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[skip deploy] Update renv.lock file for RNA-seq app
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github-actions[bot] committed Apr 12, 2024
1 parent e684f9f commit b877406
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Showing 2 changed files with 37 additions and 18 deletions.
12 changes: 6 additions & 6 deletions RNA-seq/renv.lock
Original file line number Diff line number Diff line change
Expand Up @@ -2078,13 +2078,13 @@
},
"matrixStats": {
"Package": "matrixStats",
"Version": "1.2.0",
"Version": "1.3.0",
"Source": "Repository",
"Repository": "RSPM",
"Repository": "BioC.CRAN",
"Requirements": [
"R"
],
"Hash": "33a3ca9e732b57244d14f5d732ffc9eb"
"Hash": "4b3ea27a19d669c0405b38134d89a9d1"
},
"memoise": {
"Package": "memoise",
Expand Down Expand Up @@ -2580,13 +2580,13 @@
},
"renv": {
"Package": "renv",
"Version": "1.0.5",
"Version": "1.0.7",
"Source": "Repository",
"Repository": "CRAN",
"Repository": "BioC.CRAN",
"Requirements": [
"utils"
],
"Hash": "32c3f93e8360f667ca5863272ec8ba6a"
"Hash": "397b7b2a265bc5a7a06852524dabae20"
},
"rjson": {
"Package": "rjson",
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43 changes: 31 additions & 12 deletions RNA-seq/renv/activate.R
Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,13 @@
local({

# the requested version of renv
version <- "1.0.5"
version <- "1.0.7"
attr(version, "sha") <- NULL

# the project directory
project <- getwd()
project <- Sys.getenv("RENV_PROJECT")
if (!nzchar(project))
project <- getwd()

# use start-up diagnostics if enabled
diagnostics <- Sys.getenv("RENV_STARTUP_DIAGNOSTICS", unset = "FALSE")
Expand Down Expand Up @@ -129,6 +131,21 @@ local({

}

heredoc <- function(text, leave = 0) {

# remove leading, trailing whitespace
trimmed <- gsub("^\\s*\\n|\\n\\s*$", "", text)

# split into lines
lines <- strsplit(trimmed, "\n", fixed = TRUE)[[1L]]

# compute common indent
indent <- regexpr("[^[:space:]]", lines)
common <- min(setdiff(indent, -1L)) - leave
paste(substring(lines, common), collapse = "\n")

}

startswith <- function(string, prefix) {
substring(string, 1, nchar(prefix)) == prefix
}
Expand Down Expand Up @@ -631,6 +648,9 @@ local({

# if the user has requested an automatic prefix, generate it
auto <- Sys.getenv("RENV_PATHS_PREFIX_AUTO", unset = NA)
if (is.na(auto) && getRversion() >= "4.4.0")
auto <- "TRUE"

if (auto %in% c("TRUE", "True", "true", "1"))
return(renv_bootstrap_platform_prefix_auto())

Expand Down Expand Up @@ -822,24 +842,23 @@ local({

# the loaded version of renv doesn't match the requested version;
# give the user instructions on how to proceed
remote <- if (!is.null(description[["RemoteSha"]])) {
dev <- identical(description[["RemoteType"]], "github")
remote <- if (dev)
paste("rstudio/renv", description[["RemoteSha"]], sep = "@")
} else {
else
paste("renv", description[["Version"]], sep = "@")
}

# display both loaded version + sha if available
friendly <- renv_bootstrap_version_friendly(
version = description[["Version"]],
sha = description[["RemoteSha"]]
sha = if (dev) description[["RemoteSha"]]
)

fmt <- paste(
"renv %1$s was loaded from project library, but this project is configured to use renv %2$s.",
"- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.",
"- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.",
sep = "\n"
)
fmt <- heredoc("
renv %1$s was loaded from project library, but this project is configured to use renv %2$s.
- Use `renv::record(\"%3$s\")` to record renv %1$s in the lockfile.
- Use `renv::restore(packages = \"renv\")` to install renv %2$s into the project library.
")
catf(fmt, friendly, renv_bootstrap_version_friendly(version), remote)

FALSE
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