From 872b6e322d6db78708880b18427fcd32504bef42 Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Wed, 4 Jul 2018 11:10:12 +0200 Subject: [PATCH 01/19] Switched to using conda plugin --- .buildkite/pipeline.yml | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index ffb3106..e410b86 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,11 +1,9 @@ steps: - - label: "Build Conda-environment" + - label: ":stopwatch: Running checks for Wilson" command: -# - "conda env create -f .buildkite/wilson-env.yml --force" - - ". /etc/profile.d/conda.sh" - - "conda activate wilson" -# - "Rscript -e 'install.packages(\"rje\")'" - "Rscript -e 'devtools::check()'" + plugins: + https://github.com/loosolab/conda-buildkite-plugin.git#master: # - wait From 82984fe069ee1a1ec8837b739ac677faf42189eb Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Wed, 4 Jul 2018 11:15:40 +0200 Subject: [PATCH 02/19] Renamed environment file --- .buildkite/{wilson-env.yml => environment.yml} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .buildkite/{wilson-env.yml => environment.yml} (100%) diff --git a/.buildkite/wilson-env.yml b/.buildkite/environment.yml similarity index 100% rename from .buildkite/wilson-env.yml rename to .buildkite/environment.yml From 09e3127986bddaefec8e2b2223279ec380fc3885 Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Thu, 5 Jul 2018 09:57:51 +0200 Subject: [PATCH 03/19] Added r-rje as dependency --- .buildkite/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/environment.yml b/.buildkite/environment.yml index 574754e..0207019 100644 --- a/.buildkite/environment.yml +++ b/.buildkite/environment.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 50f701e59be1b629f251d079cc2c0dc9acb47653 Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Fri, 6 Jul 2018 15:39:31 +0200 Subject: [PATCH 04/19] Cleaned pipeline step --- .buildkite/pipeline.yml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index e410b86..c1848dd 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,11 +1,7 @@ steps: - label: ":stopwatch: Running checks for Wilson" command: - - "Rscript -e 'devtools::check()'" + - Rscript -e \'devtools::check()\' plugins: https://github.com/loosolab/conda-buildkite-plugin.git#master: -# - wait - -# - label: "Package check" -# command: From ea994fc8ae9cd337f9c8376cee584ef976d5d9c4 Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Fri, 6 Jul 2018 15:46:06 +0200 Subject: [PATCH 05/19] Temporarily escaped ticks --- .buildkite/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index c1848dd..1eb5444 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,7 +1,7 @@ steps: - label: ":stopwatch: Running checks for Wilson" command: - - Rscript -e \'devtools::check()\' + - "Rscript -e \'devtools::check()\'" plugins: https://github.com/loosolab/conda-buildkite-plugin.git#master: From b5e1e5105c03b38823ef00f52644e100d87686db Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Fri, 6 Jul 2018 15:57:07 +0200 Subject: [PATCH 06/19] Removed escaped ticks --- .buildkite/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 1eb5444..f0d58c0 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,7 +1,7 @@ steps: - label: ":stopwatch: Running checks for Wilson" command: - - "Rscript -e \'devtools::check()\'" + - "Rscript -e 'devtools::check()'" plugins: https://github.com/loosolab/conda-buildkite-plugin.git#master: From c482d8f8713f22789f3cbd1c685cb67fafd7e505 Mon Sep 17 00:00:00 2001 From: HendrikSchultheis Date: Mon, 16 Jul 2018 09:26:05 +0200 Subject: [PATCH 07/19] Update environment.yml dependencies rmarkdown, testthat and vdiffr added --- .buildkite/environment.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.buildkite/environment.yml b/.buildkite/environment.yml index 0207019..edf27f7 100644 --- a/.buildkite/environment.yml +++ b/.buildkite/environment.yml @@ -43,3 +43,6 @@ dependencies: - r-devtools - "readline==6.3" - r-roxygen2 + - r-rmarkdown + - r-testthat +# - r-vdiffr # not yet in conda-forge From 42e5bc6657fc98411770eeeef6cc7ab46176b204 Mon Sep 17 00:00:00 2001 From: HendrikSchultheis Date: Mon, 16 Jul 2018 11:25:48 +0200 Subject: [PATCH 08/19] Update pipeline.yml upload check log as artifact --- .buildkite/pipeline.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index f0d58c0..45dc7b2 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -4,4 +4,5 @@ steps: - "Rscript -e 'devtools::check()'" plugins: https://github.com/loosolab/conda-buildkite-plugin.git#master: - + artifact_paths: + - "wilson.Rcheck/00check.log" From e53371838abf796633ce779d9aa7b25e959a8bba Mon Sep 17 00:00:00 2001 From: HendrikSchultheis Date: Mon, 16 Jul 2018 11:30:49 +0200 Subject: [PATCH 09/19] Update pipeline.yml --- .buildkite/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 45dc7b2..aa36a9d 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -5,4 +5,4 @@ steps: plugins: https://github.com/loosolab/conda-buildkite-plugin.git#master: artifact_paths: - - "wilson.Rcheck/00check.log" + - "wilson.Rcheck/*" From 2f61038d68cd9b633d634cee188c1f5502c2bb7e Mon Sep 17 00:00:00 2001 From: HendrikSchultheis Date: Mon, 16 Jul 2018 11:42:37 +0200 Subject: [PATCH 10/19] Update pipeline.yml --- .buildkite/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index aa36a9d..46feab6 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -5,4 +5,4 @@ steps: plugins: https://github.com/loosolab/conda-buildkite-plugin.git#master: artifact_paths: - - "wilson.Rcheck/*" + - "/tmp/**/wilson.Rcheck/*" From dc48218a03c3c14cf993b0db50d0a58e7ff4588d Mon Sep 17 00:00:00 2001 From: HendrikSchultheis Date: Mon, 16 Jul 2018 12:28:00 +0200 Subject: [PATCH 11/19] Update pipeline.yml replace devtools::check with R CMD build & check --- .buildkite/pipeline.yml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 46feab6..bf7beff 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -1,8 +1,9 @@ steps: - label: ":stopwatch: Running checks for Wilson" command: - - "Rscript -e 'devtools::check()'" + - "R CMD build ." + - "R CMD check *tar.gz --as-cran" plugins: https://github.com/loosolab/conda-buildkite-plugin.git#master: artifact_paths: - - "/tmp/**/wilson.Rcheck/*" + - "wilson.Rcheck/*" From f8a92c4fe26609e770e90a0b8ef11e46c2d8ca29 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jens=20Preu=C3=9Fner?= Date: Tue, 17 Jul 2018 08:25:26 +0200 Subject: [PATCH 12/19] Update environment.yml --- .buildkite/environment.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.buildkite/environment.yml b/.buildkite/environment.yml index edf27f7..ff19792 100644 --- a/.buildkite/environment.yml +++ b/.buildkite/environment.yml @@ -1,8 +1,8 @@ name: wilson channels: - - defaults - - conda-forge - bioconda + - conda-forge + - defaults dependencies: - r-base - r-shiny From 7eaa529fafddaed7fcdaf8a851d5bc53f3262ae0 Mon Sep 17 00:00:00 2001 From: bioi Date: Tue, 17 Jul 2018 15:47:00 +0200 Subject: [PATCH 13/19] Pinned stringi dependecy --- .buildkite/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/environment.yml b/.buildkite/environment.yml index ff19792..4365dad 100644 --- a/.buildkite/environment.yml +++ b/.buildkite/environment.yml @@ -40,8 +40,8 @@ dependencies: - r-openssl # - r-methods # base package - r-r6 + - r-stringi >=1.2.3 - r-devtools - - "readline==6.3" - r-roxygen2 - r-rmarkdown - r-testthat From 307efcd7fb4a9a5cc4b2ce6f7f8f1686efa32387 Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Thu, 19 Jul 2018 13:30:55 +0200 Subject: [PATCH 14/19] Reflected upstream changes --- .buildkite/pipeline.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index bf7beff..79d89b6 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -5,5 +5,7 @@ steps: - "R CMD check *tar.gz --as-cran" plugins: https://github.com/loosolab/conda-buildkite-plugin.git#master: + environment: .buildkite/environment.yml + update: true artifact_paths: - "wilson.Rcheck/*" From 294cb5155a83a07634f3be91d6c2b0e938c9fdc6 Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Thu, 19 Jul 2018 14:38:35 +0200 Subject: [PATCH 15/19] Pinned plugin to initial tag --- .buildkite/pipeline.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.buildkite/pipeline.yml b/.buildkite/pipeline.yml index 79d89b6..2032985 100644 --- a/.buildkite/pipeline.yml +++ b/.buildkite/pipeline.yml @@ -4,7 +4,7 @@ steps: - "R CMD build ." - "R CMD check *tar.gz --as-cran" plugins: - https://github.com/loosolab/conda-buildkite-plugin.git#master: + https://github.com/loosolab/conda-buildkite-plugin.git#v0.1.0: environment: .buildkite/environment.yml update: true artifact_paths: From d887f039e35b0494e8c68323cf2371f47d86d1cf Mon Sep 17 00:00:00 2001 From: Jens Preussner Date: Fri, 20 Jul 2018 11:43:42 +0200 Subject: [PATCH 16/19] Cleaned testing environment --- .buildkite/environment.yml | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/.buildkite/environment.yml b/.buildkite/environment.yml index 4365dad..84ff75b 100644 --- a/.buildkite/environment.yml +++ b/.buildkite/environment.yml @@ -1,4 +1,3 @@ -name: wilson channels: - bioconda - conda-forge @@ -17,12 +16,9 @@ dependencies: - 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 @@ -38,11 +34,11 @@ dependencies: - r-shinycssloaders - r-log4r - r-openssl -# - r-methods # base package - r-r6 - r-stringi >=1.2.3 - r-devtools - r-roxygen2 - r-rmarkdown - r-testthat -# - r-vdiffr # not yet in conda-forge + - r-vdiffr + - qpdf From f51c5d8ff989c5f9bcb634d6c8fae7cd71bb3737 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Fri, 3 Aug 2018 11:07:11 +0200 Subject: [PATCH 17/19] message tempfile --- tests/testthat/test-download.R | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/testthat/test-download.R b/tests/testthat/test-download.R index f5f7dd4..34587b5 100644 --- a/tests/testthat/test-download.R +++ b/tests/testthat/test-download.R @@ -6,6 +6,7 @@ test_that("ggplot is downloadable", { height <- 20 file <- tempfile(fileext = ".zip") filename <- "plot" + message(file) expect_false(file.exists(file)) expect_silent(download(file = file, filename = filename, plot = plot, width = width, height = height)) From deaddc55aaa0c5e683d5ae8753da7cb262bf39a1 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Fri, 3 Aug 2018 11:21:10 +0200 Subject: [PATCH 18/19] print instead of message --- tests/testthat/test-download.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-download.R b/tests/testthat/test-download.R index 34587b5..8810ed1 100644 --- a/tests/testthat/test-download.R +++ b/tests/testthat/test-download.R @@ -6,7 +6,7 @@ test_that("ggplot is downloadable", { height <- 20 file <- tempfile(fileext = ".zip") filename <- "plot" - message(file) + print(file) expect_false(file.exists(file)) expect_silent(download(file = file, filename = filename, plot = plot, width = width, height = height)) From 661ce56fca8286bab1cd0cc3e2ba854f316d43d0 Mon Sep 17 00:00:00 2001 From: Schultheis Date: Fri, 3 Aug 2018 13:07:05 +0200 Subject: [PATCH 19/19] removed print --- tests/testthat/test-download.R | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/testthat/test-download.R b/tests/testthat/test-download.R index 8810ed1..f5f7dd4 100644 --- a/tests/testthat/test-download.R +++ b/tests/testthat/test-download.R @@ -6,7 +6,6 @@ test_that("ggplot is downloadable", { height <- 20 file <- tempfile(fileext = ".zip") filename <- "plot" - print(file) expect_false(file.exists(file)) expect_silent(download(file = file, filename = filename, plot = plot, width = width, height = height))