P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2024-12-26 06:46:11 +01:00
Code Releases Activity

R release test

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends 2019-01-05 22:18:49 +01:00
parent f01d62ee5d
commit d0c679e884
2 changed files with 7 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

11
.gitlab-ci.yml
View File

@ -25,7 +25,7 @@ stages:
- deploy - deploy
# debian stretch only contains R 3.3... # debian stretch only contains R 3.3...
image: debian:buster-slim #image: debian:buster-slim
before_script: before_script:
- apt-get update -qq - apt-get update -qq
@ -41,11 +41,12 @@ before_script:
- echo 'R_LIBS="installed_deps"' > .Renviron - echo 'R_LIBS="installed_deps"' > .Renviron
- echo 'R_LIBS_USER="installed_deps"' >> .Renviron - echo 'R_LIBS_USER="installed_deps"' >> .Renviron
- echo 'R_LIBS_SITE="installed_deps"' >> .Renviron - echo 'R_LIBS_SITE="installed_deps"' >> .Renviron
# set language
- echo 'LANGUAGE="en_US.utf8"' >> .Renviron - echo 'LANGUAGE="en_US.utf8"' >> .Renviron
- echo 'LANG="en_US.utf8"' >> .Renviron
- echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron - echo 'LANGUAGE="en_US.utf8"' > ~/.Renviron
#- Rscript -e '.libPaths()'
# install missing and outdated packages
- Rscript -e 'sessionInfo()' - Rscript -e 'sessionInfo()'
# install missing and outdated packages
- Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)' - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)'
cache: cache:
@ -53,7 +54,8 @@ cache:
paths: paths:
- installed_deps/ - installed_deps/
R 3: R-release:
image: rocker/r-ver:release
stage: build stage: build
allow_failure: true allow_failure: true
script: script:
@ -67,7 +69,6 @@ R 3:
artifacts: artifacts:
paths: paths:
- '*.Rcheck/*' - '*.Rcheck/*'
name: 'Rcheck log'
expire_in: '1 month' expire_in: '1 month'
coverage: coverage:

2
docs/news/index.html
View File

@ -592,7 +592,7 @@
<ul> <ul>
<li>Full support for Windows, Linux and macOS</li> <li>Full support for Windows, Linux and macOS</li>
<li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li> <li>Full support for old R versions, only R-3.0.0 (April 2013) or later is needed (needed packages may have other dependencies)</li>
<li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><a href="https://www.rdocumentation.org/packages/dplyr/topics/summarise">dplyr::summarise</a></code>, see ?rsi</li> <li>Function <code>n_rsi</code> to count cases where antibiotic test results were available, to be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">dplyr::summarise</a></code>, see ?rsi</li>
<li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li> <li>Function <code>guess_bactid</code> to <strong>determine the ID</strong> of a microorganism based on genus/species or known abbreviations like MRSA</li>
<li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li> <li>Function <code>guess_atc</code> to <strong>determine the ATC</strong> of an antibiotic based on name, trade name, or known abbreviations</li>
<li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li> <li>Function <code>freq</code> to create <strong>frequency tables</strong>, with additional info in a header</li>