Submit R code
bsub_chunk(code,
name = NULL,
packages = bsub_opt$packages,
image = bsub_opt$image,
variables = character(),
share = character(),
working_dir = bsub_opt$working_dir,
hours = 1,
memory = 1,
cores = 1,
R_version = bsub_opt$R_version,
temp_dir = bsub_opt$temp_dir,
output_dir = bsub_opt$output_dir,
dependency = NULL,
enforce = bsub_opt$enforce,
local = bsub_opt$local,
script = NULL,
start = NULL,
end = NULL,
save_var = FALSE,
sh_head = bsub_opt$sh_head)The code chunk, it should be embraced by { }.
If name is not specified, an internal name calculated by digest on the chunk is automatically assigned.
A character vector with package names that will be loaded before running the script. There is a special name _in_session_ that loads all the packages loaded in current R session.
A character vector of RData/rda files that will be loaded before running the script. When image is set to TRUE, all variables in .GlobalEnv will be saved into a temporary file and all attached packages will be recorded. The temporary files will be removed after the job is finished.
A character vector of variable names that will be loaded before running the script. There is a special name _all_functions_ that saves all functions defined in the global environment.
A character vector of variables names for which the variables are shared between jobs. Note the temporary .RData files are not deleted automatically.
The working directory.
Running time of the job.
Memory usage of the job. It is measured in GB.
Number of cores.
R version.
Path of temporary folder where the temporary R/bash scripts will be put.
Path of output folder where the output/flag files will be put.
A vector of job IDs that current job depends on.
If a flag file for the job is found, whether to enforce to rerun the job.
Run job locally (not submitting to the LSF cluster)?
Path of a script where code chunks will be extracted and sent to the cluster.It is always used with start and end arguments.
A numeric vector that contains line indices of the starting code chunk or a character vector that contain regular expression to match the start of code chunks.
Same setting as start.
Whether save the last variable in the code chunk? Later the variable can be retrieved by retrieve_var.
Commands that are written as head of the sh script.
Job ID.
bsub_script submits R scripts.
bsub_cmdsubmits shell commands.
# NOT RUN {
bsub_chunk(name = "example", memory = 10, hours = 10, cores = 4,
{
Sys.sleep(5)
})
# }
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