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useDynLib("BiocParallel", .registration = TRUE)
import(methods)
importFrom(stats, setNames, terms, runif)
importFrom(utils, capture.output, find, head, tail, relist,
setTxtProgressBar, txtProgressBar)
importFrom(parallel, nextRNGStream, nextRNGSubStream)
importFrom(codetools, findGlobals)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 classes
###
exportClass(
BiocParallelParam,
MulticoreParam,
SnowParam,
DoparParam,
SerialParam,
BatchtoolsParam,
BPValidate
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export non-generic functions
###
export(
MulticoreParam, SnowParam, DoparParam, SerialParam,
BatchtoolsParam,
## register
register, registered, bpparam,
## accessor
bpnworkers,
## error handlers
bptry,
## accessor for the errors
bpresult,
## helpers
bploop, # worker, manager loops
multicoreWorkers, snowWorkers,
batchtoolsWorkers, batchtoolsCluster, batchtoolsRegistryargs,
batchtoolsTemplate,
bpvalidate, bpok, bperrorTypes,
bprunMPIworker,
## iteration
bpiterateAlong,
## ipcmutex
ipcid, ipcremove, ipclock, ipctrylock, ipcunlock, ipclocked,
ipcyield, ipcvalue, ipcreset,
bpoptions, .registerOption
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 generics and methods defined in BiocParallel
###
export(
bplapply, bpvec, bpvectorize, bpmapply, bpaggregate, bpiterate,
## bp-controls
bpworkers, "bpworkers<-", bpbackend, "bpbackend<-",
bptasks, "bptasks<-", bpjobname, "bpjobname<-",
bpstart, bpstop, bpisup,
bpstopOnError, "bpstopOnError<-",
bpprogressbar, "bpprogressbar<-", bpRNGseed, "bpRNGseed<-",
bptimeout, "bptimeout<-", bpexportglobals, "bpexportglobals<-",
bpexportvariables, "bpexportvariables<-",
bpforceGC, "bpforceGC<-",
bpfallback, "bpfallback<-",
bplog, "bplog<-", bplogdir, "bplogdir<-",
bpthreshold, "bpthreshold<-", bpresultdir, "bpresultdir<-",
## schedule
bpschedule
)
### Same list as above.
exportMethods(
bplapply, bpvec, bpvectorize, bpmapply, bpaggregate, bpiterate,
## bp-controls
bpworkers, "bpworkers<-", bpbackend, "bpbackend<-",
bptasks, "bptasks<-", bpjobname, "bpjobname<-",
bpstart, bpstop, bpisup,
bpstopOnError, "bpstopOnError<-",
bpprogressbar, "bpprogressbar<-", bpRNGseed, "bpRNGseed<-",
bptimeout, "bptimeout<-", bplog, "bplog<-", bplogdir, "bplogdir<-",
bpthreshold, "bpthreshold<-", bpresultdir, "bpresultdir<-",
## schedule
bpschedule
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S4 methods for generics not defined in BiocParallel
###
exportMethods(
show
)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export S3 methods
###
S3method(print, remote_error)
S3method(print, bplist_error)
S3method(bploop, lapply)
S3method(bploop, iterate)
### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
### Export 'developer' API for extending BiocParallelParam
###
export(
.BiocParallelParam_prototype, .prototype_update, .prettyPath,
.send_to, .recv_any, .send, .recv, .close, .send_all, .recv_all,
.bpstart_impl, .bpstop_impl, .bpworker_impl,
.bplapply_impl, .bpiterate_impl,
.error_worker_comm,
.manager, .manager_send, .manager_recv,
.manager_send_all, .manager_recv_all,
.manager_capacity,
.manager_flush, .manager_cleanup,
.task_const, .task_dynamic, .task_remake
)
|
