From a8b9b9fdb5bacded771f9974b32220afc43de214 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Fri, 22 Jun 2018 10:13:56 +0200 Subject: [PATCH 01/10] buildkite pipeline added --- .Rbuildignore | 3 +++ .buildkite/check.R | 2 ++ .buildkite/pipeline.yml | 3 +++ 3 files changed, 8 insertions(+) create mode 100644 .Rbuildignore create mode 100644 .buildkite/check.R create mode 100644 .buildkite/pipeline.yml diff --git a/.Rbuildignore b/.Rbuildignore new file mode 100644 index 0000000..4d88d31 --- /dev/null +++ b/.Rbuildignore @@ -0,0 +1,3 @@ +^.*\.Rproj$ +^\.Rproj\.user$ +^\.buildkite.* diff --git a/.buildkite/check.R b/.buildkite/check.R new file mode 100644 index 0000000..f5c0fd5 --- /dev/null +++ b/.buildkite/check.R @@ -0,0 +1,2 @@ +if (!require(devtools)) install.packages("devtools") +devtools::check() diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml new file mode 100644 index 0000000..c0b4fb4 --- /dev/null +++ b/.buildkite/pipeline.yml @@ -0,0 +1,3 @@ +steps: + - label: Package check + command: Rscript /.buildkite/check.R From 9d9b95b4147e96b6e0bddf0be4cc463c0cb4c544 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Fri, 22 Jun 2018 13:53:06 +0200 Subject: [PATCH 02/10] install dependencies prior to check --- .buildkite/check.R | 1 + 1 file changed, 1 insertion(+) diff --git a/.buildkite/check.R b/.buildkite/check.R index f5c0fd5..2bee08e 100644 --- a/.buildkite/check.R +++ b/.buildkite/check.R @@ -1,2 +1,3 @@ if (!require(devtools)) install.packages("devtools") +devtools::install_deps() devtools::check() From 82c410f11c2d5e1e9dbd727ac8a61985aa249a69 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Tue, 26 Jun 2018 14:01:44 +0200 Subject: [PATCH 03/10] conde environment added --- .buildkite/check.R | 2 +- .buildkite/pipeline.yml | 11 ++++++++-- .buildkite/wilson-env.yml | 43 +++++++++++++++++++++++++++++++++++++++ 3 files changed, 53 insertions(+), 3 deletions(-) create mode 100644 .buildkite/wilson-env.yml diff --git a/.buildkite/check.R b/.buildkite/check.R index 2bee08e..d90a566 100644 --- a/.buildkite/check.R +++ b/.buildkite/check.R @@ -1,3 +1,3 @@ if (!require(devtools)) install.packages("devtools") -devtools::install_deps() +# devtools::install_deps() devtools::check() diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index c0b4fb4..01c4aa1 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,3 +1,10 @@ steps: - - label: Package check - command: Rscript /.buildkite/check.R + - label: "Build Conda-environment" + command: + - "conda env create -f .buildkite/wilson-env.yml" + - "source activate wilson" + + - wait + + - label: "Package check" + command: "Rscript .buildkite/check.R" diff --git a/.buildkite/wilson-env.yml b/.buildkite/wilson-env.yml new file mode 100644 index 0000000..965b589 --- /dev/null +++ b/.buildkite/wilson-env.yml @@ -0,0 +1,43 @@ +name: wilson +channels: + - defaults + - conda-forge + - bioconda +dependencies: + - r-base + - r-shiny + - r-data.table + - r-ggplot2 + - r-plotly + - r-scales + - r-shinydashboard + - "r-dt>=0.3" + - r-colourpicker + - r-RColorBrewer + - r-shinyjs + - r-viridis + - r-rje +# - r-grdevices # base package +# - r-grid # base package + - r-plyr + - r-circlize + - bioconductor-complexheatmap +# - r-stats # base package + - r-gplots + - r-reshape + - r-rintrojs + - r-webshot + - r-rjsonio + - "r-ggrepel>=0.6.12" + - bioconductor-deseq2 + - r-rjson + - r-factominer + - r-factoextra + - "r-heatmaply>=0.14.1" + - r-shinythemes + - r-shinycssloaders + - r-log4r + - r-openssl +# - r-methods # base package + - r-r6 + - r-devtools \ No newline at end of file From 6e1d670a9f17fa784256e134ceea3a00be565308 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Tue, 26 Jun 2018 14:12:40 +0200 Subject: [PATCH 04/10] install rje package with Rscript --- .buildkite/pipeline.yml | 3 ++- .buildkite/wilson-env.yml | 2 +- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 01c4aa1..cf09672 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -3,8 +3,9 @@ steps: command: - "conda env create -f .buildkite/wilson-env.yml" - "source activate wilson" + - "Rscript -e 'install.packages(\"rje\")'" - wait - label: "Package check" - command: "Rscript .buildkite/check.R" + command: "Rscript -e 'devtools::check()'" diff --git a/.buildkite/wilson-env.yml b/.buildkite/wilson-env.yml index 965b589..f00a25d 100644 --- a/.buildkite/wilson-env.yml +++ b/.buildkite/wilson-env.yml @@ -16,7 +16,7 @@ dependencies: - r-RColorBrewer - r-shinyjs - r-viridis - - r-rje +# - r-rje # - r-grdevices # base package # - r-grid # base package - r-plyr From 1b6ffe9b38e1ed2c2487b8884565075a0f1bb3de Mon Sep 17 00:00:00 2001 From: Schultheis Date: Tue, 26 Jun 2018 15:00:19 +0200 Subject: [PATCH 05/10] removed check.R, install readline 6.3 in wilson-env --- .buildkite/check.R | 3 --- .buildkite/wilson-env.yml | 3 ++- 2 files changed, 2 insertions(+), 4 deletions(-) delete mode 100644 .buildkite/check.R diff --git a/.buildkite/check.R b/.buildkite/check.R deleted file mode 100644 index d90a566..0000000 --- a/.buildkite/check.R +++ /dev/null @@ -1,3 +0,0 @@ -if (!require(devtools)) install.packages("devtools") -# devtools::install_deps() -devtools::check() diff --git a/.buildkite/wilson-env.yml b/.buildkite/wilson-env.yml index f00a25d..5db785a 100644 --- a/.buildkite/wilson-env.yml +++ b/.buildkite/wilson-env.yml @@ -40,4 +40,5 @@ dependencies: - r-openssl # - r-methods # base package - r-r6 - - r-devtools \ No newline at end of file + - r-devtools + - "readline==6.3" From d194f7df0531c3974a5b5ee23c83ff0829620f4f Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 27 Jun 2018 08:21:44 +0200 Subject: [PATCH 06/10] force creation of new environment --- .buildkite/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index cf09672..c4d1b90 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,7 +1,7 @@ steps: - label: "Build Conda-environment" command: - - "conda env create -f .buildkite/wilson-env.yml" + - "conda env create -f .buildkite/wilson-env.yml --force" - "source activate wilson" - "Rscript -e 'install.packages(\"rje\")'" From 138d1cf205b20901867dbd26cf50fa9412a3ab4f Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 27 Jun 2018 08:58:47 +0200 Subject: [PATCH 07/10] static wilson solution --- .buildkite/pipeline.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index c4d1b90..2f696d5 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,9 +1,10 @@ steps: - label: "Build Conda-environment" command: - - "conda env create -f .buildkite/wilson-env.yml --force" +# - "conda env create -f .buildkite/wilson-env.yml --force" + - ". /etc/profile.d/conda.sh" - "source activate wilson" - - "Rscript -e 'install.packages(\"rje\")'" +# - "Rscript -e 'install.packages(\"rje\")'" - wait From 55964a878114e25b81fd786bc3f338a23acff5fe Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 27 Jun 2018 09:03:16 +0200 Subject: [PATCH 08/10] source -> conda --- .buildkite/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 2f696d5..adc9024 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -3,7 +3,7 @@ steps: command: # - "conda env create -f .buildkite/wilson-env.yml --force" - ". /etc/profile.d/conda.sh" - - "source activate wilson" + - "conda activate wilson" # - "Rscript -e 'install.packages(\"rje\")'" - wait From e5c78f005cd056edda7ec387c25eedc2da882176 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Wed, 27 Jun 2018 09:05:34 +0200 Subject: [PATCH 09/10] moved 'check' command --- .buildkite/pipeline.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index adc9024..ffb3106 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -5,8 +5,9 @@ steps: - ". /etc/profile.d/conda.sh" - "conda activate wilson" # - "Rscript -e 'install.packages(\"rje\")'" + - "Rscript -e 'devtools::check()'" - - wait +# - wait - - label: "Package check" - command: "Rscript -e 'devtools::check()'" +# - label: "Package check" +# command: From 96d58685d78d1989c27d288c2faf50022cce9b27 Mon Sep 17 00:00:00 2001 From: bioi Date: Wed, 27 Jun 2018 09:55:02 +0200 Subject: [PATCH 10/10] [ci skip] Updated environment --- .buildkite/wilson-env.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.buildkite/wilson-env.yml b/.buildkite/wilson-env.yml index 5db785a..32b23f0 100644 --- a/.buildkite/wilson-env.yml +++ b/.buildkite/wilson-env.yml @@ -42,3 +42,5 @@ dependencies: - r-r6 - r-devtools - "readline==6.3" + - r-roxygen2 + - r-shinybs