From cb76b16b69bcd6b5582dba9010a63a1ce40831a4 Mon Sep 17 00:00:00 2001 From: Matthijs Berends Date: Wed, 5 Oct 2022 00:11:22 +0200 Subject: [PATCH] final --- .github/workflows/check.yaml | 2 +- .github/workflows/lintr.yaml | 2 +- DESCRIPTION | 4 ++-- NEWS.md | 2 +- inst/tinytest/test-disk.R | 4 ++-- inst/tinytest/test-mic.R | 4 ++-- 6 files changed, 9 insertions(+), 9 deletions(-) diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml index 4cb95c42..00d26914 100644 --- a/.github/workflows/check.yaml +++ b/.github/workflows/check.yaml @@ -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: '4.0', 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: '3.5', 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: '3.3', 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"} diff --git a/.github/workflows/lintr.yaml b/.github/workflows/lintr.yaml index aa3a7182..00f06381 100644 --- a/.github/workflows/lintr.yaml +++ b/.github/workflows/lintr.yaml @@ -63,7 +63,7 @@ jobs: # lose deprecated linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator)_linter$", linters)] # and the ones we find unnnecessary - linters <- linters[!grepl("^(extraction_operator|implicit_integer|line_length|object_name|nonportable_path)_linter$", linters)] + linters <- linters[!grepl("^(extraction_operator|implicit_integer|line_length|object_name|nonportable_path|is)_linter$", linters)] # put the functions in a list linters <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr"))) # run them all! diff --git a/DESCRIPTION b/DESCRIPTION index 21e0785b..8d820cff 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.8.2.9029 -Date: 2022-10-04 +Version: 1.8.2.9030 +Date: 2022-10-05 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by diff --git a/NEWS.md b/NEWS.md index e285ff7f..7972c92f 100755 --- a/NEWS.md +++ b/NEWS.md @@ -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! diff --git a/inst/tinytest/test-disk.R b/inst/tinytest/test-disk.R index 47049c89..7d6d2f4a 100755 --- a/inst/tinytest/test-disk.R +++ b/inst/tinytest/test-disk.R @@ -46,11 +46,11 @@ pdf(NULL) # prevent Rplots.pdf being created 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)), 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")) { 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)), 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))) diff --git a/inst/tinytest/test-mic.R b/inst/tinytest/test-mic.R index b034bf25..ad5f6158 100755 --- a/inst/tinytest/test-mic.R +++ b/inst/tinytest/test-mic.R @@ -61,11 +61,11 @@ pdf(NULL) # prevent Rplots.pdf being created 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)), 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")) { 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, 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))))