CRAN Package Check Results for Package AMR

Last updated on 2018-09-28 12:47:37 CEST.

Check Details

Version: 0.3.0
Check: tests
Result: ERROR
     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
Flavor: r-patched-solaris-x86