From e444b922695ef82a7b1cfcfebbd65f5aba91b4bc Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sat, 16 May 2020 18:06:26 +0200 Subject: [PATCH 01/12] this is not going to work --- .github/workflows/R_CMD_check.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/R_CMD_check.yml b/.github/workflows/R_CMD_check.yml index b0df295..85ca56d 100644 --- a/.github/workflows/R_CMD_check.yml +++ b/.github/workflows/R_CMD_check.yml @@ -67,6 +67,12 @@ jobs: remotes::install_cran("rcmdcheck") shell: Rscript {0} + - name: Build and install packages + run: | + R CMD build . --no-build-vignettes + Rscript -e "install.packages('*.tar.gz')" + rm *.tar.gz + - name: Check env: _R_CHECK_CRAN_INCOMING_REMOTE_: false From 641bb6b02961bda9ab640bf83e679726d7b249e5 Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sat, 16 May 2020 18:30:48 +0200 Subject: [PATCH 02/12] also this will not work... --- .github/workflows/R_CMD_check.yml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.github/workflows/R_CMD_check.yml b/.github/workflows/R_CMD_check.yml index 85ca56d..6bb92ed 100644 --- a/.github/workflows/R_CMD_check.yml +++ b/.github/workflows/R_CMD_check.yml @@ -3,7 +3,7 @@ on: branches: - master - development - - fix-master + - github-actions pull_request: branches: - master @@ -69,14 +69,12 @@ jobs: - name: Build and install packages run: | - R CMD build . --no-build-vignettes - Rscript -e "install.packages('*.tar.gz')" - rm *.tar.gz + Rscript -e "remotes::install_github('caravagn/mobster', ref=$(git rev-parse --short "$GITHUB_SHA"))" - name: Check env: _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check") + run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "errors", check_dir = "check") shell: Rscript {0} - name: Upload check results From bbbadffe7a07210ae9a0bf5ba06819642cad5996 Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sat, 16 May 2020 18:41:38 +0200 Subject: [PATCH 03/12] missing ' ' --- .github/workflows/R_CMD_check.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R_CMD_check.yml b/.github/workflows/R_CMD_check.yml index 6bb92ed..b5df909 100644 --- a/.github/workflows/R_CMD_check.yml +++ b/.github/workflows/R_CMD_check.yml @@ -69,7 +69,7 @@ jobs: - name: Build and install packages run: | - Rscript -e "remotes::install_github('caravagn/mobster', ref=$(git rev-parse --short "$GITHUB_SHA"))" + Rscript -e "remotes::install_github('caravagn/mobster', ref='$(git rev-parse --short "$GITHUB_SHA")')" - name: Check env: From c74b242f8e3545d5ba95c1c593ea5096b203d8c1 Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sat, 16 May 2020 18:51:18 +0200 Subject: [PATCH 04/12] let's try with the simple version... --- .github/workflows/R_CMD_check.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R_CMD_check.yml b/.github/workflows/R_CMD_check.yml index b5df909..b5eb4db 100644 --- a/.github/workflows/R_CMD_check.yml +++ b/.github/workflows/R_CMD_check.yml @@ -69,7 +69,7 @@ jobs: - name: Build and install packages run: | - Rscript -e "remotes::install_github('caravagn/mobster', ref='$(git rev-parse --short "$GITHUB_SHA")')" + Rscript -e "remotes::install_github('caravagn/mobster')" - name: Check env: From e26cda2cf6c150d69819234c140958faeb716d9a Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sat, 16 May 2020 19:00:46 +0200 Subject: [PATCH 05/12] maybe... --- .github/workflows/R_CMD_check.yml | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R_CMD_check.yml b/.github/workflows/R_CMD_check.yml index b5eb4db..4c24fb8 100644 --- a/.github/workflows/R_CMD_check.yml +++ b/.github/workflows/R_CMD_check.yml @@ -67,14 +67,19 @@ jobs: remotes::install_cran("rcmdcheck") shell: Rscript {0} + + - name: Build and install packages run: | - Rscript -e "remotes::install_github('caravagn/mobster')" + echo "GITHUB_SHA: ${GITHUB_SHA}" + echo "::set-output name=sha_short::$(git rev-parse --short HEAD)" + echo "Sha: ${{ steps.vars.outputs.sha_short }}" + Rscript -e "remotes::install_github('caravagn/mobster', ref='${{ steps.vars.outputs.sha_short }}')" - name: Check env: _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "errors", check_dir = "check") + run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "error", check_dir = "check") shell: Rscript {0} - name: Upload check results From 3a2ed4ec43e44e439b1b9021345da4e1c93fae3a Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sat, 16 May 2020 19:10:16 +0200 Subject: [PATCH 06/12] I should have read the doc first! --- .github/workflows/R_CMD_check.yml | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/.github/workflows/R_CMD_check.yml b/.github/workflows/R_CMD_check.yml index 4c24fb8..d068cad 100644 --- a/.github/workflows/R_CMD_check.yml +++ b/.github/workflows/R_CMD_check.yml @@ -67,13 +67,24 @@ jobs: remotes::install_cran("rcmdcheck") shell: Rscript {0} - - - - name: Build and install packages + - name: Shell GIT env + shell: bash + run: | + SHA=${{ github.event.pull_request.head.sha }} + echo "github.event.pull_request.head.sha = ${SHA}" + echo "GITHUB_SHA = ${GITHUB_SHA}" + echo "GITHUB_REF = ${GITHUB_REF}" + echo "BRANCH = ${GITHUB_REF#refs/heads/}" + - name: Declare some vars to use on other actions + id: vars + shell: bash run: | echo "GITHUB_SHA: ${GITHUB_SHA}" + echo "##[set-output name=branch;]$(echo ${GITHUB_REF#refs/heads/})" echo "::set-output name=sha_short::$(git rev-parse --short HEAD)" - echo "Sha: ${{ steps.vars.outputs.sha_short }}" + + - name: Build and install packages + run: | Rscript -e "remotes::install_github('caravagn/mobster', ref='${{ steps.vars.outputs.sha_short }}')" - name: Check From bcaf611a3ece23312a5bc7bcbe30f7cff0316ff3 Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sat, 16 May 2020 19:30:44 +0200 Subject: [PATCH 07/12] missing ref to gganimate this is just a gift for Giulio <3 --- vignettes/a7_Example_tumour_simulation.Rmd | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/vignettes/a7_Example_tumour_simulation.Rmd b/vignettes/a7_Example_tumour_simulation.Rmd index 482e127..88f0362 100644 --- a/vignettes/a7_Example_tumour_simulation.Rmd +++ b/vignettes/a7_Example_tumour_simulation.Rmd @@ -37,10 +37,11 @@ We have simulated a tumour with 2 clones. The tumours starts with the ancestral We load the simulation object [simulationdata.Rdata](./simulationdata.Rdata). ```{r, warning=FALSE, message=FALSE} -require(mobster) -require(dplyr) -require(tibble) -require(ggplot2) +library(mobster) +library(dplyr) +library(tibble) +library(ggplot2) +library(gganimate) # Load input data from Marc load('simulationdata.Rdata') From 76f76b43bf6e439c7280e5698b1638e440b27218 Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sat, 16 May 2020 19:50:31 +0200 Subject: [PATCH 08/12] wops, gganimate missing in DESCRIPTION --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 1644d08..459fd82 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -45,7 +45,8 @@ Suggests: knitr, CNAqc, ggmuller, png, - plotly + plotly, + gganimate Remotes: caravagn/easypar, caravagn/pio, From 32440ef04e19c60dee1c20f8696b4fd75ec334e7 Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sat, 16 May 2020 22:11:10 +0200 Subject: [PATCH 09/12] magick missing! --- DESCRIPTION | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 459fd82..28179c8 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -46,7 +46,8 @@ Suggests: knitr, ggmuller, png, plotly, - gganimate + gganimate, + magick Remotes: caravagn/easypar, caravagn/pio, From 45f5125091e9403e620003aea57eaf55a3a1ad17 Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sun, 17 May 2020 11:02:09 +0200 Subject: [PATCH 10/12] a different version of pandoc ti fight against: cannot popen '/usr/bin/which 'pandoc-citeproc' 2>/dev/null', probable reason 'Cannot allocate memory' --- .github/workflows/R_CMD_check.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R_CMD_check.yml b/.github/workflows/R_CMD_check.yml index d068cad..3db26dc 100644 --- a/.github/workflows/R_CMD_check.yml +++ b/.github/workflows/R_CMD_check.yml @@ -36,7 +36,9 @@ jobs: with: r-version: ${{ matrix.config.r }} - - uses: r-lib/actions/setup-pandoc@master + - uses: r-lib/actions/setup-pandoc@v1 + with: + pandoc-version: '2.9.2.1' # The pandoc version to download (if necessary) and use. - name: Query dependencies run: | From 4bdd101140b3e6b04d7b590bf75cfef7ccb431ae Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sun, 17 May 2020 13:28:50 +0200 Subject: [PATCH 11/12] maybe travis now will work? --- .travis.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/.travis.yml b/.travis.yml index 261365f..32dea5f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,6 +2,21 @@ language: R +addons: + apt: + update: true + packages: + - libmagick++-dev + - librsvg2-dev + - libwebp-dev + - libpoppler-cpp-dev + - libtesseract-dev + - libleptonica-dev + - tesseract-ocr-eng + - libfftw3-dev + - cargo + - gsfonts + cache: # Main R library packages: true From e85f009d62a99a6eadcc29e31eb5f37549534f06 Mon Sep 17 00:00:00 2001 From: Luca De Sano Date: Sun, 17 May 2020 13:39:57 +0200 Subject: [PATCH 12/12] warnings are good! --- .travis.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.travis.yml b/.travis.yml index 32dea5f..330e478 100644 --- a/.travis.yml +++ b/.travis.yml @@ -2,6 +2,8 @@ language: R +warnings_are_errors: false + addons: apt: update: true