diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml deleted file mode 100644 index e40db5b..0000000 --- a/.github/workflows/main.yml +++ /dev/null @@ -1,83 +0,0 @@ -on: - push: - branches: - - master - - devel - pull_request: - branches: - - master - - devel - -name: R-CMD-check - -jobs: - R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - { os: windows-latest, r: '3.6', args: '--no-manual'} - - { os: macOS-latest, r: '3.6'} - - { os: macOS-latest, r: 'devel'} - - { os: ubuntu-16.04, r: '3.4', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} - - { os: ubuntu-16.04, r: '3.5', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} - - { os: ubuntu-16.04, r: '3.6', cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"} - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - CRAN: ${{ matrix.config.cran }} - - steps: - - uses: actions/checkout@v1 - - - uses: r-lib/actions/setup-r@master - with: - r-version: ${{ matrix.config.r }} - - - uses: r-lib/actions/setup-pandoc@master - - - uses: r-lib/actions/setup-tinytex@master - if: contains(matrix.config.args, 'no-manual') == false - - - name: Query dependencies - run: > - Rscript -e "install.packages(c('remotes', 'roxygen2'))" -e "saveRDS(remotes::dev_package_deps(dependencies = TRUE), 'depends.Rds', version = 2)" - - - name: Cache R packages - uses: actions/cache@v1 - if: runner.os != 'Windows' - with: - path: ${{ env.R_LIBS_USER }} - key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('**/DESCRIPTION') }} - restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}- - - - name: Install system dependencies - if: runner.os == 'Linux' - env: - RHUB_PLATFORM: linux-x86_64-ubuntu-gcc - run: | - Rscript -e "remotes::install_github('r-hub/sysreqs')" - sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))") - sudo -s eval "$sysreqs" - - - name: Install dependencies - run: > - Rscript -e "library('remotes')" -e "update(readRDS('depends.Rds'))" -e "remotes::install_cran('rcmdcheck')" - - - name: Document - run: Rscript -e 'roxygen2::roxygenise()' - - - name: Check - run: > - Rscript -e "rcmdcheck::rcmdcheck(args = '--no-manual', error_on = 'note', check_dir = 'check')" - - - name: Upload check results - if: failure() - uses: actions/upload-artifact@master - with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check diff --git a/DESCRIPTION b/DESCRIPTION index 2cbb01d..7360a23 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -27,4 +27,3 @@ URL: https://github.com/bedapub/ribiosGraph BugReports: https://github.com/bedapub/ribiosGraph/issues Encoding: UTF-8 RoxygenNote: 7.3.3 -Remotes: github::bedapub/ribiosUtils diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..efc1b98 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,56 @@ +# ribiosGraph 1.1.0 + +* Initial CRAN submission +* Package prepared for CRAN submission with comprehensive documentation +* Depends on ribiosUtils (on CRAN) and igraph + +# ribiosGraph 1.0.11 (2013-06-05) + +* Add TextMining_I2E and manual as supported databases + +# ribiosGraph 1.0.10 (2013-03-27) + +* Add aux function `fixNodeLabel` to fix dash-only gene labels + +# ribiosGraph 1.0.9 (2013-03-22) + +* Add ronet-evaluation.Rscript for internal evaluation +* Bit-flags can specify which databases to use + +# ribiosGraph 1.0.8 (2012-12-04) + +* ronet.Rscript: bug fix for input GeneID/GeneSymbols trimming + +# ribiosGraph 1.0.7 (2012-12-03) + +* ronet.Rscript: add "-genesymbol" option +* Output graph converts GeneIDs to GeneSymbols + +# ribiosGraph 1.0.6 (2012-11-30) + +* `exportGML`: fixed node indices starting from 0 instead of 1 + +# ribiosGraph 1.0.5 (2012-07-30) + +* ronet.Rscript: package namespace "graph" appended before edges function + +# ribiosGraph 1.0.4 (2012-07-11) + +* Add pathSigTree.Rscript for pathway signature tree visualization + +# ribiosGraph 1.0.3 (2012-04-12) + +* `exportGML` refactored into ribiosNetwork package + +# ribiosGraph 1.0.2 (2012-04-11) + +* ronet.Rscript: output isInput attribute of nodes + +# ribiosGraph 1.0.1 (2012-03-27) + +* ronet.Rscript: support edge type and automatic output format recognition + +# ribiosGraph 1.0.0 (2012-03-26) + +* Initial release of ribiosGraph (originally ribiosNetwork) +* Add ronet.Rscript and testing files