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.gitlab-ci.yml
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.gitlab-ci.yml
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variables:
PKGNAME: "OUTRIDER"
PKGDIR: "./"
R_LIBS_U: "tmp_lib"
# RVER: "3.5.0-Bioc3.7"
RVER: "000-devel-3.5.0-Bioc3.8"
TEXVER: "2016"
# CI_DEBUG_TRACE: "true"
stages:
- testing
before_script:
- module load "i12g/R/$RVER"
- module load "i12g/texlive/$TEXVER"
- export R_LIBS_U="`realpath ${CI_JOB_ID}_${R_LIBS_U}`"
- mkdir $R_LIBS_U
- R --vanilla CMD build --no-build-vignettes --no-manual $PKGDIR
- PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1)
- R_LIBS_USER=$R_LIBS_U Rscript --vanilla -e "install.packages('${PKG_FILE_NAME}', lib='$R_LIBS_U', repo=NULL)"
R-check:
stage: testing
when: always
tags: [shell]
script:
- R_LIBS_USER=$R_LIBS_U R --vanilla CMD check --no-vignettes --timings "${PKG_FILE_NAME}"
R-BiocCheck:
stage: testing
when: always
tags: [shell]
script:
- R_LIBS_USER=$R_LIBS_U R --vanilla CMD BiocCheck --no-check-vignettes "${PKG_FILE_NAME}"
R-coverage:
stage: testing
when: always
tags: [shell]
script:
- R_LIBS_USER=$R_LIBS_U Rscript --vanilla -e "library('$PKGNAME'); covr::package_coverage('$PKGDIR')"
R-check_vignettes:
stage: testing
when: always
tags: [shell]
script:
- cd "$PKGDIR/vignettes/" && R_LIBS_USER=$R_LIBS_U R --vanilla CMD Sweave --engine=knitr::knitr --pdf "$PKGNAME.Rnw"