-
Notifications
You must be signed in to change notification settings - Fork 88
222 lines (189 loc) · 8.38 KB
/
cmd-check.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
## Read more about GitHub actions the features of this GitHub Actions workflow
## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action
##
## For more details, check the biocthis developer notes vignette at
## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html
##
## You can add this workflow to other packages using:
## > biocthis::use_bioc_github_action()
##
## Using GitHub Actions exposes you to many details about how R packages are
## compiled and installed in several operating system.s
### If you need help, please follow the steps listed at
## https://github.com/r-lib/actions#where-to-find-help
##
## If you found an issue specific to biocthis's GHA workflow, please report it
## with the information that will make it easier for others to help you.
## Thank you!
## Acronyms:
## * GHA: GitHub Action
## * OS: operating system
on:
push:
pull_request:
name: R-CMD-check
## These environment variables control whether to run GHA code later on that is
## specific to testthat, covr, and pkgdown.
##
## If you need to clear the cache of packages, update the number inside
## cache-version as discussed at https://github.com/r-lib/actions/issues/86.
## Note that you can always run a GHA test without the cache by using the word
## "/nocache" in the commit message.
env:
has_testthat: 'false'
run_covr: 'false'
run_pkgdown: 'false'
has_RUnit: 'false'
cache-version: 'cache-v3'
run_docker: 'false'
jobs:
build-check:
if: "!contains(github.event.head_commit.message, 'ci-skip')"
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
container: ${{ matrix.config.cont }}
## Environment variables unique to this job.
strategy:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: '4.4', bioc: '3.19', cont: "bioconductor/bioconductor_docker:RELEASE_3_19", rspm: "https://packagemanager.posit.co/cran/__linux__/focal/latest" }
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 }}
steps:
## Set the R library to the directory matching the
## R packages cache step further below when running on Docker (Linux).
- name: Set R Library home on Linux
if: runner.os == 'Linux'
run: |
mkdir /__w/_temp/Library
echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile
## Most of these steps are the same as the ones in
## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml
## If they update their steps, we will also need to update ours.
- name: Checkout Repository
uses: actions/checkout@v2
## R is already included in the Bioconductor docker images
- name: Setup R from r-lib
if: runner.os != 'Linux'
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
- name: Query dependencies
run: |
install.packages('remotes')
saveRDS(remotes::dev_package_deps(), ".github/depends.Rds", version = 2)
shell: Rscript {0}
- 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-RELEASE_3_12-r-4.0-2${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-2
- 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-RELEASE_3_12-r-4.0-2${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-2
- name: Install Linux system dependencies
if: runner.os == 'Linux'
run: |
sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
echo $sysreqs
sudo -s eval "$sysreqs"
- 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" >> $GITHUB_ENV
## Required to install magick as noted at
## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2
brew install imagemagick@6
## For textshaping, required by ragg, and required by pkgdown
brew install harfbuzz fribidi
## For installing usethis's dependency gert
brew install libgit2
- name: Install Windows system dependencies
if: runner.os == 'Windows'
run: |
## Edit below if you have any Windows system dependencies
shell: Rscript {0}
- name: Install BiocManager
run: |
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_cran("BiocManager")
shell: Rscript {0}
- name: Set BiocVersion
run: |
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE)
shell: Rscript {0}
- 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
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
remotes::install_local(repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
continue-on-error: true
shell: Rscript {0}
- 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(repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
remotes::install_cran("rcmdcheck")
BiocManager::install("BiocCheck")
shell: Rscript {0}
- name: Install BiocGenerics
if: env.has_RUnit == 'true'
run: |
## Install BiocGenerics
BiocManager::install("BiocGenerics")
shell: Rscript {0}
- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
- name: Run CMD check
env:
_R_CHECK_CRAN_INCOMING_: false
_R_CHECK_DEPENDS_ONLY_: true
_R_CHECK_FORCE_SUGGESTS_: false
run: |
rcmdcheck::rcmdcheck(
args = c("--no-build-vignettes", "--no-manual", "--timings"),
build_args = c("--no-manual", "--no-resave-data"),
error_on = "warning",
check_dir = "check"
)
shell: Rscript {0}
## Might need an to add this to the if: && runner.os == 'Linux'
- name: Reveal testthat details
if: env.has_testthat == 'true'
run: find . -name testthat.Rout -exec cat '{}' ';'
- name: Install package
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: R CMD INSTALL .
- name: Upload check results
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-RELEASE_3_12-r-4.0-results
path: check