{ "_id": "6a106fc9acfb0bcc41cab7a5", "Package": "BatchJobs", "Title": "Batch Computing with R", "Version": "1.10", "Authors@R": "c(\nperson(\"Bernd\", \"Bischl\", , \"bernd_bischl@gmx.net\", role = c(\"aut\", \"cre\")),\nperson(\"Michel\", \"Lang\", , \"michellang@gmail.com\", role = \"aut\"),\nperson(\"Henrik\", \"Bengtsson\", , \"henrikb@braju.com\", role = \"aut\")\n)", "Description": "Provides Map, Reduce and Filter variants to generate jobs\non batch computing systems like PBS/Torque, LSF, SLURM and Sun\nGrid Engine. Multicore and SSH systems are also supported. For\nfurther details see the project web page.", "License": "BSD_2_clause + file LICENSE", "URL": "https://github.com/tudo-r/BatchJobs", "BugReports": "https://github.com/tudo-r/BatchJobs/issues", "Encoding": "UTF-8", "MailingList": "batchjobs@googlegroups.com", "RoxygenNote": "7.3.2", "Config/pak/sysreqs": "libicu-dev", "Repository": "https://tudo-r.r-universe.dev", "Date/Publication": "2025-09-09 06:23:41 UTC", "RemoteUrl": "https://github.com/tudo-r/batchjobs", "RemoteRef": "HEAD", "RemoteSha": "74b541b8ce8da74f41bac289a970dd75c8fdf197", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-07 07:28:58 UTC", "User": "root" }, "Author": "Bernd Bischl [aut, cre],\nMichel Lang [aut],\nHenrik Bengtsson [aut]", "Maintainer": "Bernd Bischl ", "MD5sum": "8e95441a7d5e8b2e7b1457968a8f7a31", "_user": "tudo-r", "_type": "src", "_file": "BatchJobs_1.10.tar.gz", "_fileid": "02b567de63abb3167751494be52e6086e485177d72abd8d1713525c19d158d5c", "_filesize": 391753, "_sha256": 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"callFunctionOnSSHWorkers", "cfBrewTemplate", "cfHandleUnknownSubmitError", "cfKillBatchJob", "cfReadBrewTemplate", "checkIds", "copyRequiredJobFiles", "dbCreateJobDefTable", "dbGetJobs", "debugMulticore", "debugSSH", "filterResults", "findDisappeared", "findDone", "findErrors", "findExpired", "findJobs", "findMissingResults", "findNotDone", "findNotErrors", "findNotOnSystem", "findNotRunning", "findNotStarted", "findNotSubmitted", "findNotTerminated", "findOnSystem", "findRunning", "findStarted", "findSubmitted", "findTerminated", "getConfig", "getErrorMessages", "getJob", "getJobIds", "getJobInfo", "getJobLocation", "getJobNr", "getJobParamDf", "getJobResources", "getJobs", "getLogFiles", "getResources", "getSSHWorkersInfo", "getStatus", "grepLogs", "installPackagesOnSSHWorkers", "killJobs", "loadConfig", "loadExports", "loadRegistry", "loadResult", "loadResults", "makeClusterFunctions", "makeClusterFunctionsInteractive", "makeClusterFunctionsLocal", "makeClusterFunctionsLSF", "makeClusterFunctionsMulticore", "makeClusterFunctionsOpenLava", "makeClusterFunctionsSGE", "makeClusterFunctionsSLURM", "makeClusterFunctionsSSH", "makeClusterFunctionsTorque", "makeJob", "makeRegistry", "makeSSHWorker", "makeSubmitJobResult", "reduceResults", "reduceResultsDataFrame", "reduceResultsDataTable", "reduceResultsList", "reduceResultsMatrix", "reduceResultsVector", "removeRegistry", "removeRegistryPackages", "removeRegistrySourceDirs", "removeRegistrySourceFiles", "resetJobs", "sanitizePath", "setConfig", "setJobFunction", "setJobNames", "setRegistryPackages", "showClusterStatus", "showLog", "showStatus", "sourceRegistryFiles", "submitJobs", "sweepRegistry", "syncRegistry", "testJob", "updateRegistry", "waitForJobs" ], "_help": [ { "page": "addRegistryPackages", "title": "Add packages to registry.", "concept": [ "exports" ], "topics": [ "addRegistryPackages" ] }, { "page": "addRegistrySourceDirs", "title": "Add source dirs to registry.", "concept": [ "exports" ], "topics": [ "addRegistrySourceDirs" ] }, { "page": "addRegistrySourceFiles", "title": "Add source files to registry.", "concept": [ "exports" ], "topics": [ "addRegistrySourceFiles" ] }, { "page": "batchExpandGrid", "title": "Map function over all combinations.", "topics": [ "batchExpandGrid" ] }, { "page": "batchExport", "title": "Export R object to be available on the slaves.", "concept": [ "exports" ], "topics": [ "batchExport" ] }, { "page": "BatchJobs", "title": "The BatchJobs package", "topics": [ "BatchJobs-package", "BatchJobs" ] }, { "page": "batchMap", "title": "Maps a function over lists or vectors, adding jobs to a registry.", "topics": [ "batchMap" ] }, { "page": "batchMapQuick", "title": "Combination of makeRegistry, batchMap and submitJobs.", "topics": [ "batchMapQuick" ] }, { "page": "batchMapResults", "title": "Maps a function over the results of a registry by using batchMap.", "topics": [ "batchMapResults" ] }, { "page": "batchQuery", "title": "Manually query the BatchJobs database", "topics": [ "batchQuery" ] }, { "page": "batchReduce", "title": "Reduces via a binary function over a list adding jobs to a registry.", "topics": [ "batchReduce" ] }, { "page": "batchReduceResults", "title": "Reduces results via a binary function and adds jobs for this to a registry.", "topics": [ "batchReduceResults" ] }, { "page": "batchUnexport", "title": "Unload exported R objects.", "concept": [ "exports" ], "topics": [ "batchUnexport" ] }, { "page": "callFunctionOnSSHWorkers", "title": "Call an arbitrary function on specified SSH workers.", "topics": [ "callFunctionOnSSHWorkers" ] }, { "page": "cfBrewTemplate", "title": "Cluster functions helper: Brew your template into a job description file.", "topics": [ "cfBrewTemplate" ] }, { "page": "cfHandleUnknownSubmitError", "title": "Cluster functions helper: Handle an unknown error during job submission.", "topics": [ "cfHandleUnknownSubmitError" ] }, { "page": "cfKillBatchJob", "title": "Cluster functions helper: Kill a batch job via OS command", "topics": [ "cfKillBatchJob" ] }, { "page": "cfReadBrewTemplate", "title": "Cluster functions helper: Read in your brew template file.", "topics": [ "cfReadBrewTemplate" ] }, { "page": "checkIds", "title": "Check job ids.", "topics": [ "checkIds" ] }, { "page": "configuration", "title": "BatchJobs configuration.", "concept": [ "conf" ], "topics": [ ".BatchJobs.R", "configuration" ] }, { "page": "debugMulticore", "title": "Helper function to debug multicore mode.", "concept": [ "debug" ], "topics": [ "debugMulticore" ] }, { "page": "debugSSH", "title": "Helper function to debug SSH mode.", "concept": [ "debug" ], "topics": [ "debugSSH" ] }, { "page": "filterResults", "title": "Find all results where a specific condition is true.", "topics": [ "filterResults" ] }, { "page": "findState", "title": "Find jobs depending on computional state.", "topics": [ "findDisappeared", "findDone", "findErrors", "findExpired", "findMissingResults", "findNotDone", "findNotErrors", "findNotOnSystem", "findNotRunning", "findNotStarted", "findNotSubmitted", "findNotTerminated", "findOnSystem", "findRunning", "findStarted", "findSubmitted", "findTerminated" ] }, { "page": "findJobs", "title": "Finds ids of jobs that match a query.", "topics": [ "findJobs" ] }, { "page": "getConfig", "title": "Returns a list of BatchJobs configuration settings", "concept": [ "conf" ], "topics": [ "getConfig" ] }, { "page": "getErrorMessages", "title": "Get error messages of jobs.", "concept": [ "debug" ], "topics": [ "getErrorMessages" ] }, { "page": "getJob", "title": "Get job from registry by id.", "topics": [ "getJob" ] }, { "page": "getJobIds", "title": "Get ids of jobs in registry.", "topics": [ "getJobIds" ] }, { "page": "getJobInfo", "title": "Get computational information of jobs.", "concept": [ "debug" ], "topics": [ "getJobInfo" ] }, { "page": "getJobLocation", "title": "Get the physical location of job files on the hard disk.", "topics": [ "getJobLocation" ] }, { "page": "getJobNr", "title": "Get number of jobs in registry.", "topics": [ "getJobNr" ] }, { "page": "getJobParamDf", "title": "Retrieve Job Parameters.", "topics": [ "getJobParamDf" ] }, { "page": "getJobResources", "title": "Function to get the resources that were submitted for some jobs.", "topics": [ "getJobResources" ] }, { "page": "getJobs", "title": "Get jobs from registry by id.", "topics": [ "getJobs" ] }, { "page": "getLogFiles", "title": "Get log file paths for jobs.", "concept": [ "debug" ], "topics": [ "getLogFiles" ] }, { "page": "getResources", "title": "Function to get job resources in job function.", "topics": [ "getResources" ] }, { "page": "getSSHWorkersInfo", "title": "Print and return R installation and other information for SSH workers.", "topics": [ "getSSHWorkersInfo" ] }, { "page": "grepLogs", "title": "Grep log files for a pattern.", "concept": [ "debug" ], "topics": [ "grepLogs" ] }, { "page": "installPackagesOnSSHWorkers", "title": "Install packages on SSH workers.", "topics": [ "installPackagesOnSSHWorkers" ] }, { "page": "killJobs", "title": "Kill some jobs on the batch system.", "concept": [ "debug" ], "topics": [ "killJobs" ] }, { "page": "loadConfig", "title": "Load a specific configuration file.", "concept": [ "conf" ], "topics": [ "loadConfig" ] }, { "page": "loadExports", "title": "Load exported R data objects.", "concept": [ "exports" ], "topics": [ "loadExports" ] }, { "page": "loadRegistry", "title": "Load a previously saved registry.", "topics": [ "loadRegistry" ] }, { "page": "loadResult", "title": "Loads a specific result file.", "topics": [ "loadResult" ] }, { "page": "loadResults", "title": "Loads result files for id vector.", "topics": [ "loadResults" ] }, { "page": "makeClusterFunctions", "title": "Create a ClusterFuntions object.", "concept": [ "clusterFunctions" ], "topics": [ "ClusterFunctions", "makeClusterFunctions" ] }, { "page": "makeClusterFunctionsInteractive", "title": "Create cluster functions for sequential execution in same session.", "concept": [ "clusterFunctions" ], "topics": [ "makeClusterFunctionsInteractive" ] }, { "page": "makeClusterFunctionsLocal", "title": "Create cluster functions for sequential execution on local host.", "concept": [ "clusterFunctions" ], "topics": [ "makeClusterFunctionsLocal" ] }, { "page": "makeClusterFunctionsLSF", "title": "Create cluster functions for LSF systems.", "concept": [ "clusterFunctions" ], "topics": [ "makeClusterFunctionsLSF" ] }, { "page": "makeClusterFunctionsMulticore", "title": "Use multiple cores on local Linux machine to spawn parallel jobs.", "concept": [ "clusterFunctions" ], "topics": [ "makeClusterFunctionsMulticore" ] }, { "page": "makeClusterFunctionsOpenLava", "title": "Create cluster functions for OpenLava systems.", "concept": [ "clusterFunctions" ], "topics": [ "makeClusterFunctionsOpenLava" ] }, { "page": "makeClusterFunctionsSGE", "title": "Create cluster functions for Sun Grid Engine systems.", "concept": [ "clusterFunctions" ], "topics": [ "makeClusterFunctionsSGE" ] }, { "page": "makeClusterFunctionsSLURM", "title": "Create cluster functions for SLURM-based systems.", "concept": [ "clusterFunctions" ], "topics": [ "makeClusterFunctionsSLURM" ] }, { "page": "makeClusterFunctionsSSH", "title": "Create an SSH cluster to execute jobs.", "concept": [ "clusterFunctions" ], "topics": [ "makeClusterFunctionsSSH" ] }, { "page": "makeClusterFunctionsTorque", "title": "Create cluster functions for torque-based systems.", "concept": [ "clusterFunctions" ], "topics": [ "makeClusterFunctionsTorque" ] }, { "page": "makeJob", "title": "Creates a job description.", "topics": [ "Job", "makeJob" ] }, { "page": "makeRegistry", "title": "Construct a registry object.", "topics": [ "makeRegistry", "Registry" ] }, { "page": "makeSSHWorker", "title": "Create SSH worker for SSH cluster functions.", "topics": [ "makeSSHWorker", "SSHWorker" ] }, { "page": "makeSubmitJobResult", "title": "Create a SubmitJobResult object.", "topics": [ "makeSubmitJobResult", "SubmitJobResult" ] }, { "page": "reduceResults", "title": "Reduce results from result directory.", "topics": [ "reduceResults", "reduceResultsDataFrame", "reduceResultsDataTable", "reduceResultsList", "reduceResultsMatrix", "reduceResultsVector" ] }, { "page": "removeRegistry", "title": "Remove a registry object.", "topics": [ "removeRegistry" ] }, { "page": "removeRegistryPackages", "title": "Remove packages from registry.", "concept": [ "exports" ], "topics": [ "removeRegistryPackages" ] }, { "page": "removeRegistrySourceDirs", "title": "Remove packages from registry.", "concept": [ "exports" ], "topics": [ "removeRegistrySourceDirs" ] }, { "page": "removeRegistrySourceFiles", "title": "Remove source files from registry.", "concept": [ "exports" ], "topics": [ "removeRegistrySourceFiles" ] }, { "page": "resetJobs", "title": "Reset computational state of jobs.", "concept": [ "debug" ], "topics": [ "resetJobs" ] }, { "page": "sanitizePath", "title": "Sanitize a path", "topics": [ "sanitizePath" ] }, { "page": "setConfig", "title": "Set and overwrite configuration settings", "concept": [ "conf" ], "topics": [ "setConfig" ] }, { "page": "setJobFunction", "title": "Sets the job function for already existing jobs.", "concept": [ "debug" ], "topics": [ "setJobFunction" ] }, { "page": "setJobNames", "title": "Set job names.", "topics": [ "setJobNames" ] }, { "page": "setRegistryPackages", "title": "Set packages for a registry.", "concept": [ "exports" ], "topics": [ "setRegistryPackages" ] }, { "page": "showClusterStatus", "title": "Show information about available computational resources on cluster.", "topics": [ "showClusterStatus" ] }, { "page": "showLog", "title": "Display the contents of a log file.", "concept": [ "debug" ], "topics": [ "showLog" ] }, { "page": "showStatus", "title": "Retrieve or show status information about jobs.", "topics": [ "getStatus", "showStatus" ] }, { "page": "sourceRegistryFiles", "title": 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