From fe2a851a5a70b178aa1b27739eae5b67da09187b Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Mon, 19 Aug 2024 14:34:37 -0400 Subject: [PATCH 1/3] Add an Rproj file --- .Rbuildignore | 2 ++ .gitignore | 1 + slurmjobs.Rproj | 21 +++++++++++++++++++++ 3 files changed, 24 insertions(+) create mode 100644 slurmjobs.Rproj diff --git a/.Rbuildignore b/.Rbuildignore index b14d5a7..c615301 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -4,3 +4,5 @@ ^\.github$ ^codecov\.yml$ ^data-raw$ +^.*\.Rproj$ +^\.Rproj\.user$ diff --git a/.gitignore b/.gitignore index 17e349e..b56176a 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ inst/doc dev/interactive_testing/logs +.Rproj.user diff --git a/slurmjobs.Rproj b/slurmjobs.Rproj new file mode 100644 index 0000000..020fcd1 --- /dev/null +++ b/slurmjobs.Rproj @@ -0,0 +1,21 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 4 +Encoding: UTF-8 + +RnwWeave: knitr +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes +LineEndingConversion: Posix + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source From 09404779d9eba0ffd48bf44e2c98a17a1ec593b5 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Mon, 19 Aug 2024 14:35:22 -0400 Subject: [PATCH 2/3] Use URL syntax , which will be detected by pkgdown --- DESCRIPTION | 2 +- R/job_single.R | 2 +- man/job_single.Rd | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 5cec07e..8a36358 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -14,7 +14,7 @@ URL: https://github.com/LieberInstitute/slurmjobs BugReports: https://support.bioconductor.org/tag/slurmjobs Encoding: UTF-8 Roxygen: list(markdown = TRUE) -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 Suggests: BiocStyle, knitr, diff --git a/R/job_single.R b/R/job_single.R index 40957d7..655bb53 100644 --- a/R/job_single.R +++ b/R/job_single.R @@ -21,7 +21,7 @@ #' your job will request is `cores` multiplied by `memory`. #' @param time_limit character(1): time limit specified in a format accepted by #' the \code{--time} parameter to \code{sbatch} (e.g. "4:00:00"). Defaults to 1 -#' day, following the JHPCE default (https://jhpce.jhu.edu/knowledge-base/setting-a-time-limit-for-your-slurm-job-on-jhpce/). +#' day, following the JHPCE default (). #' @param email The email reporting option for the email address ("BEGIN", #' "END", "FAIL", or "ALL") #' @param logdir The directory to contain the log, as an absolute or relative diff --git a/man/job_single.Rd b/man/job_single.Rd index 3f18bc8..e3175a2 100644 --- a/man/job_single.Rd +++ b/man/job_single.Rd @@ -38,7 +38,7 @@ your job will request is \code{cores} multiplied by \code{memory}.} \item{time_limit}{character(1): time limit specified in a format accepted by the \code{--time} parameter to \code{sbatch} (e.g. "4:00:00"). Defaults to 1 -day, following the JHPCE default (https://jhpce.jhu.edu/knowledge-base/setting-a-time-limit-for-your-slurm-job-on-jhpce/).} +day, following the JHPCE default (\url{https://jhpce.jhu.edu/knowledge-base/setting-a-time-limit-for-your-slurm-job-on-jhpce/}).} \item{email}{The email reporting option for the email address ("BEGIN", "END", "FAIL", or "ALL")} From 74fc163faa2827f6df5be90d0a1666fe583f6048 Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Mon, 19 Aug 2024 14:36:58 -0400 Subject: [PATCH 3/3] Update URL --- R/job_single.R | 2 +- man/job_single.Rd | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/R/job_single.R b/R/job_single.R index 655bb53..d004505 100644 --- a/R/job_single.R +++ b/R/job_single.R @@ -21,7 +21,7 @@ #' your job will request is `cores` multiplied by `memory`. #' @param time_limit character(1): time limit specified in a format accepted by #' the \code{--time} parameter to \code{sbatch} (e.g. "4:00:00"). Defaults to 1 -#' day, following the JHPCE default (). +#' day, following the JHPCE default (). #' @param email The email reporting option for the email address ("BEGIN", #' "END", "FAIL", or "ALL") #' @param logdir The directory to contain the log, as an absolute or relative diff --git a/man/job_single.Rd b/man/job_single.Rd index e3175a2..9053714 100644 --- a/man/job_single.Rd +++ b/man/job_single.Rd @@ -38,7 +38,7 @@ your job will request is \code{cores} multiplied by \code{memory}.} \item{time_limit}{character(1): time limit specified in a format accepted by the \code{--time} parameter to \code{sbatch} (e.g. "4:00:00"). Defaults to 1 -day, following the JHPCE default (\url{https://jhpce.jhu.edu/knowledge-base/setting-a-time-limit-for-your-slurm-job-on-jhpce/}).} +day, following the JHPCE default (\url{https://jhpce.jhu.edu/slurm/time-limits/}).} \item{email}{The email reporting option for the email address ("BEGIN", "END", "FAIL", or "ALL")}