mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 17:26:12 +01:00
introduction of Packrat
This commit is contained in:
parent
cf44d94552
commit
fd646fe1fc
@ -1,17 +1,20 @@
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^Meta$
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^doc$
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^CRAN-RELEASE$
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^.*\.Rproj$
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^\.gitlab-ci.yml$
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^\.Rprofile$
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^\.Rproj\.user$
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^\.travis.yml$
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^appveyor.yml$
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^\.gitlab-ci.yml$
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^\.zenodo.json$
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^_noinclude$
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^cran-comments\.md$
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^git.sh$
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^public$
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^docs$
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^_pkgdown\.yml$
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^pkgdown$
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^appveyor.yml$
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^ci.R$
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^cran-comments\.md$
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^CRAN-RELEASE$
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^doc$
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^docs$
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^git.sh$
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^index\.md$
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^Meta$
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^packrat/
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^pkgdown$
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^public$
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3
.gitignore
vendored
3
.gitignore
vendored
@ -15,5 +15,8 @@ _noinclude
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*.dll
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vignettes/*.R
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.DS_Store
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.Rprofile
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^CRAN-RELEASE$
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git.sh
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packrat/lib*/
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packrat/src/
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@ -1,54 +1,69 @@
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# from https://stackoverflow.com/questions/51866926
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# and https://github.com/jangorecki/r.gitlab.ci
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# and https://docs.gitlab.com/ce/ci/yaml/README.html
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# how the Docker+R images work: https://hub.docker.com/r/rocker/r-ver/
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This package is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This R package is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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# https://r-posts.com/gitlab-ci-for-r-package-development/
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image: rocker/r-base
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stages:
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- build
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- setup
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- test
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- deploy
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image: rocker/r-ver:3 # test on R v3.*.*
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cache:
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# Ommit key to use the same cache across all pipelines and branches
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key: "$CI_COMMIT_REF_SLUG"
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paths:
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- packrat/lib/
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before_script:
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- apt-get update
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# install dependencies for package
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- apt-get install --yes --no-install-recommends libxml2-dev libssl-dev libcurl4-openssl-dev zlib1g-dev pandoc
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- Rscript -e 'install.packages(c("devtools", "rlang"), repos = "https://cran.rstudio.com")'
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- Rscript -e 'devtools::install_dev_deps(repos = "https://cran.rstudio.com")'
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R 3:
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stage: build
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allow_failure: true
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setup:
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stage: setup
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script:
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# remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file
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- rm -rf vignettes
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- Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")'
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# build package
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- R CMD build . --no-build-vignettes --no-manual
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- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
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- R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran
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# code coverage
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- apt-get install --yes git
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- Rscript -e 'cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = "50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca"); cat("Code coverage:", covr::percent_coverage(cc))'
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- R -e 'source("ci.R"); ci_setup()'
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check:
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stage: test
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dependencies:
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- setup
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when: on_success
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script:
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- R -e 'source("ci.R"); ci_check()'
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coverage:
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stage: test
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dependencies:
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- setup
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when: on_success
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only:
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- master
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script:
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- R -e 'source("ci.R"); ci_coverage()'
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coverage: '/Code coverage: \d+\.\d+/'
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artifacts:
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paths:
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- '*.Rcheck/*.log'
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- '*.Rcheck/*.out'
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# - '*.Rcheck/*.fail'
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- '*.Rcheck/*.Rout'
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name: 'Rcheck log'
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expire_in: '1 month'
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pages:
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stage: deploy
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dependencies:
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- setup
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when: on_success
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only:
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- master
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script:
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- Rscript -e "install.packages('pkgdown', repos = 'https://cran.rstudio.com')"
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- Rscript -e "devtools::install(build = TRUE, upgrade = FALSE)"
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# - R -e "pkgdown::build_favicon()"
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- R -e "pkgdown::build_site(examples = FALSE, override = list(destination = 'public'))"
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- R -e 'source("ci.R"); ci_pages()'
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artifacts:
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paths:
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- public
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only:
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- master
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18
_pkgdown.yml
18
_pkgdown.yml
@ -1,3 +1,21 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This package is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This R package is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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url: https://msberends.gitlab.io
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title: 'AMR (for R)'
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48
ci.R
Normal file
48
ci.R
Normal file
@ -0,0 +1,48 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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||||
# LICENCE #
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||||
# This package is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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||||
# as published by the Free Software Foundation. #
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# #
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# This R package is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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||||
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License version 2.0 for more details. #
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# ==================================================================== #
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install_if_needed <- function(package_to_install) {
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package_path <- find.package(package_to_install, quiet = TRUE)
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if(length(package_path) == 0){
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# Only install if not present
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install.packages(package_to_install)
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}
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}
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ci_setup <- function() {
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install_if_needed("packrat")
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packrat::restore()
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}
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ci_check <- function() {
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install_if_needed("devtools")
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devtools::check()
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}
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ci_coverage <- function() {
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install_if_needed("covr")
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cc <- covr::package_coverage(type = c("tests", "examples"))
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covr::codecov(coverage = cc, token = "50ffa0aa-fee0-4f8b-a11d-8c7edc6d32ca")
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cat("Code coverage:", covr::percent_coverage(cc))
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}
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ci_pages <- function() {
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install_if_needed("pkgdown")
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pkgdown::build_site(examples = FALSE, override = list(destination = "public"))
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}
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15
index.md
15
index.md
@ -10,30 +10,35 @@ We created this package for academic research at the Faculty of Medical Sciences
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This package is ready-to-use for a professional environment by specialists in the following fields:
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* Medical Microbiology
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Medical Microbiology:
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* Epidemiologists (both clinical microbiological and research)
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* Research Microbiologists
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* Biomedical Researchers
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* Research Pharmacologists
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* Veterinary Microbiology
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Veterinary Microbiology:
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* Research Veterinarians
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* Veterinary Epidemiologists
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* Biomedical Researchers
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* Microbial Ecology
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Microbial Ecology:
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||||
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||||
* Soil Microbiologists
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* Extremophile Researchers
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* Astrobiologists
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||||
* Other specialists in any of the above fields:
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||||
Other specialists in any of the above fields:
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||||
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||||
* Data Scientists/Data Analysts
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||||
* Biotechnologists
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||||
* Biochemists
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||||
* Geneticists
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||||
* Molecular Biologists/Microbiologists
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||||
|
||||
* Developers
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||||
Developers:
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||||
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||||
* Package developers for R
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||||
* Software developers
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||||
* Web application developers
|
||||
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||||
226
packrat/init.R
Normal file
226
packrat/init.R
Normal file
@ -0,0 +1,226 @@
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local({
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||||
## Helper function to get the path to the library directory for a
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## given packrat project.
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getPackratLibDir <- function(projDir = NULL) {
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path <- file.path("packrat", "lib", R.version$platform, getRversion())
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if (!is.null(projDir)) {
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## Strip trailing slashes if necessary
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projDir <- sub("/+$", "", projDir)
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||||
## Only prepend path if different from current working dir
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if (!identical(normalizePath(projDir), normalizePath(getwd())))
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path <- file.path(projDir, path)
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||||
}
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||||
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||||
path
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||||
}
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||||
|
||||
## Ensure that we set the packrat library directory relative to the
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||||
## project directory. Normally, this should be the working directory,
|
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## but we also use '.rs.getProjectDirectory()' if necessary (e.g. we're
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||||
## rebuilding a project while within a separate directory)
|
||||
libDir <- if (exists(".rs.getProjectDirectory"))
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getPackratLibDir(.rs.getProjectDirectory())
|
||||
else
|
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getPackratLibDir()
|
||||
|
||||
## Unload packrat in case it's loaded -- this ensures packrat _must_ be
|
||||
## loaded from the private library. Note that `requireNamespace` will
|
||||
## succeed if the package is already loaded, regardless of lib.loc!
|
||||
if ("packrat" %in% loadedNamespaces())
|
||||
try(unloadNamespace("packrat"), silent = TRUE)
|
||||
|
||||
if (suppressWarnings(requireNamespace("packrat", quietly = TRUE, lib.loc = libDir))) {
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||||
|
||||
# Check 'print.banner.on.startup' -- when NA and RStudio, don't print
|
||||
print.banner <- packrat::get_opts("print.banner.on.startup")
|
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if (print.banner == "auto" && is.na(Sys.getenv("RSTUDIO", unset = NA))) {
|
||||
print.banner <- TRUE
|
||||
} else {
|
||||
print.banner <- FALSE
|
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}
|
||||
return(packrat::on(print.banner = print.banner))
|
||||
}
|
||||
|
||||
## Escape hatch to allow RStudio to handle bootstrapping. This
|
||||
## enables RStudio to provide print output when automagically
|
||||
## restoring a project from a bundle on load.
|
||||
if (!is.na(Sys.getenv("RSTUDIO", unset = NA)) &&
|
||||
is.na(Sys.getenv("RSTUDIO_PACKRAT_BOOTSTRAP", unset = NA))) {
|
||||
Sys.setenv("RSTUDIO_PACKRAT_BOOTSTRAP" = "1")
|
||||
setHook("rstudio.sessionInit", function(...) {
|
||||
# Ensure that, on sourcing 'packrat/init.R', we are
|
||||
# within the project root directory
|
||||
if (exists(".rs.getProjectDirectory")) {
|
||||
owd <- getwd()
|
||||
setwd(.rs.getProjectDirectory())
|
||||
on.exit(setwd(owd), add = TRUE)
|
||||
}
|
||||
source("packrat/init.R")
|
||||
})
|
||||
return(invisible(NULL))
|
||||
}
|
||||
|
||||
## Bootstrapping -- only performed in interactive contexts,
|
||||
## or when explicitly asked for on the command line
|
||||
if (interactive() || "--bootstrap-packrat" %in% commandArgs(TRUE)) {
|
||||
|
||||
needsRestore <- "--bootstrap-packrat" %in% commandArgs(TRUE)
|
||||
|
||||
message("Packrat is not installed in the local library -- ",
|
||||
"attempting to bootstrap an installation...")
|
||||
|
||||
## We need utils for the following to succeed -- there are calls to functions
|
||||
## in 'restore' that are contained within utils. utils gets loaded at the
|
||||
## end of start-up anyhow, so this should be fine
|
||||
library("utils", character.only = TRUE)
|
||||
|
||||
## Install packrat into local project library
|
||||
packratSrcPath <- list.files(full.names = TRUE,
|
||||
file.path("packrat", "src", "packrat")
|
||||
)
|
||||
|
||||
## No packrat tarballs available locally -- try some other means of installation
|
||||
if (!length(packratSrcPath)) {
|
||||
|
||||
message("> No source tarball of packrat available locally")
|
||||
|
||||
## There are no packrat sources available -- try using a version of
|
||||
## packrat installed in the user library to bootstrap
|
||||
if (requireNamespace("packrat", quietly = TRUE) && packageVersion("packrat") >= "0.2.0.99") {
|
||||
message("> Using user-library packrat (",
|
||||
packageVersion("packrat"),
|
||||
") to bootstrap this project")
|
||||
}
|
||||
|
||||
## Couldn't find a user-local packrat -- try finding and using devtools
|
||||
## to install
|
||||
else if (requireNamespace("devtools", quietly = TRUE)) {
|
||||
message("> Attempting to use devtools::install_github to install ",
|
||||
"a temporary version of packrat")
|
||||
library(stats) ## for setNames
|
||||
devtools::install_github("rstudio/packrat")
|
||||
}
|
||||
|
||||
## Try downloading packrat from CRAN if available
|
||||
else if ("packrat" %in% rownames(available.packages())) {
|
||||
message("> Installing packrat from CRAN")
|
||||
install.packages("packrat")
|
||||
}
|
||||
|
||||
## Fail -- couldn't find an appropriate means of installing packrat
|
||||
else {
|
||||
stop("Could not automatically bootstrap packrat -- try running ",
|
||||
"\"'install.packages('devtools'); devtools::install_github('rstudio/packrat')\"",
|
||||
"and restarting R to bootstrap packrat.")
|
||||
}
|
||||
|
||||
# Restore the project, unload the temporary packrat, and load the private packrat
|
||||
if (needsRestore)
|
||||
packrat::restore(prompt = FALSE, restart = TRUE)
|
||||
|
||||
## This code path only reached if we didn't restart earlier
|
||||
unloadNamespace("packrat")
|
||||
requireNamespace("packrat", lib.loc = libDir, quietly = TRUE)
|
||||
return(packrat::on())
|
||||
|
||||
}
|
||||
|
||||
## Multiple packrat tarballs available locally -- try to choose one
|
||||
## TODO: read lock file and infer most appropriate from there; low priority because
|
||||
## after bootstrapping packrat a restore should do the right thing
|
||||
if (length(packratSrcPath) > 1) {
|
||||
warning("Multiple versions of packrat available in the source directory;",
|
||||
"using packrat source:\n- ", shQuote(packratSrcPath))
|
||||
packratSrcPath <- packratSrcPath[[1]]
|
||||
}
|
||||
|
||||
|
||||
lib <- file.path("packrat", "lib", R.version$platform, getRversion())
|
||||
if (!file.exists(lib)) {
|
||||
dir.create(lib, recursive = TRUE)
|
||||
}
|
||||
|
||||
message("> Installing packrat into project private library:")
|
||||
message("- ", shQuote(lib))
|
||||
|
||||
surround <- function(x, with) {
|
||||
if (!length(x)) return(character())
|
||||
paste0(with, x, with)
|
||||
}
|
||||
|
||||
|
||||
## Invoke install.packages() in clean R session
|
||||
peq <- function(x, y) paste(x, y, sep = " = ")
|
||||
installArgs <- c(
|
||||
peq("pkgs", surround(packratSrcPath, with = "'")),
|
||||
peq("lib", surround(lib, with = "'")),
|
||||
peq("repos", "NULL"),
|
||||
peq("type", surround("source", with = "'"))
|
||||
)
|
||||
|
||||
fmt <- "utils::install.packages(%s)"
|
||||
installCmd <- sprintf(fmt, paste(installArgs, collapse = ", "))
|
||||
|
||||
## Write script to file (avoid issues with command line quoting
|
||||
## on R 3.4.3)
|
||||
installFile <- tempfile("packrat-bootstrap", fileext = ".R")
|
||||
writeLines(installCmd, con = installFile)
|
||||
on.exit(unlink(installFile), add = TRUE)
|
||||
|
||||
fullCmd <- paste(
|
||||
surround(file.path(R.home("bin"), "R"), with = "\""),
|
||||
"--vanilla",
|
||||
"--slave",
|
||||
"-f",
|
||||
surround(installFile, with = "\"")
|
||||
)
|
||||
system(fullCmd)
|
||||
|
||||
## Tag the installed packrat so we know it's managed by packrat
|
||||
## TODO: should this be taking information from the lockfile? this is a bit awkward
|
||||
## because we're taking an un-annotated packrat source tarball and simply assuming it's now
|
||||
## an 'installed from source' version
|
||||
|
||||
## -- InstallAgent -- ##
|
||||
installAgent <- "InstallAgent: packrat 0.5.0"
|
||||
|
||||
## -- InstallSource -- ##
|
||||
installSource <- "InstallSource: source"
|
||||
|
||||
packratDescPath <- file.path(lib, "packrat", "DESCRIPTION")
|
||||
DESCRIPTION <- readLines(packratDescPath)
|
||||
DESCRIPTION <- c(DESCRIPTION, installAgent, installSource)
|
||||
cat(DESCRIPTION, file = packratDescPath, sep = "\n")
|
||||
|
||||
# Otherwise, continue on as normal
|
||||
message("> Attaching packrat")
|
||||
library("packrat", character.only = TRUE, lib.loc = lib)
|
||||
|
||||
message("> Restoring library")
|
||||
if (needsRestore)
|
||||
packrat::restore(prompt = FALSE, restart = FALSE)
|
||||
|
||||
# If the environment allows us to restart, do so with a call to restore
|
||||
restart <- getOption("restart")
|
||||
if (!is.null(restart)) {
|
||||
message("> Packrat bootstrap successfully completed. ",
|
||||
"Restarting R and entering packrat mode...")
|
||||
return(restart())
|
||||
}
|
||||
|
||||
# Callers (source-erers) can define this hidden variable to make sure we don't enter packrat mode
|
||||
# Primarily useful for testing
|
||||
if (!exists(".__DONT_ENTER_PACKRAT_MODE__.") && interactive()) {
|
||||
message("> Packrat bootstrap successfully completed. Entering packrat mode...")
|
||||
packrat::on()
|
||||
}
|
||||
|
||||
Sys.unsetenv("RSTUDIO_PACKRAT_BOOTSTRAP")
|
||||
|
||||
}
|
||||
|
||||
})
|
||||
354
packrat/packrat.lock
Normal file
354
packrat/packrat.lock
Normal file
@ -0,0 +1,354 @@
|
||||
PackratFormat: 1.4
|
||||
PackratVersion: 0.5.0
|
||||
RVersion: 3.5.2
|
||||
Repos: CRAN=https://cloud.r-project.org
|
||||
|
||||
Package: BH
|
||||
Source: CRAN
|
||||
Version: 1.66.0-1
|
||||
Hash: 4cc8883584b955ed01f38f68bc03af6d
|
||||
|
||||
Package: R6
|
||||
Source: CRAN
|
||||
Version: 2.3.0
|
||||
Hash: 8eccabbf292b5aba632985cde6406fc3
|
||||
|
||||
Package: RColorBrewer
|
||||
Source: CRAN
|
||||
Version: 1.1-2
|
||||
Hash: c0d56cd15034f395874c870141870c25
|
||||
|
||||
Package: Rcpp
|
||||
Source: CRAN
|
||||
Version: 1.0.0
|
||||
Hash: c7273c0f0bc9f5e41f4c52a8cf571f0f
|
||||
|
||||
Package: assertthat
|
||||
Source: CRAN
|
||||
Version: 0.2.0
|
||||
Hash: e8805df54c65ac96d50235c44a82615c
|
||||
|
||||
Package: backports
|
||||
Source: CRAN
|
||||
Version: 1.1.2
|
||||
Hash: 5ae7b3466e529e4400951ca18c137e40
|
||||
|
||||
Package: base64enc
|
||||
Source: CRAN
|
||||
Version: 0.1-3
|
||||
Hash: c590d29e555926af053055e23ee79efb
|
||||
|
||||
Package: cli
|
||||
Source: CRAN
|
||||
Version: 1.0.1
|
||||
Hash: a742a3229dbf7085c3a737af10e5065b
|
||||
Requires: assertthat, crayon
|
||||
|
||||
Package: colorspace
|
||||
Source: CRAN
|
||||
Version: 1.3-2
|
||||
Hash: 0bf8618b585fa98eb23414cd3ab95118
|
||||
|
||||
Package: covr
|
||||
Source: CRAN
|
||||
Version: 3.2.1
|
||||
Hash: b1dab7f44fae6114c222cee94d6acd63
|
||||
Requires: crayon, digest, httr, jsonlite, rex, withr
|
||||
|
||||
Package: crayon
|
||||
Source: CRAN
|
||||
Version: 1.3.4
|
||||
Hash: ff2840dd9b0d563fc80377a5a45510cd
|
||||
|
||||
Package: curl
|
||||
Source: CRAN
|
||||
Version: 3.2
|
||||
Hash: 82a7cf5bb702ef52329b6d23ea6132a7
|
||||
|
||||
Package: data.table
|
||||
Source: CRAN
|
||||
Version: 1.11.8
|
||||
Hash: 67c877937c790a0cadb71284febb6b34
|
||||
|
||||
Package: digest
|
||||
Source: CRAN
|
||||
Version: 0.6.18
|
||||
Hash: 65f62365ec69ddd17230d2ffe891a6ab
|
||||
|
||||
Package: dplyr
|
||||
Source: github
|
||||
Version: 0.7.99.9000
|
||||
Hash: 2ad5ae0fa33abb1278da08b574c03c74
|
||||
Requires: BH, R6, Rcpp, assertthat, glue, magrittr, pkgconfig, plogr,
|
||||
rlang, tibble, tidyselect
|
||||
GithubRepo: dplyr
|
||||
GithubUsername: tidyverse
|
||||
GithubRef: master
|
||||
GithubSha1: 45894214a543e63c01f66e8b1fb4cc77a5978f40
|
||||
RemoteHost: api.github.com
|
||||
RemoteRepo: dplyr
|
||||
RemoteUsername: tidyverse
|
||||
RemoteRef: master
|
||||
RemoteSha: 45894214a543e63c01f66e8b1fb4cc77a5978f40
|
||||
|
||||
Package: evaluate
|
||||
Source: CRAN
|
||||
Version: 0.12
|
||||
Hash: c32505adba4f6eca5aa20dd32300b019
|
||||
|
||||
Package: fansi
|
||||
Source: CRAN
|
||||
Version: 0.4.0
|
||||
Hash: f147621f72b561485bfffcae78c4f5d5
|
||||
|
||||
Package: ggplot2
|
||||
Source: CRAN
|
||||
Version: 3.1.0
|
||||
Hash: ef541b05dda10b209d509b5bbaf46ea3
|
||||
Requires: digest, gtable, lazyeval, plyr, reshape2, rlang, scales,
|
||||
tibble, viridisLite, withr
|
||||
|
||||
Package: glue
|
||||
Source: CRAN
|
||||
Version: 1.3.0
|
||||
Hash: 1fbde6dec830370be696eee8ef31c9e4
|
||||
|
||||
Package: gtable
|
||||
Source: CRAN
|
||||
Version: 0.2.0
|
||||
Hash: cd78381a9d3fea966ac39bd0daaf5554
|
||||
|
||||
Package: highr
|
||||
Source: CRAN
|
||||
Version: 0.7
|
||||
Hash: 20757f5c393ed0ecf96c9e8e6d8d514c
|
||||
|
||||
Package: hms
|
||||
Source: CRAN
|
||||
Version: 0.4.2
|
||||
Hash: b4096a4f6a6736138e9a825c2baaacf0
|
||||
Requires: pkgconfig, rlang
|
||||
|
||||
Package: htmltools
|
||||
Source: CRAN
|
||||
Version: 0.3.6
|
||||
Hash: 9707abea0a9b7406e98fb1242e97e1f6
|
||||
Requires: Rcpp, digest
|
||||
|
||||
Package: httr
|
||||
Source: CRAN
|
||||
Version: 1.3.1
|
||||
Hash: 2d32e01e53d532c812052e27a1021441
|
||||
Requires: R6, curl, jsonlite, mime, openssl
|
||||
|
||||
Package: jsonlite
|
||||
Source: CRAN
|
||||
Version: 1.5
|
||||
Hash: 9c51936d8dd00b2f1d4fe9d10499694c
|
||||
|
||||
Package: knitr
|
||||
Source: CRAN
|
||||
Version: 1.20
|
||||
Hash: 9c6b215d1d02b97586c8232e94533e6a
|
||||
Requires: evaluate, highr, markdown, stringr, yaml
|
||||
|
||||
Package: labeling
|
||||
Source: CRAN
|
||||
Version: 0.3
|
||||
Hash: ecf589b42cd284b03a4beb9665482d3e
|
||||
|
||||
Package: lazyeval
|
||||
Source: CRAN
|
||||
Version: 0.2.1
|
||||
Hash: 88926ad9c43581fd0822a37c8ed09f05
|
||||
|
||||
Package: magrittr
|
||||
Source: CRAN
|
||||
Version: 1.5
|
||||
Hash: bdc4d48c3135e8f3b399536ddf160df4
|
||||
|
||||
Package: markdown
|
||||
Source: CRAN
|
||||
Version: 0.8
|
||||
Hash: 045d7c594d503b41f1c28946d076c8aa
|
||||
Requires: mime
|
||||
|
||||
Package: mime
|
||||
Source: CRAN
|
||||
Version: 0.6
|
||||
Hash: 2ed8f98b8284ad733f3907fc6e2f1334
|
||||
|
||||
Package: munsell
|
||||
Source: CRAN
|
||||
Version: 0.5.0
|
||||
Hash: 38d0efee9bb99bef143bde41c4ce715c
|
||||
Requires: colorspace
|
||||
|
||||
Package: openssl
|
||||
Source: CRAN
|
||||
Version: 1.0.2
|
||||
Hash: 12a42cbd5aecdb887782247856ccbafd
|
||||
|
||||
Package: packrat
|
||||
Source: CRAN
|
||||
Version: 0.5.0
|
||||
Hash: 498643e765d1442ba7b1160a1df3abf9
|
||||
|
||||
Package: pillar
|
||||
Source: CRAN
|
||||
Version: 1.3.1
|
||||
Hash: 9ed4c2a5d3047bfba3e852ad5e806d91
|
||||
Requires: cli, crayon, fansi, rlang, utf8
|
||||
|
||||
Package: pkgconfig
|
||||
Source: CRAN
|
||||
Version: 2.0.2
|
||||
Hash: b0fd6ed908e150b77e5f00c6478bd58c
|
||||
|
||||
Package: plogr
|
||||
Source: CRAN
|
||||
Version: 0.2.0
|
||||
Hash: 81a8008a5e7858552503935f1abe48aa
|
||||
|
||||
Package: plyr
|
||||
Source: CRAN
|
||||
Version: 1.8.4
|
||||
Hash: ec185c885aab7ec91693d78c20cb5d1a
|
||||
Requires: Rcpp
|
||||
|
||||
Package: praise
|
||||
Source: CRAN
|
||||
Version: 1.0.0
|
||||
Hash: 77da8f1df873a4b91e5c4a68fe2fb1b6
|
||||
|
||||
Package: purrr
|
||||
Source: CRAN
|
||||
Version: 0.2.5
|
||||
Hash: 8b0c16db10c7e20b70cd37779a673a8b
|
||||
Requires: magrittr, rlang, tibble
|
||||
|
||||
Package: reshape2
|
||||
Source: CRAN
|
||||
Version: 1.4.3
|
||||
Hash: c950c8ac85b81209635acb3ce21b4cce
|
||||
Requires: Rcpp, plyr, stringr
|
||||
|
||||
Package: rex
|
||||
Source: CRAN
|
||||
Version: 1.1.2
|
||||
Hash: 57541aaae58f1a284a398f5c62c95097
|
||||
Requires: lazyeval, magrittr
|
||||
|
||||
Package: rlang
|
||||
Source: CRAN
|
||||
Version: 0.3.0.1
|
||||
Hash: 35fb7a51d5d756c56f793ed9c381fb84
|
||||
|
||||
Package: rmarkdown
|
||||
Source: CRAN
|
||||
Version: 1.10
|
||||
Hash: 02f1aac33000c63986c6b5585e36e7ae
|
||||
Requires: base64enc, evaluate, htmltools, jsonlite, knitr, mime,
|
||||
rprojroot, stringr, tinytex, yaml
|
||||
|
||||
Package: rprojroot
|
||||
Source: CRAN
|
||||
Version: 1.3-2
|
||||
Hash: a25c3f70c166fb3fbabc410eb32b6366
|
||||
Requires: backports
|
||||
|
||||
Package: rstudioapi
|
||||
Source: CRAN
|
||||
Version: 0.8
|
||||
Hash: 9ba7fe76dcaf96966c449527ca04bb78
|
||||
|
||||
Package: rvest
|
||||
Source: CRAN
|
||||
Version: 0.3.2
|
||||
Hash: c69f7526520bad66fd2111ebe8b1364b
|
||||
Requires: httr, magrittr, selectr, xml2
|
||||
|
||||
Package: scales
|
||||
Source: CRAN
|
||||
Version: 1.0.0
|
||||
Hash: 7d9b717abcec656ae7c5c982d72b75e5
|
||||
Requires: R6, RColorBrewer, Rcpp, labeling, munsell, viridisLite
|
||||
|
||||
Package: selectr
|
||||
Source: CRAN
|
||||
Version: 0.4-1
|
||||
Hash: b12802c11e35dec9d16a74d30ed0f3ed
|
||||
Requires: R6, stringr
|
||||
|
||||
Package: stringi
|
||||
Source: CRAN
|
||||
Version: 1.2.4
|
||||
Hash: 03ab60ef7fa4627b38ad67c95ce6b04c
|
||||
|
||||
Package: stringr
|
||||
Source: CRAN
|
||||
Version: 1.3.1
|
||||
Hash: 9f417a1d899ed1f080942ab36998e8b5
|
||||
Requires: glue, magrittr, stringi
|
||||
|
||||
Package: testthat
|
||||
Source: CRAN
|
||||
Version: 2.0.1
|
||||
Hash: 777eb6e94f5a62bf6320fecf0175bbbb
|
||||
Requires: R6, cli, crayon, digest, magrittr, praise, rlang, withr
|
||||
|
||||
Package: tibble
|
||||
Source: CRAN
|
||||
Version: 1.4.2
|
||||
Hash: 83895360ce4f8d2ce92eee00526b5b0b
|
||||
Requires: cli, crayon, pillar, rlang
|
||||
|
||||
Package: tidyr
|
||||
Source: CRAN
|
||||
Version: 0.8.2
|
||||
Hash: 9ff92b9b3c11dfcd94d179b75b85c668
|
||||
Requires: Rcpp, dplyr, glue, magrittr, purrr, rlang, stringi, tibble,
|
||||
tidyselect
|
||||
|
||||
Package: tidyselect
|
||||
Source: CRAN
|
||||
Version: 0.2.5
|
||||
Hash: fad1cf10c5c4996fca6ca68e0716d2e6
|
||||
Requires: Rcpp, glue, purrr, rlang
|
||||
|
||||
Package: tinytex
|
||||
Source: CRAN
|
||||
Version: 0.9
|
||||
Hash: a4ffe98c58eace5a95644d8fd6ca5a50
|
||||
Requires: xfun
|
||||
|
||||
Package: utf8
|
||||
Source: CRAN
|
||||
Version: 1.1.4
|
||||
Hash: f3f97ce59092abc8ed3fd098a59e236c
|
||||
|
||||
Package: viridisLite
|
||||
Source: CRAN
|
||||
Version: 0.3.0
|
||||
Hash: 78bb072c4f9e729a283d4c40ec93f9c6
|
||||
|
||||
Package: withr
|
||||
Source: CRAN
|
||||
Version: 2.1.2
|
||||
Hash: d534108bcd5f34ec73e9eb523751ba20
|
||||
|
||||
Package: xfun
|
||||
Source: CRAN
|
||||
Version: 0.4
|
||||
Hash: 76004125b45195c0330ec71904849995
|
||||
|
||||
Package: xml2
|
||||
Source: CRAN
|
||||
Version: 1.2.0
|
||||
Hash: 3f00e5347a6d7ccad2237fe1bc1df6d0
|
||||
Requires: Rcpp
|
||||
|
||||
Package: yaml
|
||||
Source: CRAN
|
||||
Version: 2.2.0
|
||||
Hash: a5ad5616d83d89f8d84cbf3cf4034e13
|
||||
19
packrat/packrat.opts
Normal file
19
packrat/packrat.opts
Normal file
@ -0,0 +1,19 @@
|
||||
auto.snapshot: TRUE
|
||||
use.cache: FALSE
|
||||
print.banner.on.startup: auto
|
||||
vcs.ignore.lib: TRUE
|
||||
vcs.ignore.src: TRUE
|
||||
external.packages:
|
||||
local.repos:
|
||||
load.external.packages.on.startup: TRUE
|
||||
ignored.packages:
|
||||
ignored.directories:
|
||||
data
|
||||
inst
|
||||
quiet.package.installation: TRUE
|
||||
snapshot.recommended.packages: FALSE
|
||||
snapshot.fields:
|
||||
Imports
|
||||
Depends
|
||||
LinkingTo
|
||||
symlink.system.packages: TRUE
|
||||
@ -2,7 +2,8 @@
|
||||
$('head').append('<!-- Updated Font Awesome library --><link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.6.3/css/all.css" integrity="sha384-UHRtZLI+pbxtHCWp1t77Bi1L4ZtiqrqD80Kn4Z8NTSRyMA2Fd33n5dQ8lWUE00s/" crossorigin="anonymous">');
|
||||
|
||||
/* edit footer */
|
||||
var footer_txt = $('footer .copyright p').html();
|
||||
footer_txt = footer_txt.replace("Developed by", "Developed at the University of Groningen. Authors:");
|
||||
$('footer').html('<p>' + footer_txt + '</p>');
|
||||
$('footer').html('<p>' +
|
||||
$('footer .copyright p').html().replace("Developed by",
|
||||
"<code>AMR</code> (for R). Developed at the University of Groningen.<br>Authors:") +
|
||||
'</p>');
|
||||
//$('footer').prepend("<div class='university'/>");
|
||||
|
||||
Loading…
Reference in New Issue
Block a user