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Correcting redir in README.Rmd
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@gvegayon
gvegayon committed Jun 21, 2022
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2 changes: 1 addition & 1 deletion README.Rmd
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Expand Up @@ -7,7 +7,7 @@ output:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.01493/status.svg)](https://doi.org/10.21105/joss.01493)
[![R CI release](https://github.com/USCbiostats/slurmR/actions/workflows/ci.yml/badge.svg)](https://github.com/USCbiostats/slurmR/actions/workflows/ci.yml)
[![codecov](https://codecov.io/gh/USCbiostats/slurmR/branch/master/graph/badge.svg)](https://codecov.io/gh/USCbiostats/slurmR)
[![codecov](https://codecov.io/gh/USCbiostats/slurmR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/USCbiostats/slurmR)
[![CRAN status](https://www.r-pkg.org/badges/version/slurmR)](https://CRAN.R-project.org/package=slurmR)
[![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/slurmR)](https://cran.r-project.org/package=slurmR)
[![status](https://tinyverse.netlify.com/badge/slurmR)](https://CRAN.R-project.org/package=slurmR)
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44 changes: 22 additions & 22 deletions README.md
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Expand Up @@ -2,7 +2,7 @@
[![DOI](http://joss.theoj.org/papers/10.21105/joss.01493/status.svg)](https://doi.org/10.21105/joss.01493)
[![R CI
release](https://github.com/USCbiostats/slurmR/actions/workflows/ci.yml/badge.svg)](https://github.com/USCbiostats/slurmR/actions/workflows/ci.yml)
[![codecov](https://codecov.io/gh/USCbiostats/slurmR/branch/master/graph/badge.svg)](https://codecov.io/gh/USCbiostats/slurmR)
[![codecov](https://codecov.io/gh/USCbiostats/slurmR/branch/master/graph/badge.svg)](https://app.codecov.io/gh/USCbiostats/slurmR)
[![CRAN
status](https://www.r-pkg.org/badges/version/slurmR)](https://CRAN.R-project.org/package=slurmR)
[![CRAN
Expand Down Expand Up @@ -122,10 +122,10 @@ We can use the function `Slurm_lapply` to distribute computations
``` r
ans <- Slurm_lapply(x, mean, plan = "none")
# Warning in normalizePath(file.path(tmp_path, job_name)): path[1]="/home/
# george/Documents/development/slurmR/slurmr-job-27165393bf6bf": No such file or
# george/Documents/development/slurmR/slurmr-job-2855312d50503": No such file or
# directory
# Warning: [submit = FALSE] The job hasn't been submitted yet. Use sbatch() to submit the job, or you can submit it via command line using the following:
# sbatch --job-name=slurmr-job-27165393bf6bf /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/01-bash.sh
# sbatch --job-name=slurmr-job-2855312d50503 /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/01-bash.sh
Slurm_clean(ans) # Cleaning after you
```

Expand All @@ -137,10 +137,10 @@ get more info, we can set the verbose mode on
opts_slurmR$verbose_on()
ans <- Slurm_lapply(x, mean, plan = "none")
# Warning in normalizePath(file.path(tmp_path, job_name)): path[1]="/home/
# george/Documents/development/slurmR/slurmr-job-27165393bf6bf": No such file or
# george/Documents/development/slurmR/slurmr-job-2855312d50503": No such file or
# directory
# --------------------------------------------------------------------------------
# [VERBOSE MODE ON] The R script that will be used is located at: /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/00-rscript.r and has the following contents:
# [VERBOSE MODE ON] The R script that will be used is located at: /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/00-rscript.r and has the following contents:
# --------------------------------------------------------------------------------
# .libPaths(c("/home/george/R/x86_64-pc-linux-gnu-library/4.2", "/usr/local/lib/R/site-library", "/usr/lib/R/site-library", "/usr/lib/R/library"))
# message("[slurmR info] Loading variables and functions... ", appendLF = FALSE)
Expand Down Expand Up @@ -168,7 +168,7 @@ ans <- Slurm_lapply(x, mean, plan = "none")
# sprintf("%s/%s/%s", tmp_path, job_name, type)
# }
# TMP_PATH <- "/home/george/Documents/development/slurmR"
# JOB_NAME <- "slurmr-job-27165393bf6bf"
# JOB_NAME <- "slurmr-job-2855312d50503"
#
# # The -tcq- function is a wrapper of tryCatch that on error tries to recover
# # the message and saves the outcome so that slurmR can return OK.
Expand All @@ -195,19 +195,19 @@ ans <- Slurm_lapply(x, mean, plan = "none")
# }
# message("done loading variables and functions.")
# tcq({
# INDICES <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/INDICES.rds")
# INDICES <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/INDICES.rds")
# })
# tcq({
# X <- readRDS(sprintf("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/X_%04d.rds", ARRAY_ID))
# X <- readRDS(sprintf("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/X_%04d.rds", ARRAY_ID))
# })
# tcq({
# FUN <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/FUN.rds")
# FUN <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/FUN.rds")
# })
# tcq({
# mc.cores <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/mc.cores.rds")
# mc.cores <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/mc.cores.rds")
# })
# tcq({
# seeds <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/seeds.rds")
# seeds <- readRDS("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/seeds.rds")
# })
# set.seed(seeds[ARRAY_ID], kind = NULL, normal.kind = NULL)
# tcq({
Expand All @@ -217,24 +217,24 @@ ans <- Slurm_lapply(x, mean, plan = "none")
# mc.cores = mc.cores
# )
# })
# saveRDS(ans, sprintf("/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/03-answer-%03i.rds", ARRAY_ID), compress = TRUE)
# saveRDS(ans, sprintf("/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/03-answer-%03i.rds", ARRAY_ID), compress = TRUE)
# message("[slurmR info] job-status: OK.\n")
# --------------------------------------------------------------------------------
# The bash file that will be used is located at: /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/01-bash.sh and has the following contents:
# The bash file that will be used is located at: /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/01-bash.sh and has the following contents:
# --------------------------------------------------------------------------------
# #!/bin/sh
# #SBATCH --job-name=slurmr-job-27165393bf6bf
# #SBATCH --output=/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/02-output-%A-%a.out
# #SBATCH --job-name=slurmr-job-2855312d50503
# #SBATCH --output=/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/02-output-%A-%a.out
# #SBATCH --array=1-2
# #SBATCH --job-name=slurmr-job-27165393bf6bf
# #SBATCH --job-name=slurmr-job-2855312d50503
# #SBATCH --cpus-per-task=1
# #SBATCH --ntasks=1
# /usr/lib/R/bin/Rscript /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/00-rscript.r
# /usr/lib/R/bin/Rscript /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/00-rscript.r
# --------------------------------------------------------------------------------
# EOF
# --------------------------------------------------------------------------------
# Warning: [submit = FALSE] The job hasn't been submitted yet. Use sbatch() to submit the job, or you can submit it via command line using the following:
# sbatch --job-name=slurmr-job-27165393bf6bf /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/01-bash.sh
# sbatch --job-name=slurmr-job-2855312d50503 /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/01-bash.sh
Slurm_clean(ans) # Cleaning after you
```

Expand Down Expand Up @@ -381,15 +381,15 @@ ans <- Slurm_lapply(1:10, mean, plan = "none", preamble = "module load pandoc")
# Printing out the bashfile
cat(readLines(ans$bashfile), sep = "\n")
# #!/bin/sh
# #SBATCH --job-name=slurmr-job-27165393bf6bf
# #SBATCH --output=/home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/02-output-%A-%a.out
# #SBATCH --job-name=slurmr-job-2855312d50503
# #SBATCH --output=/home/george/Documents/development/slurmR/slurmr-job-2855312d50503/02-output-%A-%a.out
# #SBATCH --array=1-2
# #SBATCH --job-name=slurmr-job-27165393bf6bf
# #SBATCH --job-name=slurmr-job-2855312d50503
# #SBATCH --cpus-per-task=1
# #SBATCH --ntasks=1
# module load gcc/6.0
# module load pandoc
# /usr/lib/R/bin/Rscript /home/george/Documents/development/slurmR/slurmr-job-27165393bf6bf/00-rscript.r
# /usr/lib/R/bin/Rscript /home/george/Documents/development/slurmR/slurmr-job-2855312d50503/00-rscript.r

Slurm_clean(ans) # Cleaning after you
```
Expand Down

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