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.travis.yml
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# which branches to trigger builds on
branches:
only:
- master
# language settings
language: r
sudo: required
cran: http://cran.rstudio.com
latex: false
pandoc: true
warnings_are_errors: false
cache:
directories:
- "$HOME/.local/share/renv"
- "$TRAVIS_BUILD_DIR/renv/library"
- "$HOME/.TinyTeX/"
# which versions of R should we build on
r:
#- release
# NOTE: can we grab this from the renv.lockfile?
- 4.0.4
# public key to allow Travis to push to gh-pages
env:
global:
secure: 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
# build reports via included Make recipes, in independent simultaneous jobs
jobs:
include:
- name: Moderna CoR Report
env:
- REPORT_TYPE=COR
- TRIAL=moderna_mock
script:
- echo "Building correlates of risk report"
#- make data_processed
#- make risk_report
- make cor_report
- name: Janssen Pooled CoR Report
env:
- REPORT_TYPE=COR
- TRIAL=janssen_pooled_mock
script:
- echo "Building correlates of risk report"
#- make data_processed
#- make risk_report
- make cor_report
# - name: Moderna CoP Report
# env:
# - REPORT_TYPE=COP
# - TRIAL=moderna_mock
# script:
# - echo "Building correlates of protection report"
# - make data_processed
# - make risk_report
# - make cop_report
#- name: Janssen Data Processing
# env:
# - REPORT_TYPE=IMMUNO
# - TRIAL=janssen_pooled_mock
# script:
# - echo "Processing data"
# - make data_processed
#- name: Moderna Immuno Report
# env:
# - REPORT_TYPE=IMMUNO
# - TRIAL=moderna_mock
# script:
# - echo "Building immunogenicity report"
# - make data_processed
# - make immuno_report
#- name: Janssen Pooled Immuno Report
# env:
# - REPORT_TYPE=IMMUNO
# - TRIAL=janssen_pooled_mock
# script:
# - echo "Building immunogenicity report"
# - make data_processed
# - make immuno_report
# - name: Janssen Pooled Risk Score Report
# env:
# - REPORT_TYPE=RISK
# - TRIAL=janssen_pooled_mock
# script:
# - echo "Building risk score report"
# - make risk_report
apt_packages:
- libxml2-dev
- libssl-dev
- libcurl4-openssl-dev
before_install:
- sudo apt-get install -y texlive-extra-utils ghostscript
# R packages cannot be installed in TRAVIS_BUILD_DIR; they need to be installed
# separately from the lockfile
# tinytex installs tlmgr to a directory that is symlinked to $HOME/bin
install:
- cd .. && Rscript -e "install.packages(c('here', 'renv', 'tinytex'))"
- echo insecure >> ~/.curlrc && Rscript -e "tinytex::install_tinytex()"
- export PATH=$HOME/bin:${PATH}
- cd $TRAVIS_BUILD_DIR && Rscript -e "renv::restore()"
# turn down number of bootstraps and permutations in CoR for faster builds
before_script:
- echo "B <- 5" >> $TRAVIS_BUILD_DIR/cor_coxph/code/params.R
- echo "numPerm <- 5" >> $TRAVIS_BUILD_DIR/cor_coxph/code/params.R
- echo "B <- 5" >> $TRAVIS_BUILD_DIR/cor_nonlinear/code/params.R
# push reports to gh-pages branch
after_script:
- chmod +x _deploy_reports.sh && ./_deploy_reports.sh
notifications:
email:
on_success: change
on_failure: always
recipients: