.travis.yml

# this uses the r-travis native syntax for 1/16/16 travis implementation
#
# See README.md for instructions, or for more configuration options,
# see the wiki:
#   https://github.com/craigcitro/r-travis/wiki
#  checking now from ramsinghLab ~ master

#this tests TxDbLite build of geneWiseAnalysis which runs annotateFeatures and build TxDbLite libraries from scratch before running gwa. this is for human only testing.  

language: 
    - r
    - c
bioc_required: true

#pandoc: true


sudo: required
dist: trusty

env:
    matrix:
    - BIOC_USE_DEVEL="FALSE"

r_github_packages:
    - hadley/devtools

apt_packages:
   - gcc-4.6-base
   - cpp-4.6 
   - libgomp1
   - libquadmath0
   - libc6-dev
   - build-essential 
   - zlib1g-dev 
   - libc6-dev 
   - libcurl4-openssl-dev 
   - r-cran-xml
   - curl 
   - cmake 
   - zlibc 
   - zlib1g-dev
   - libhdf5-dev
   - git
#   - pandoc
 #  - texlive-latex-base
 #  - texlive-fonts-recommended
 #  - texlive-fonts-extra
 #  - texlive-latex-extra
   - libcurl4-openssl-dev
   - libxml2-dev
   - samtools
before_install:
    - curl -OL http://raw.github.com/craigcitro/r-travis/master/scripts/travis-tool.sh
    - chmod 755 ./travis-tool.sh
    - sudo apt-get --yes install curl cmake zlibc zlib1g-dev
    - sudo apt-get install -y libhdf5-dev
   # - cwd=$(pwd) && sudo mkdir ./KallistoSource && cd ./KallistoSource && sudo git clone https://github.com/pachterlab/kallisto.git && cd ./kallisto && sudo mkdir ./build && cd ./build && sudo cmake .. && sudo make && sudo make install && cd $cwd
    - sudo R -e 'source("http://bioconductor.org/biocLite.R"); biocLite("BiocInstaller")'
    - sudo R -e 'library(BiocInstaller);biocLite(c("rtracklayer","XML","biomaRt","RCurl"),ask=FALSE)'
    - sudo R -e 'library(BiocInstaller);biocLite(c("org.Hs.eg.db","parallel","jsonlite","GenomeInfoDb","limma","Biobase","SummarizedExperiment","clusterProfiler","rhdf5","matrixStats","GenomicRanges","GenomicFeatures","Matrix","pathview","KEGGREST","beeswarm","tools","graphite","roxygen2","knitr"),ask=FALSE )'
     - sudo R -e 'library(BiocInstaller);biocLite(c("Homo.sapiens","Mus.musculus","RUVSeq","erccdashboard"),ask=FALSE)'
     - sudo  R -e 'library(BiocInstaller);biocLite(c("DBI","RSQLite","ensembldb","stringdist","Biostrings","OrganismDbi","Rsamtools", "qusage","rmarkdown","na.utils"),ask=FALSE)'
 

bioc_packages: 
#    - rversions
 #   - annotate
  #  - genefilter
 #   - RColorBrewer
 #   - geneplotter
 #   - bitops
 #   - BiocParallel
 #   - latticeExtra
 #   - hwriter
 #   - GenomicAlignments
 #   - ShortRead
 #   - EDASeq
 #   - rmarkdown
 #   - pathview
 #   - edgeR
 #   - ggplot2

r_github_packages:
    - arcolombo/TxDbLite
    - arcolombo/RepDbLite.Hsapiens.2012
    - arcolombo/EnsDbLite.Hsapiens.83
    - arcolombo/arkas
    - arcolombo/arkasData    

script:
      - sudo R -e 'library(rmarkdown); render("./vignettes/makeTxDbLiteAnnotationLibrary.Rmd")'    
after_failure:
    - sudo ./travis-tool.sh dump_logs

notifications:
  email:
    on_success: change
    on_failure: change