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 |
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