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remove unwanted deps on renv.lock #180

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merged 5 commits into from
Jan 17, 2024
Merged

remove unwanted deps on renv.lock #180

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2241362
remove unwanted deps on renv.lock
pharmaverse-bot Jan 17, 2024
a764cb2
remove duplicate
pharmaverse-bot Jan 17, 2024
dbde79f
update DEPS_IGNORE
pharmaverse-bot Jan 17, 2024
f91ad3a
fix cat cmd
pharmaverse-bot Jan 17, 2024
c506e54
apply suggestions
pharmaverse-bot Jan 17, 2024
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27 changes: 20 additions & 7 deletions .github/workflows/r-cmd-check.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -40,23 +40,35 @@ jobs:
R_KEEP_PKG_SOURCE: true
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
R_REPOS: "https://cran.r-project.org"
DEPS_IGNORE: >-
pharmaversesdtm,
pharmaverseadam,
admiral,
admiraldev,
admiralophtha,
admiralonco,
admiralvaccine,
staged.dependencies

# DEPS_IGNORE: env variable to ignore package when building renv.lock (step Upload dependencies artifact)
# (improvments ideas : get this list of deps to ignore from staged.dependencies yml file)
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steps:
##################### BEGIN boilerplate steps #####################
- name: Get branch names
id: branch-name
uses: tj-actions/branch-names@v5.4
uses: tj-actions/branch-names@v8

- name: Checkout repo (PR) 🛎
uses: actions/checkout@v3
uses: actions/checkout@v4
if: |
github.event_name == 'pull_request'
with:
ref: ${{ steps.branch-name.outputs.head_ref_branch }}
repository: ${{ github.event.pull_request.head.repo.full_name }}

- name: Checkout repository
uses: actions/checkout@v3
uses: actions/checkout@v4
if: |
github.event_name != 'pull_request'
with:
Expand Down Expand Up @@ -100,14 +112,15 @@ jobs:
dir.create("/workspace/tmp")
library(dplyr)
installed_packages <- as.data.frame(installed.packages())
packages_to_remove <- Sys.getenv("DEPS_IGNORE", "")
packages_to_remove <- unlist(strsplit(packages_to_remove, ","))
installed_packages <- installed_packages %>% filter(LibPath != "/usr/local/lib/R/library") %>% # remove pre-built deps
filter(!Package %in% packages_to_remove)
# save deps as csv file
write.csv(installed_packages, "/workspace/tmp/deps-${{ matrix.r_version }}.csv", row.names = FALSE)
# create also renv.lock file
setwd("/workspace/tmp")

installed_packages <- as.data.frame(installed.packages())
installed_packages <- installed_packages %>% filter(LibPath != "/usr/local/lib/R/library")

renv_lock <- list(
"R" = list(
"Version" = paste(R.version$major, R.version$minor, sep=".")
Expand Down Expand Up @@ -152,7 +165,7 @@ jobs:
# Write the list to a JSON file (renv.lock)
writeLines(jsonlite::toJSON(renv_lock, pretty = TRUE, auto_unbox = TRUE), "renv-${{ matrix.r_version }}.lock")
print("generated renv.lock content")
system("cat renv.lock")
system("cat renv-${{ matrix.r_version }}.lock")
shell: Rscript {0}

- name: Upload deps.csv and renv.lock artifacts
Expand Down
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