diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
index 62c35ab4..3a0c14de 100644
--- a/.github/workflows/check.yaml
+++ b/.github/workflows/check.yaml
@@ -56,6 +56,10 @@ jobs:
- {os: windows-latest, r: 'devel', allowfail: false}
- {os: windows-latest, r: 'release', allowfail: false}
- {os: windows-latest, r: 'oldrel', allowfail: false}
+ - {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ - {os: ubuntu-20.04, r: 'release', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ - {os: ubuntu-20.04, r: 'oldrel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+ - {os: ubuntu-20.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- {os: ubuntu-16.04, r: 'devel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: 'release', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: 'oldrel', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
@@ -67,12 +71,6 @@ jobs:
- {os: ubuntu-16.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {os: ubuntu-16.04, r: '3.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- - {os: ubuntu-20.04, r: 'devel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: 'release', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: 'oldrel', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: '3.2', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: '3.1', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
- - {os: ubuntu-20.04, r: '3.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -95,7 +93,7 @@ jobs:
shell: Rscript {0}
- name: Cache R packages
- if: runner.os != 'Windows'
+ if: runner.os != 'Windows' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
uses: actions/cache@v1
with:
path: ${{ env.R_LIBS_USER }}
@@ -103,7 +101,16 @@ jobs:
restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-
- name: Install Linux dependencies
- if: runner.os == 'Linux'
+ if: runner.os == 'Linux' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
+ env:
+ RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
+ run: |
+ Rscript -e "remotes::install_github('r-hub/sysreqs')"
+ sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
+ sudo -s eval "$sysreqs"
+
+ - name: Install Linux dependencies on old R versions
+ if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
@@ -117,8 +124,10 @@ jobs:
brew install mariadb-connector-c
- name: Install dependencies
+ if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
run: |
- utils::update.packages(ask = FALSE)
+ remotes::install_deps(dependencies = TRUE)
+ remotes::install_cran("rcmdcheck")
shell: Rscript {0}
- name: Session info
@@ -128,32 +137,27 @@ jobs:
as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
shell: Rscript {0}
- - name: Run R CMD check
- if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
- env:
- _R_CHECK_CRAN_INCOMING_: false
- run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
- shell: Rscript {0}
+ # - name: Run R CMD check
+ # if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
+ # env:
+ # _R_CHECK_CRAN_INCOMING_: false
+ # run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
+ # shell: Rscript {0}
- name: Run R CMD check on older R versions
- if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
+ # if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
env:
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_FORCE_SUGGESTS_: false
- # these are set already in --as-cran:
_R_CHECK_LENGTH_1_CONDITION_: verbose
_R_CHECK_LENGTH_1_LOGIC2_: verbose
run: |
- R CMD check data-raw/AMR_*.tar.gz --no-manual
+ R CMD check data-raw/AMR_*.tar.gz --no-manual --as-cran
- name: Show testthat output
if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash
-
- - name: Install packages to check for new deps
- run: |
- R CMD INSTALL data-raw/AMR_*.tar.gz
- name: Upload check results
if: failure()
diff --git a/DESCRIPTION b/DESCRIPTION
index 516052e5..fc8083e2 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
Package: AMR
-Version: 1.4.0.9057
+Version: 1.4.0.9058
Date: 2021-01-04
Title: Antimicrobial Resistance Analysis
Authors@R: c(
diff --git a/NEWS.md b/NEWS.md
index 7e8509a3..40a68ab8 100755
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,4 +1,4 @@
-# AMR 1.4.0.9057
+# AMR 1.4.0.9058
## Last updated: 4 January 2021
### New
* Functions `get_episode()` and `is_new_episode()` to determine (patient) episodes which are not necessarily based on microorganisms. The `get_episode()` function returns the index number of the episode per group, while the `is_new_episode()` function returns values `TRUE`/`FALSE` to indicate whether an item in a vector is the start of a new episode. They also support `dplyr`s grouping (i.e. using `group_by()`):
diff --git a/data-raw/AMR_1.4.0.9057.tar.gz b/data-raw/AMR_1.4.0.9058.tar.gz
similarity index 81%
rename from data-raw/AMR_1.4.0.9057.tar.gz
rename to data-raw/AMR_1.4.0.9058.tar.gz
index a9f84586..4bdc18cc 100644
Binary files a/data-raw/AMR_1.4.0.9057.tar.gz and b/data-raw/AMR_1.4.0.9058.tar.gz differ
diff --git a/docs/404.html b/docs/404.html
index 4c364517..dc184c34 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9057
+ 1.4.0.9058
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index 93db29cb..f8426757 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9057
+ 1.4.0.9058
diff --git a/docs/articles/index.html b/docs/articles/index.html
index ce30f144..4116a500 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9057
+ 1.4.0.9058
diff --git a/docs/authors.html b/docs/authors.html
index 11961739..cb175c91 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9057
+ 1.4.0.9058
diff --git a/docs/index.html b/docs/index.html
index 6a843cd7..8f977006 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -43,7 +43,7 @@
AMR (for R)
- 1.4.0.9057
+ 1.4.0.9058
diff --git a/docs/news/index.html b/docs/news/index.html
index e47eb46f..52d71f3a 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.4.0.9057
+ 1.4.0.9058
@@ -236,9 +236,9 @@
Source: NEWS.md
-
-