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dr. M.S. (Matthijs) Berends
2022-10-05 00:11:22 +02:00
parent 4e9de9eb5d
commit cb76b16b69
6 changed files with 9 additions and 9 deletions
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.github/workflows/check.yaml
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@@ -61,7 +61,7 @@ jobs:
- {os: ubuntu-22.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.5', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '3.5.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"} - {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
.github/workflows/lintr.yaml
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@@ -63,7 +63,7 @@ jobs:
# lose deprecated # lose deprecated
linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator)_linter$", linters)] linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator)_linter$", linters)]
# and the ones we find unnnecessary # and the ones we find unnnecessary
linters <- linters[!grepl("^(extraction_operator|implicit_integer|line_length|object_name|nonportable_path)_linter$", linters)] linters <- linters[!grepl("^(extraction_operator|implicit_integer|line_length|object_name|nonportable_path|is)_linter$", linters)]
# put the functions in a list # put the functions in a list
linters <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr"))) linters <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr")))
# run them all! # run them all!
DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.8.2.9029 Version: 1.8.2.9030
Date: 2022-10-04 Date: 2022-10-05
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by
NEWS.md
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@@ -1,4 +1,4 @@
# AMR 1.8.2.9029 # AMR 1.8.2.9030
This version will eventually become v2.0! We're happy to reach a new major milestone soon! This version will eventually become v2.0! We're happy to reach a new major milestone soon!
inst/tinytest/test-disk.R
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@@ -46,11 +46,11 @@ pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.disk(c(10, 20, 40)))) expect_silent(barplot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40)))) expect_silent(plot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE)) expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
expect_silent(plot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr")) expect_silent(plot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"))
if (AMR:::pkg_is_available("ggplot2")) { if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(autoplot(as.disk(c(10, 20, 40))), "gg") expect_inherits(autoplot(as.disk(c(10, 20, 40))), "gg")
expect_inherits(autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg") expect_inherits(autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
expect_inherits(autoplot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"), "gg") expect_inherits(autoplot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"), "gg")
} }
expect_stdout(print(as.disk(12))) expect_stdout(print(as.disk(12)))
inst/tinytest/test-mic.R
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@@ -61,11 +61,11 @@ pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.mic(c(1, 2, 4, 8)))) expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
expect_silent(plot(as.mic(c(1, 2, 4, 8)))) expect_silent(plot(as.mic(c(1, 2, 4, 8))))
expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE)) expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "esco", ab = "cipr")) expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "Escherichia coli", ab = "cipr"))
if (AMR:::pkg_is_available("ggplot2")) { if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8))), "gg") expect_inherits(autoplot(as.mic(c(1, 2, 4, 8))), "gg")
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg") expect_inherits(autoplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "esco", ab = "cipr"), "gg") expect_inherits(autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "Escherichia coli", ab = "cipr"), "gg")
} }
expect_stdout(print(as.mic(c(1, 2, 4, 8)))) expect_stdout(print(as.mic(c(1, 2, 4, 8))))