
  Staphylococcus-- 1. Error: EUCAST rules work (@test-eucast_rules.R#28)  ----------------------
  'data' must be of a vector type, was 'NULL'
  1: expect_identical(colnames(septic_patients), colnames(suppressWarnings(eucast_rules(septic_patients)))) at testthat/test-eucast_rules.R:28
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: colnames(suppressWarnings(eucast_rules(septic_patients)))
  5: is.data.frame(x)
  6: suppressWarnings(eucast_rules(septic_patients))
  7: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  8: eucast_rules(septic_patients)
  9: edit_rsi(to = "S", rule = c(rule_group, rule), rows = which(tbl$genus == "Staphylococcus" & 
         tbl[, norf] == "S"), cols = c(cipr, levo, moxi, oflo))
  10: which(tbl$genus == "Staphylococcus" & tbl[, norf] == "S")
  11: Ops.data.frame(tbl[, norf], "S")
  12: matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr, dimnames = list(rn, 
         cn))
  
  [Criterion] Inclusion based on key antibiotics, ignoring I.
  [Criterion] Inclusion based on key antibiotics, ignoring I.
  [Criterion] Inclusion based on key antibiotics, not ignoring I.
  [Criterion] Inclusion based on key antibiotics, using points threshold of 2.
  
  [Criterion] Excluded isolates from ICU.
  [Criterion] Excluded other than specimen group 'Urine'
  [Criterion] Excluded other than specimen group 'Urine'
  [Criterion] Excluded isolates from ICU.
  [Criterion] Excluded other than specimen group 'something_unexisting'
  Determining multidrug-resistant organisms (MDRO), according to:
  Guideline: EUCAST Expert Rules, "Intrinsic Resistance and Exceptional Phenotypes Tables", Version 3.1
  Country  : (European guidelines)
  Source   : http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf
  
  Determining multidrug-resistant organisms (MDRO), according to:
  Guideline: EUCAST Expert Rules, "Intrinsic Resistance and Exceptional Phenotypes Tables", Version 3.1
  Country  : (European guidelines)
  Source   : http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf
  
  Determining multidrug-resistant organisms (MDRO), according to:
  Guideline: EUCAST Expert Rules, "Intrinsic Resistance and Exceptional Phenotypes Tables", Version 3.1
  Country  : (European guidelines)
  Source   : http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf
  
  Determining multidrug-resistant organisms (MDRO), according to:
  Guideline: WIP-Richtlijn BRMO, Revision as of December 2017
  Country  : The Netherlands
  Source   : https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH
  
  Determining multidrug-resistant organisms (MDRO), according to:
  Guideline: , 
  Country  : Germany
  Source   : 
  
  Class 'mic'
  [1] 1 2 4 8
  Escherichia blattae (Burgess et al., 1973) was renamed Shimwellia blattae (Priest et al., 2010) (B_SHMWL_BLA)2 unique result(s) guessed with uncertainty:
  (1 = renamed, 2 = uncertain, 3 = very uncertain)
  
   [2]  "Streptococcus suis (bovis gr)" -> Streptococcus suis (B_STRPT_SUI)
   [2]  "Raoultella (here some text) terrigena" -> Raoultella terrigena (B_RLTLL_TER)
  Logistic regression model (logit) with binomial distribution
  ------------------------------------------------------------
  
  Call:
  glm(formula = df_matrix ~ year, family = binomial)
  
  Deviance Residuals: 
      Min       1Q   Median       3Q      Max  
  -3.2579  -0.9245   0.0336   1.4185   3.0981  
  
  Coefficients:
               Estimate Std. Error z value Pr(>|z|)  
  (Intercept) -97.54685   49.32757  -1.978    0.048 *
  year          0.04850    0.02453   1.977    0.048 *
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 42.518  on 13  degrees of freedom
  Residual deviance: 38.575  on 12  degrees of freedom
  AIC: 93.28
  
  Number of Fisher Scoring iterations: 3
  
  
  Logistic regression model (logit) with binomial distribution
  ------------------------------------------------------------
  
  Call:
  glm(formula = df_matrix ~ year, family = binomial)
  
  Deviance Residuals: 
       Min        1Q    Median        3Q       Max  
  -2.65799  -0.59136   0.08025   0.77236   2.21610  
  
  Coefficients:
               Estimate Std. Error z value Pr(>|z|)
  (Intercept)  9.079733  25.139103   0.361    0.718
  year        -0.004401   0.012507  -0.352    0.725
  
  (Dispersion parameter for binomial family taken to be 1)
  
      Null deviance: 23.780  on 15  degrees of freedom
  Residual deviance: 23.656  on 14  degrees of freedom
  AIC: 103.33
  
  Number of Fisher Scoring iterations: 3
  
  Class 'rsi'
  [1] S I R
  == testthat results  ===========================================================
  OK: 494 SKIPPED: 0 FAILED: 1
  1. Error: EUCAST rules work (@test-eucast_rules.R#28) 
  
  Error: testthat unit tests failed
  Execution halted