diff --git a/.gitignore b/.gitignore index 3269e90f2..23e1979c4 100644 --- a/.gitignore +++ b/.gitignore @@ -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 diff --git a/renv/activate.R b/renv/activate.R index dcef95c4d..3f52a662a 100644 --- a/renv/activate.R +++ b/renv/activate.R @@ -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 @@ -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 @@ -734,6 +746,7 @@ local({ } else { NULL } + } renv_bootstrap_install <- function(version, tarball, library) { diff --git a/scripts/start/submit.R b/scripts/start/submit.R index cb0f1ee10..eb0dfd5a1 100644 --- a/scripts/start/submit.R +++ b/scripts/start/submit.R @@ -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) }