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.travis.yml
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notifications:
slack: fertiglab:LZeNoaS7BnLfqP6XuHiDYdts
addons:
apt:
packages: ccache
cache: ccache
jobs:
fast_finish: true
allow_failures:
- name: Linting
- name: Code Formatting
- name: Bioconductor Devel Testing - Linux
- name: Bioconductor Devel Testing - OSX
include:
- name: "Bioconductor Release Testing - Linux"
os: linux
if: tag IS NOT present
language: r
r: bioc-release
repos:
CRAN: http://cran.rstudio.com/
before_install:
- mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
- name: "Bioconductor Devel Testing - Linux"
os: linux
if: tag IS NOT present
language: r
r: bioc-devel
repos:
CRAN: http://cran.rstudio.com/
before_install:
- mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
- name: "Bioconductor Release Testing - OSX"
os: osx
if: tag IS NOT present
language: r
r: bioc-release
repos:
CRAN: http://cran.rstudio.com/
- name: "Bioconductor Devel Testing - OSX"
os: osx
if: tag IS NOT present
language: r
r: bioc-devel
repos:
CRAN: http://cran.rstudio.com/
- name: "Test Running in Debug Mode"
if: tag IS NOT present
language: r
r: release
before_install:
- mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
install:
- R -e 'install.packages(c("BiocManager", "desc"), repos="http://cran.rstudio.com/")'
- R -e 'BiocManager::install(desc::desc_get_deps()$package, site_repository=c("http://cran.rstudio.com/"))'
- R CMD build --no-build-vignettes .
- R CMD INSTALL --configure-args=" --enable-debug " *tar.gz
script: R -f inst/scripts/debugRuns.R
- name: "Linting"
if: tag IS NOT present
script: echo "linting not implemented"
- name: "Code Formatting"
if: tag IS NOT present
script: echo "formatting not implemented"
#- stage: Valgrind Analysis
# before_install:
# - mkdir $HOME/.R && echo -e 'VER=\nCCACHE=ccache\nCC=$(CCACHE) gcc$(VER) -std=gnu99\nCXX=$(CCACHE) g++$(VER)\nC11=$(CCACHE) g++$(VER)\nC14=$(CCACHE) g++$(VER)\nFC=$(CCACHE) gfortran$(VER)\nF77=$(CCACHE) gfortran$(VER)' > $HOME/.R/Makevars
# - sudo apt-get update -qq
# - sudo apt-get install -qq valgrind
# install:
# - R -e 'install.packages(c("BiocManager", "desc"))'
# - R -e 'BiocManager::install(desc::desc_get_deps()$package)'
# - R CMD build --no-build-vignettes .
# - R CMD INSTALL --configure-args=" --disable-openmp " *tar.gz
# script: R -d "valgrind --tool=memcheck --leak-check=yes" -e 'library(CoGAPS); data(GIST); CoGAPS(GIST.matrix, nIterations=1000, outputFrequency=250)'