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# OslerInHealth Template no ANTs
language: r
warnings_are_errors: true
cache: packages
bioc_required: true
cran: http://cran.rstudio.com
dist: trusty
addons:
apt:
packages:
- libcurl4-openssl-dev
- libxml2-dev
- libfftw3-dev
- libgsl0-dev
- mesa-common-dev
- libglu1-mesa-dev
- devscripts
- jags
os:
- linux
- osx
osx_image: xcode9.4
services:
- xvfb
r:
- 3.3
- 3.4
- 3.5
- release
- devel
jobs:
allow_failures:
- r: devel
env:
global:
- RGL_USE_NULL=TRUE
- PROJECT_NAME=oslerinhealth
- DISPLAY=:99.0
- R_REMOTES_NO_ERRORS_FROM_WARNINGS=true
- _R_CHECK_FORCE_SUGGESTS_=false
- CACHE_NAME="${TRAVIS_OS_NAME}-R-${TRAVIS_R_VERSION}"
r_check_args: --as-cran --install-args=--build
before_install:
- if [ "$TRAVIS_DIST" = "trusty" ]; then sudo apt-get -y install libgsl0ldbl ; fi
- ulimit -n 2048
- export PROJ_DIR=`basename $PWD`
- fname=travis_helpers.sh
- wget -O ${fname} http://bit.ly/travis_helpers
- cat ${fname}; source ${fname}; rm ${fname}
- cat DESCRIPTION
- codename=`linux_codename`;
- start_xvfb ;
- export rver=`r_version`; echo $rver ;
- x=`export_clang_cxx`; eval ${x}
- if [ "$TRAVIS_OS_NAME" = "osx" ];
then
no_open_mp ;
brew install -v freetype ;
fi
- jags_install || true;
- if `need_v8`; then v8_install || true; fi
- dcmtk_install || true;
- gsl_install 2.1 || true ; # now checking version
- echo "CC=${CC}, CXX=${CXX}, CXX1X=${CXX1X}"
- echo "CXX1XSTD=${CXX1XSTD}, CXX11=${CXX11}"
- echo "CXX1XSTD=${CXX1XSTD}, CXX11=${CXX11}"
- clang_cxx
- export cmake_version="3.11"
- cmake --version
- x=`cmake_setup`; echo "${x}"; eval ${x};
- cmake --version
- remove_neuroc_packages
- cat DESCRIPTION
- install_remotes_no_dep
- cat DESCRIPTION
- export PACKAGE_NAME=`package_name`
- echo "Package Name is $PACKAGE_NAME"
- setup_python 3.6 false ;
- install_python_requirements ;
- R CMD javareconf ;
# - ralias; R -e "cat('test')"; ls travis_*.log
after_success:
- dump_logs
after_failure:
- dump_logs
# need this explicitly
# for naming convention
before_deploy:
# - travis_wait 100 R CMD INSTALL --build ${PKG_TARBALL}
# so no overwrite of linux build
- if [ "$TRAVIS_OS_NAME" = "osx" ];
then
PKG_TARBALL=$(ls -1t *.tgz | head -n 1);
PKG_TARBALL_WITH_R=`echo $PKG_TARBALL | sed 's/.tgz/_'"R${rver}"'.tgz/'` ;
mv ${PKG_TARBALL} ${PKG_TARBALL_WITH_R} ;
echo "Built tarball is ${PKG_TARBALL_WITH_R}" ;
fi
- if [ "$TRAVIS_OS_NAME" = "linux" ];
then
PKG_TARBALL=$(ls -1t *.tar.gz | head -n 1);
PKG_TARBALL_WITH_R=`echo $PKG_TARBALL | sed 's/.tar.gz/_'"R${rver}"'.tar.gz/'` ;
mv ${PKG_TARBALL} ${PKG_TARBALL_WITH_R} ;
echo "Built tarball is ${PKG_TARBALL_WITH_R}" ;
fi
- if [[ "${TRAVIS_OS_NAME}" = "osx" ]];
then
rm -f *.tar.gz;
fi
deploy:
provider: releases
skip_cleanup: true
token: $GITHUB_TOKEN
file_glob: true
overwrite: true
file: ${PACKAGE_NAME}*.t*gz
'on':
tags: true
after_deploy:
- echo "${PROJECT_NAME}" | grep -q "releases"; if [[ $? -eq 0 ]]; then run_coverage="false"; else run_coverage=; fi;
- if [[ "${TRAVIS_OS_NAME}" == "linux" && ${TRAVIS_R_VERSION_STRING} = "release" && -z "${run_coverage}" ]];
then
echo 'covr::coveralls(type = "all", quiet = FALSE)' > osler_covr.R ;
travis_wait 100 Rscript osler_covr.R ;
rm osler_covr.R ;
fi
# r:
# - release
# - devel
# matrix:
# allow_failures:
# - r: devel
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