CRAN Package Check Results for Package AMR

Last updated on 2019-04-19 02:46:32 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.6.1 20.39 565.49 585.88 OK
r-devel-linux-x86_64-debian-gcc 0.6.1 16.71 409.94 426.65 OK
r-devel-linux-x86_64-fedora-clang 0.6.1 567.13 NOTE
r-devel-linux-x86_64-fedora-gcc 0.6.1 559.17 NOTE
r-devel-windows-ix86+x86_64 0.6.1 48.00 500.00 548.00 OK
r-patched-linux-x86_64 0.6.1 20.81 478.13 498.94 OK
r-patched-solaris-x86 0.6.1 629.00 NOTE
r-release-linux-x86_64 0.6.1 16.65 459.94 476.59 OK
r-release-windows-ix86+x86_64 0.6.1 24.00 397.00 421.00 OK
r-release-osx-x86_64 0.6.1 NOTE
r-oldrel-windows-ix86+x86_64 0.6.1 29.00 338.00 367.00 ERROR
r-oldrel-osx-x86_64 0.6.1 ERROR

Check Details

Version: 0.6.1
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘microbenchmark’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.1
Check: data for non-ASCII characters
Result: NOTE
     Note: found 7 marked UTF-8 strings
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.6.1
Check: installed package size
Result: NOTE
     installed size is 5.4Mb
     sub-directories of 1Mb or more:
     data 3.0Mb
Flavor: r-patched-solaris-x86

Version: 0.6.1
Check: examples
Result: ERROR
    Running examples in 'AMR-Ex.R' failed
    The error most likely occurred in:
    
    > ### Name: eucast_rules
    > ### Title: EUCAST rules
    > ### Aliases: eucast_rules EUCAST_rules interpretive_reading
    > ### Keywords: eucast interpretive reading resistance
    >
    > ### ** Examples
    >
    > a <- eucast_rules(septic_patients)
    NOTE: Using column `mo` as input for `col_mo`.
    Warning: Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.
    
    Rules by the European Committee on Antimicrobial Susceptibility Testing (EUCAST)
    
    EUCAST Clinical Breakpoints (v9.0, 2019)
    Enterobacteriales (Order) (no changes)
    StaphylococcusError in matrix(unlist(value, recursive = FALSE, use.names = FALSE), nrow = nr, :
     'data' must be of a vector type, was 'NULL'
    Calls: eucast_rules -> edit_rsi -> which -> Ops.data.frame -> matrix
    Execution halted
Flavors: r-oldrel-windows-ix86+x86_64, r-oldrel-osx-x86_64

Version: 0.6.1
Check: tests
Result: ERROR
     Running 'testthat.R' [134s]
    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
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.6.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Joining, by = "patient_id"
    Warning: Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.
    Quitting from lines 177-178 (AMR.Rmd)
    Error: processing vignette 'AMR.Rmd' failed with diagnostics:
    'data' must be of a vector type, was 'NULL'
    Execution halted
Flavor: r-oldrel-windows-ix86+x86_64

Version: 0.6.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [284s/103s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
    
     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
Flavor: r-oldrel-osx-x86_64

Version: 0.6.1
Check: re-building of vignette outputs
Result: WARN
    Error in re-building vignettes:
     ...
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    
    Attaching package: 'dplyr'
    
    The following objects are masked from 'package:stats':
    
     filter, lag
    
    The following objects are masked from 'package:base':
    
     intersect, setdiff, setequal, union
    
    Joining, by = "patient_id"
    Warning: Some columns do not exist -- THIS MAY STRONGLY INFLUENCE THE OUTCOME.
    Quitting from lines 177-178 (AMR.Rmd)
    Error: processing vignette 'AMR.Rmd' failed with diagnostics:
    'data' must be of a vector type, was 'NULL'
    Execution halted
Flavor: r-oldrel-osx-x86_64