-
Notifications
You must be signed in to change notification settings - Fork 7
306 lines (266 loc) · 11.8 KB
/
build.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
## Acronyms:
## * GHA: GitHub Action
## * OS: operating system
on:
push:
pull_request:
# Define the GitHub Actions workflow for R CMD check of the MetFamily package
name: R-CMD-check-MetFamily
# Define environment variables for the workflow
env:
has_testthat: 'true'
# run_covr: 'true' # Disabled until later
run_covr: 'false'
# run_pkgdown: 'true' # Disabled until later
run_pkgdown: 'false'
has_RUnit: 'false'
has_BiocCheck: 'false'
cache-version: 'cache-v1'
# Define the jobs for different operating systems
jobs:
build-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
container: ${{ matrix.config.cont }}
# Define the matrix for different configurations
strategy:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
# - { os: ubuntu-latest, r: 'devel', bioc: 'devel', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
# Disabling additional architectures until later
# - { os: macOS-latest, r: 'next', bioc: '3.18'}
# - { os: windows-latest, r: 'next', bioc: '3.18'}
# Define environment variables for the job
env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}
NOT_CRAN: true
TZ: UTC
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
# Define the steps to be executed
steps:
# Step 1: Set R Library home on Linux
- name: Set R Library home on Linux
if: runner.os == 'Linux'
run: |
mkdir /__w/_temp/Library
echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
# Step 2: Checkout the repository
- name: Checkout Repository
uses: actions/checkout@v2
# Step 3: Setup R from r-lib
- name: Setup R from r-lib
if: runner.os != 'Linux'
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
extra-repositories: https://janmarvin.r-universe.dev
# Step 4: Setup pandoc from r-lib
- name: Setup pandoc from r-lib
if: runner.os != 'Linux'
uses: r-lib/actions/setup-pandoc@v2
# Step 5: Query dependencies and save RDS file
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
shell: Rscript {0}
# Step 6: Cache R packages based on configuration
- name: Cache R packages
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'"
uses: actions/cache@v2
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
# Step 7: Cache R packages on Linux
- name: Cache R packages on Linux
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
uses: actions/cache@v2
with:
path: /home/runner/work/_temp/Library
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-devel-
# Step 8: Install Linux system dependencies
- name: Install Linux system dependencies
if: runner.os == 'Linux'
run: |
sysreqs=$(Rscript -e 'cat("apt-get update -y && ", paste(remotes::system_requirements("ubuntu", "20.04"), collapse = " && "))')
echo $sysreqs
sudo -s eval "$sysreqs"
# Step 9: Install macOS system dependencies
- name: Install macOS system dependencies
if: matrix.config.os == 'macOS-latest'
run: |
## Enable installing XML from source if needed
brew install libxml2
echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV
## Required to install magick as noted at
## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
brew install imagemagick@6
## For textshaping, required by ragg, and required by pkgdown
brew install harfbuzz fribidi
## For installing usethis's dependency gert
brew install libgit2
## required for ncdf4
## brew install netcdf ## Does not work as it is compiled with gcc
## Use pre-compiled libraries from https://mac.r-project.org/libs-4/
curl -O https://mac.r-project.org/libs-4/netcdf-4.7.4-darwin.17-x86_64.tar.gz
tar fvxzm netcdf-4.7.4-darwin.17-x86_64.tar.gz -C /
rm netcdf-4.7.4-darwin.17-x86_64.tar.gz
curl -O https://mac.r-project.org/libs-4/hdf5-1.12.0-darwin.17-x86_64.tar.gz
tar fvxzm hdf5-1.12.0-darwin.17-x86_64.tar.gz -C /
rm hdf5-1.12.0-darwin.17-x86_64.tar.gz
curl -O https://mac.r-project.org/libs-4/szip-2.1.1-darwin.17-x86_64.tar.gz
tar fvxzm szip-2.1.1-darwin.17-x86_64.tar.gz -C /
rm szip-2.1.1-darwin.17-x86_64.tar.gz
# Step 10: Install Windows system dependencies
- name: Install Windows system dependencies
if: runner.os == 'Windows'
run: |
## Edit below if you have any Windows system dependencies
shell: Rscript {0}
# Step 11: Install BiocManager
- name: Install BiocManager
run: |
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_cran("BiocManager")
shell: Rscript {0}
# Step 12: Set BiocVersion
- name: Set BiocVersion
run: |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
shell: Rscript {0}
# Step 13: Install dependencies pass 1
- name: Install dependencies pass 1
run: |
## Try installing the package dependencies in steps. First the local
## dependencies, then any remaining dependencies to avoid the
## issues described at
## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## Pass #1 at installing dependencies
BiocManager::install(c(
"mzR", "htmltools", "shiny", "shinyBS", "shinyjs", "shinybusy",
"DT", "colourpicker", "Matrix", "squash", "FactoMineR", "mixOmics",
"pcaMethods", "cba", "tools", "stringr", "xcms", "matrixStats",
"plotrix"
))
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
BiocManager::install(c("rmarkdown", "BiocStyle"))
continue-on-error: true
shell: Rscript {0}
# Step 14: Install dependencies pass 2
- name: Install dependencies pass 2
run: |
## Pass #2 at installing dependencies
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
## Manually install packages that seem to be skipped.
message(paste('****', Sys.time(), 'force installation of selected packages ****'))
BiocManager::install("mzR", type = "source", force = TRUE)
BiocManager::install("Spectra")
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
remotes::install_cran("rcmdcheck")
BiocManager::install(c("BiocCheck", "DBI"))
shell: Rscript {0}
# Step 15: Install BiocGenerics
- name: Install BiocGenerics
if: env.has_RUnit == 'true'
run: |
## Install BiocGenerics
BiocManager::install("BiocGenerics")
shell: Rscript {0}
# Step 16: Install covr
- name: Install covr
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("covr")
shell: Rscript {0}
# Step 17: Install pkgdown
- name: Install pkgdown
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
remotes::install_github("r-lib/pkgdown")
shell: Rscript {0}
# Step 18: Session info
- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
# Step 19: Run CMD check
- name: Run CMD check
env:
_R_CHECK_CRAN_INCOMING_: false
run: |
rcmdcheck::rcmdcheck(
args = c("--no-build-vignettes", "--no-manual", "--timings"),
build_args = c("--no-manual", "--no-resave-data"),
error_on = "error",
check_dir = "check"
)
shell: Rscript {0}
# Step 20: Reveal testthat details
- name: Reveal testthat details
if: env.has_testthat == 'true' && runner.os == 'Linux'
run: find . -name testthat.Rout -exec cat '{}' ';'
# Step 21: Run RUnit tests
- name: Run RUnit tests
if: env.has_RUnit == 'true' && runner.os == 'Linux'
run: |
BiocGenerics:::testPackage()
shell: Rscript {0}
# Step 22: Run BiocCheck
- name: Run BiocCheck
if: env.has_BiocCheck == 'true' && runner.os == 'Linux'
run: |
BiocCheck::BiocCheck(
dir('check', 'tar.gz$', full.names = TRUE),
`quit-with-status` = TRUE,
`no-check-R-ver` = TRUE,
`no-check-bioc-help` = TRUE
)
shell: Rscript {0}
# Step 23: Test coverage
- name: Test coverage
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
covr::codecov()
shell: Rscript {0}
# Step 24: Install package
- name: Install package
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: R CMD INSTALL .
# Step 25: Test Shiny App in package
- name: Test Shiny App
uses: rstudio/shinytest2/actions/test-app@actions/v1
with:
app-dir: "inst/MetFamily"
# Step 26: Deploy package
- name: Deploy package
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
git config --global user.email "[email protected]"
git config --global user.name "GitHub Actions"
git config --global --add safe.directory /__w/your-package-name
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)"
shell: bash {0}
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
## at least one locally before this will work. This creates the gh-pages
## branch (erasing anything you haven't version controlled!) and
## makes the git history recognizable by pkgdown.
# Step 27: Upload check results
- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-devel-r-devel-results
path: check