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Fix slurm error propagation #2488

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Merged
simonkrogmann merged 1 commit into from
Oct 3, 2026
Merged

Fix slurm error propagation #2488

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2 changes: 1 addition & 1 deletion .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -81,8 +81,8 @@ plotRuntimeDependencies/
.Rproj.user
runtime.rds

# main renv.lock should only be commited for releases
/.Rbuildignore
renv.lock

# ignore RStudio project files
/*.Rproj
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15 changes: 14 additions & 1 deletion renv/activate.R
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Expand Up @@ -2,7 +2,7 @@
local({

# the requested version of renv
version <- "1.2.4"
version <- "1.3.0"
attr(version, "md5") <- NULL
attr(version, "sha") <- NULL

Expand Down Expand Up @@ -716,6 +716,18 @@ local({
# (512 byte) header.
renv_bootstrap_git_extract_sha1_tar <- function(bundle) {

tryCatch(
renv_bootstrap_git_extract_sha1_tar_impl(bundle),
error = function(cnd) {
catf("- Failed to extract the Git SHA from '%s': %s", bundle, conditionMessage(cnd))
NULL
}
)

}

renv_bootstrap_git_extract_sha1_tar_impl <- function(bundle) {

# open the bundle for reading
# We use gzcon for everything because (from ?gzcon)
# > Reading from a connection which does not supply a 'gzip' magic
Expand All @@ -734,6 +746,7 @@ local({
} else {
NULL
}

}

renv_bootstrap_install <- function(version, tarball, library) {
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2 changes: 1 addition & 1 deletion scripts/start/submit.R
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Expand Up @@ -133,7 +133,7 @@ submit <- function(cfg, restart = FALSE, stopOnFolderCreateError = TRUE) {
" --mail-type=END,FAIL",
" --comment=REMIND",
# Prefix RSCRIPT_SLURM_HOOK for piam-apptainer integration (empty if unset)
" --wrap=\"", trimws(paste(Sys.getenv("RSCRIPT_SLURM_HOOK", unset = ""), "Rscript")), " prepareAndRun.R \" ",
" --wrap=\"set -e; ", trimws(paste(Sys.getenv("RSCRIPT_SLURM_HOOK", unset = ""), "Rscript")), " prepareAndRun.R \" ",
cfg$slurmConfig))
Sys.sleep(1)
}
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