@@ -39,9 +39,9 @@ matrix:

         - sudo apt-get install jq

         - pip install mkdocs==1 mkdocs-material==3.0.3

         - conda install r-knitr r-devtools

-        - R -e 'remove.packages(c("curl","httr")); install.packages(c("curl", "httr"), repos="http://cran.us.r-project.org"); Sys.setenv(CURL_CA_BUNDLE="/utils/microsoft-r-open-3.5.0/lib64/R/lib/microsoft-r-cacert.pem")'

-        - R -e 'install.packages("Rd2md", repos="http://cran.us.r-project.org")'

-        - R -e 'install.packages("Rcpp", repos="http://cran.us.r-project.org")'

+        - R -e 'remove.packages(c("curl","httr")); install.packages(c("curl", "httr"), repos="http://cran.mtu.edu"); Sys.setenv(CURL_CA_BUNDLE="/utils/microsoft-r-open-3.5.0/lib64/R/lib/microsoft-r-cacert.pem")'

+        - R -e 'install.packages("Rd2md", repos="http://cran.mtu.edu")'

+        - R -e 'install.packages("Rcpp", repos="http://cran.mtu.edu")'

         - R -e 'source("https://bioconductor.org/biocLite.R"); biocLite("BiocInstaller"); library(devtools); install_github("compbiocore/RSeqAn",build_vignettes=FALSE)'

       before_script:

         - source activate test-env

@@ -3,6 +3,7 @@ matrix:

     - stage: test # groups builds by type, add your tests here

       language: r

       r: bioc-release

+      cache: packages

       os: linux

       addons:

         apt:

@@ -35,12 +35,13 @@ matrix:

         - conda info -a

         - conda create -q -n test-env python=$TRAVIS_PYTHON_VERSION

         - source activate test-env

+        - sudo apt-get install jq

         - pip install mkdocs==1 mkdocs-material==3.0.3

         - conda install r-knitr r-devtools

         - R -e 'remove.packages(c("curl","httr")); install.packages(c("curl", "httr"), repos="http://cran.us.r-project.org"); Sys.setenv(CURL_CA_BUNDLE="/utils/microsoft-r-open-3.5.0/lib64/R/lib/microsoft-r-cacert.pem")'

         - R -e 'install.packages("Rd2md", repos="http://cran.us.r-project.org")'

         - R -e 'install.packages("Rcpp", repos="http://cran.us.r-project.org")'

-        - R -e 'source("https://bioconductor.org/biocLite.R"); biocLite("BiocInstaller"); library(devtools); install_github("compbiocore/qckitfastq",build_vignettes=FALSE)'

+        - R -e 'source("https://bioconductor.org/biocLite.R"); biocLite("BiocInstaller"); library(devtools); install_github("compbiocore/RSeqAn",build_vignettes=FALSE)'

       before_script:

         - source activate test-env

       script:

@@ -48,8 +49,10 @@ matrix:

         - Rscript make.R

         - mkdir docs/styles

         - mkdir docs/images

-        - curl https://gist.githubusercontent.com/fernandogelin/08ecff3387dffc374c4abf06a577ab71/raw/083a383e51533feb20f3b03e6edcd9e86ddc59f9/dark_mode.css > docs/styles/dark_mode.css

-        - curl https://gist.githubusercontent.com/fernandogelin/b02ee98f2f35ce4263093f7a1c66582b/raw/20ca5a37eb6defe00d35e50e7e00a784b64309f9/cbc-logo.svg > docs/images/cbc-logo.svg

+        - curl https://api.github.com/repos/compbiocore/cbc-documentation-templates/contents/files/dark_mode.css\?access_token\=$GITHUB_TOKEN > dark_mode.json

+        - jq -r '.content' < dark_mode.json | base64 --decode > docs/styles/dark_mode.css

+        - curl https://api.github.com/repos/compbiocore/cbc-documentation-templates/contents/files/cbc-logo.svg\?access_token\=$GITHUB_TOKEN > logo.json

+        - jq -r '.content' < logo.json | base64 --decode > docs/images/cbc-logo.svg

         - mkdocs build --verbose --clean --strict

       deploy:

        provider: pages

@@ -39,6 +39,7 @@ matrix:

         - conda install r-knitr r-devtools

         - R -e 'remove.packages(c("curl","httr")); install.packages(c("curl", "httr"), repos="http://cran.us.r-project.org"); Sys.setenv(CURL_CA_BUNDLE="/utils/microsoft-r-open-3.5.0/lib64/R/lib/microsoft-r-cacert.pem")'

         - R -e 'install.packages("Rd2md", repos="http://cran.us.r-project.org")'

+        - R -e 'install.packages("Rcpp", repos="http://cran.us.r-project.org")'

         - R -e 'source("https://bioconductor.org/biocLite.R"); biocLite("BiocInstaller"); library(devtools); install_github("compbiocore/qckitfastq",build_vignettes=FALSE)'

       before_script:

         - source activate test-env

@@ -37,8 +37,8 @@ matrix:

         - source activate test-env

         - pip install mkdocs==1 mkdocs-material==3.0.3

         - conda install r-knitr r-devtools

-        - R -e 'remove.packages(c("curl","httr")); install.packages(c("curl", "httr")); Sys.setenv(CURL_CA_BUNDLE="/utils/microsoft-r-open-3.5.0/lib64/R/lib/microsoft-r-cacert.pem")'

-        - R -e 'install.packages("Rd2md")'

+        - R -e 'remove.packages(c("curl","httr")); install.packages(c("curl", "httr"), repos="http://cran.us.r-project.org"); Sys.setenv(CURL_CA_BUNDLE="/utils/microsoft-r-open-3.5.0/lib64/R/lib/microsoft-r-cacert.pem")'

+        - R -e 'install.packages("Rd2md", repos="http://cran.us.r-project.org")'

         - R -e 'source("https://bioconductor.org/biocLite.R"); biocLite("BiocInstaller"); library(devtools); install_github("compbiocore/qckitfastq",build_vignettes=FALSE)'

       before_script:

         - source activate test-env

@@ -1,27 +1,28 @@

 matrix:

   include: #allows to set up tests/deploys in different languages/environments.

     - stage: test # groups builds by type, add your tests here

-    # Run Travis CI for R using https://eddelbuettel.github.io/r-travis/

-      language: c

-      sudo: required

-      dist: trusty

+      language: r

+      r: bioc-release

+      os: linux

+      addons:

+        apt:

+          packages:

+            - g++-6

+          sources:

+            - ubuntu-toolchain-r-test

+      env:

+        - MATRIX_EVAL="CXX=g++-6 && CC=gcc-6"

       before_install:

-        - curl -OLs https://eddelbuettel.github.io/r-travis/run.sh && chmod 0755 run.sh

-        # optionally add our launchpad repo, but not needed here

-        # - sudo add-apt-repository -y ppa:edd/misc

-        - ./run.sh bootstrap

-      install:

-        - ./run.sh install_aptget r-cran-rmarkdown r-cran-knitr

-      script:

-        - ./run.sh run_tests

-      after_failure:

-        - ./run.sh dump_logs

-      #after_success:

-      #  - ./run.sh coverage   

-      notifications:

-        email:

-          on_success: change

-          on_failure: change

+        - eval "${MATRIX_EVAL}"

+        - bash configure.sh

+        - cat DESCRIPTION

+        - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-6 90

+        - gcc --version

+        - g++ --version

+      r_packages:

+        - covr

+      after_success:

+        - Rscript -e 'library(covr); codecov()'

     - stage: deploy # this block builds and deploys the docs, it's in Python.

       language: python

       install:

@@ -47,7 +47,7 @@ matrix:

         - mkdir docs/styles

         - mkdir docs/images

         - curl https://gist.githubusercontent.com/fernandogelin/08ecff3387dffc374c4abf06a577ab71/raw/083a383e51533feb20f3b03e6edcd9e86ddc59f9/dark_mode.css > docs/styles/dark_mode.css

-        - curl https://gist.githubusercontent.com/fernandogelin/b02ee98f2f35ce4263093f7a1c66582b/raw/8c8b8a03203f2dbc9040ea2970fc888f14e08cb6/cbc-logo.svg > docs/images/cbc-logo.svg

+        - curl https://gist.githubusercontent.com/fernandogelin/b02ee98f2f35ce4263093f7a1c66582b/raw/20ca5a37eb6defe00d35e50e7e00a784b64309f9/cbc-logo.svg > docs/images/cbc-logo.svg

         - mkdocs build --verbose --clean --strict

       deploy:

        provider: pages

@@ -46,8 +46,8 @@ matrix:

         - Rscript make.R

         - mkdir docs/styles

         - mkdir docs/images

-        - curl https://raw.githubusercontent.com/compbiocore/cbc-documentation-templates/master/docs/assets/styles/dark_mode.css > docs/styles/dark_mode.css

-        - curl https://raw.githubusercontent.com/compbiocore/cbc-documentation-templates/master/docs/assets/img/cbc-logo.svg > docs/images/cbc-logo.svg

+        - curl https://gist.githubusercontent.com/fernandogelin/08ecff3387dffc374c4abf06a577ab71/raw/083a383e51533feb20f3b03e6edcd9e86ddc59f9/dark_mode.css > docs/styles/dark_mode.css

+        - curl https://gist.githubusercontent.com/fernandogelin/b02ee98f2f35ce4263093f7a1c66582b/raw/8c8b8a03203f2dbc9040ea2970fc888f14e08cb6/cbc-logo.svg > docs/images/cbc-logo.svg

         - mkdocs build --verbose --clean --strict

       deploy:

        provider: pages

@@ -55,4 +55,4 @@ matrix:

        github_token: $GITHUB_PAT

        local_dir: site

        on:

-         branch: master

\ No newline at end of file

+         branch: master

@@ -36,8 +36,8 @@ matrix:

         - source activate test-env

         - pip install mkdocs==1 mkdocs-material==3.0.3

         - conda install r-knitr r-devtools

-        - R -e 'remove.packages(c("curl","httr")); install.packages(c("curl", "httr"), repos="http://cran.us.r-project.org"); Sys.setenv(CURL_CA_BUNDLE="/utils/microsoft-r-open-3.5.0/lib64/R/lib/microsoft-r-cacert.pem")'

-        - R -e 'install.packages("Rd2md", repos="http://cran.us.r-project.org")'

+        - R -e 'remove.packages(c("curl","httr")); install.packages(c("curl", "httr")); Sys.setenv(CURL_CA_BUNDLE="/utils/microsoft-r-open-3.5.0/lib64/R/lib/microsoft-r-cacert.pem")'

+        - R -e 'install.packages("Rd2md")'

         - R -e 'source("https://bioconductor.org/biocLite.R"); biocLite("BiocInstaller"); library(devtools); install_github("compbiocore/qckitfastq",build_vignettes=FALSE)'

       before_script:

         - source activate test-env

@@ -1,30 +1,58 @@

-# Run Travis CI for R using https://eddelbuettel.github.io/r-travis/

-

-language: c

-

-sudo: required

-

-dist: trusty

-

-before_install:

-  - curl -OLs https://eddelbuettel.github.io/r-travis/run.sh && chmod 0755 run.sh

-  # optionally add our launchpad repo, but not needed here

-  # - sudo add-apt-repository -y ppa:edd/misc

-  - ./run.sh bootstrap

-

-install:

-  - ./run.sh install_aptget r-cran-rmarkdown r-cran-knitr

-  

-script:

-  - ./run.sh run_tests

-

-after_failure:

-  - ./run.sh dump_logs

-

-#after_success:

-#  - ./run.sh coverage

-   

-notifications:

-  email:

-    on_success: change

-    on_failure: change

\ No newline at end of file

+matrix:

+  include: #allows to set up tests/deploys in different languages/environments.

+    - stage: test # groups builds by type, add your tests here

+    # Run Travis CI for R using https://eddelbuettel.github.io/r-travis/

+      language: c

+      sudo: required

+      dist: trusty

+      before_install:

+        - curl -OLs https://eddelbuettel.github.io/r-travis/run.sh && chmod 0755 run.sh

+        # optionally add our launchpad repo, but not needed here

+        # - sudo add-apt-repository -y ppa:edd/misc

+        - ./run.sh bootstrap

+      install:

+        - ./run.sh install_aptget r-cran-rmarkdown r-cran-knitr

+      script:

+        - ./run.sh run_tests

+      after_failure:

+        - ./run.sh dump_logs

+      #after_success:

+      #  - ./run.sh coverage   

+      notifications:

+        email:

+          on_success: change

+          on_failure: change

+    - stage: deploy # this block builds and deploys the docs, it's in Python.

+      language: python

+      install:

+        - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;

+        - bash miniconda.sh -b -p $HOME/miniconda

+        - export PATH="$HOME/miniconda/bin:$PATH"

+        - hash -r

+        - conda config --set always_yes yes --set changeps1 no

+        - conda update -q conda

+        - conda info -a

+        - conda create -q -n test-env python=$TRAVIS_PYTHON_VERSION

+        - source activate test-env

+        - pip install mkdocs==1 mkdocs-material==3.0.3

+        - conda install r-knitr r-devtools

+        - R -e 'remove.packages(c("curl","httr")); install.packages(c("curl", "httr"), repos="http://cran.us.r-project.org"); Sys.setenv(CURL_CA_BUNDLE="/utils/microsoft-r-open-3.5.0/lib64/R/lib/microsoft-r-cacert.pem")'

+        - R -e 'install.packages("Rd2md", repos="http://cran.us.r-project.org")'

+        - R -e 'source("https://bioconductor.org/biocLite.R"); biocLite("BiocInstaller"); library(devtools); install_github("compbiocore/qckitfastq",build_vignettes=FALSE)'

+      before_script:

+        - source activate test-env

+      script:

+        - mkdir docs

+        - Rscript make.R

+        - mkdir docs/styles

+        - mkdir docs/images

+        - curl https://raw.githubusercontent.com/compbiocore/cbc-documentation-templates/master/docs/assets/styles/dark_mode.css > docs/styles/dark_mode.css

+        - curl https://raw.githubusercontent.com/compbiocore/cbc-documentation-templates/master/docs/assets/img/cbc-logo.svg > docs/images/cbc-logo.svg

+        - mkdocs build --verbose --clean --strict

+      deploy:

+       provider: pages

+       skip_cleanup: true

+       github_token: $GITHUB_PAT

+       local_dir: site

+       on:

+         branch: master

\ No newline at end of file

@@ -12,8 +12,8 @@ before_install:

   # - sudo add-apt-repository -y ppa:edd/misc

   - ./run.sh bootstrap

-#install:

-#  - ./run.sh install_aptget 

+install:

+  - ./run.sh install_aptget r-cran-rmarkdown r-cran-knitr

 script:

   - ./run.sh run_tests

new file mode 100644

@@ -0,0 +1,30 @@

+# Run Travis CI for R using https://eddelbuettel.github.io/r-travis/

+

+language: c

+

+sudo: required

+

+dist: trusty

+

+before_install:

+  - curl -OLs https://eddelbuettel.github.io/r-travis/run.sh && chmod 0755 run.sh

+  # optionally add our launchpad repo, but not needed here

+  # - sudo add-apt-repository -y ppa:edd/misc

+  - ./run.sh bootstrap

+

+#install:

+#  - ./run.sh install_aptget 

+  

+script:

+  - ./run.sh run_tests

+

+after_failure:

+  - ./run.sh dump_logs

+

+#after_success:

+#  - ./run.sh coverage

+   

+notifications:

+  email:

+    on_success: change

+    on_failure: change

\ No newline at end of file