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HenrikBengtssonHenrikBengtsson
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More template cleanups
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14 files changed

+62
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‎DESCRIPTION‎

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Package: future.batchtools
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Version: 0.12.2-9989
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Version: 0.12.2-9990
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Depends:
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R (>= 3.2.0),
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parallelly,

‎inst/templates-for-R_CMD_check/batchtools.sge.tmpl‎

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## Resources needed:
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<%
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Should scheduler "details" be seen?
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details <- isTRUE(resources[["details"]])
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resources[["details"]] <- NULL
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modules <- resources[["modules"]]
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resources[["modules"]] <- NULL
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## SPECIAL: For R CMD check package testing on HPC environments, which
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## typically uses a temporary working directory that is local, we force
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## it to use HPC-wide working directory
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} %>
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echo "Session information:"
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echo "- timestamp: $(date)"
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echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
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echo "- hostname: $(hostname)"
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echo "- Rscript path: $(which Rscript)"
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echo "- Rscript version: $(Rscript --version)"
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writeLines(shutdown)
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} %>
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echo "End time: $(date +"%Y-%m-%d %H:%M:%S%z")"
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## Relay the exit code from Rscript
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exit "${res}"

‎inst/templates-for-R_CMD_check/batchtools.slurm.tmpl‎

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## Resources needed:
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<%
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Shell "details" code to evaluate
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details <- isTRUE(resources[["details"]])
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resources[["details"]] <- NULL
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modules <- resources[["modules"]]
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resources[["modules"]] <- NULL
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## SPECIAL: For R CMD check package testing on HPC environments, which
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## typically uses a temporary working directory that is local, we force
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## it to use HPC-wide working directory
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} %>
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echo "Session information:"
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echo "- timestamp: $(date)"
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echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
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echo "- hostname: $(hostname)"
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echo "- Rscript path: $(which Rscript)"
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echo "- Rscript version: $(Rscript --version)"
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writeLines(shutdown)
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} %>
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echo "End time: $(date +"%Y-%m-%d %H:%M:%S%z")"
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## Relay the exit code from Rscript
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exit "${res}"

‎inst/templates-for-R_CMD_check/batchtools.torque.tmpl‎

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## Resources needed:
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<%
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Should scheduler "details" be seen?
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details <- isTRUE(resources[["details"]])
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resources[["details"]] <- NULL
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modules <- resources[["modules"]]
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resources[["modules"]] <- NULL
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## SPECIAL: For R CMD check package testing on HPC environments, which
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## typically uses a temporary working directory that is local, we force
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## it to use HPC-wide working directory
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} %>
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echo "Session information:"
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echo "- timestamp: $(date)"
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echo "- timestamp: $(date +"%Y-%m-%d %H:%M:%S%z")"
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echo "- hostname: $(hostname)"
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echo "- Rscript path: $(which Rscript)"
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echo "- Rscript version: $(Rscript --version)"
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writeLines(shutdown)
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} %>
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echo "End time: $(date +"%Y-%m-%d %H:%M:%S%z")"
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## Relay the exit code from Rscript
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exit "${res}"

‎inst/templates/lsf.tmpl‎

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## Resources needed
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<%
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Should scheduler "details" be seen?
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details <- isTRUE(resources[["details"]])
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resources[["details"]] <- NULL
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modules <- resources[["modules"]]
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resources[["modules"]] <- NULL
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Remaining resources are assumed to be of type '-<key>=<value>'
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opts <- unlist(resources, use.names = TRUE)
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opts <- sprintf("-%s=%s", names(opts), opts)

‎inst/templates/openlava.tmpl‎

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## Resources needed
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<%
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Should scheduler "details" be seen?
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details <- isTRUE(resources[["details"]])
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resources[["details"]] <- NULL
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modules <- resources[["modules"]]
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resources[["modules"]] <- NULL
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Remaining resources are assumed to be of type '-<key>=<value>'
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opts <- unlist(resources, use.names = TRUE)
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opts <- sprintf("-%s=%s", names(opts), opts)

‎inst/templates/sge.tmpl‎

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## Resources needed:
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<%
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Should scheduler "details" be seen?
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details <- isTRUE(resources[["details"]])
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resources[["details"]] <- NULL
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modules <- resources[["modules"]]
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resources[["modules"]] <- NULL
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Remaining resources are assumed to be of type '-l <key>=<value>'
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opts <- unlist(resources, use.names = TRUE)
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opts <- sprintf("-l %s=%s", names(opts), opts)

‎inst/templates/slurm.tmpl‎

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## Resources needed:
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<%
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Shell "details" code to evaluate
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details <- isTRUE(resources[["details"]])
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resources[["details"]] <- NULL
@@ -32,6 +28,10 @@
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modules <- resources[["modules"]]
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resources[["modules"]] <- NULL
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Remaining resources are assumed to be of type '--<key>=<value>'
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opts <- unlist(resources, use.names = TRUE)
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opts <- sprintf("--%s=%s", names(opts), opts)

‎inst/templates/torque.tmpl‎

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## Resources needed:
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<%
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Should scheduler "details" be seen?
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details <- isTRUE(resources[["details"]])
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resources[["details"]] <- NULL
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modules <- resources[["modules"]]
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resources[["modules"]] <- NULL
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## As-is resource specifications
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job_declarations <- resources[["asis"]]
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resources[["asis"]] <- NULL
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## Remaining resources are assumed to be of type '-l <key>=<value>'
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opts <- unlist(resources, use.names = TRUE)
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opts <- sprintf("-l %s=%s", names(opts), opts)

‎man/batchtools_lsf.Rd‎

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