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Bioconductor · Jul 6, 2020 · ad46db9 · ad46db9
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Showing 8 changed files with 12 additions and 5 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: BiocParallel
 Type: Package
 Title: Bioconductor facilities for parallel evaluation
-Version: 1.23.1
+Version: 1.23.2
 Authors@R: c(
     person("Bioconductor Package Maintainer",
         email="[email protected]", role="cre"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -46,6 +46,7 @@ export(
     batchtoolsTemplate,
     bpvalidate, bpok,
     bprunMPIslave,
+    bprunMPIworker,
 
     ## ipcmutex
     ipcid, ipcremove, ipclock, ipctrylock, ipcunlock, ipclocked,

diff --git a/R/SnowParam-utils.R b/R/SnowParam-utils.R
@@ -5,6 +5,11 @@
 ###
 
 bprunMPIslave <- function() {
+    .Deprecated("bprunMPIworker")
+    bprunMPIworker()
+}
+
+bprunMPIworker <- function() {
     comm <- 1
     intercomm <- 2
     Rmpi::mpi.comm.get.parent(intercomm)

diff --git a/inst/RMPInode.sh b/inst/RMPInode.sh
@@ -5,5 +5,5 @@ ${RPROG:-R} --vanilla <<EOF > ${OUT:-/dev/null} 2>&1
 loadNamespace("Rmpi")
 loadNamespace("snow")
 
-BiocParallel::bprunMPIslave()
+BiocParallel::bprunMPIworker()
 EOF
diff --git a/inst/snow/RMPInode.R b/inst/snow/RMPInode.R
@@ -20,6 +20,6 @@ local({
     loadNamespace("Rmpi")
     loadNamespace("snow")
 
-    BiocParallel::bprunMPIslave()
+    BiocParallel::bprunMPIworker()
     quit("no")
 })
diff --git a/inst/unitTests/test_script/test-sge-template.tmpl b/inst/unitTests/test_script/test-sge-template.tmpl
@@ -22,7 +22,7 @@
 ## R settings
 module load R/3.4.3
 
-## Export value of DEBUGME environemnt var to slave
+## Export value of DEBUGME environemnt var to worker
 export DEBUGME=<%= Sys.getenv("DEBUGME") %>
 
 Rscript -e 'batchtools::doJobCollection("<%= uri %>")'

diff --git a/man/bploop.Rd b/man/bploop.Rd
@@ -9,6 +9,7 @@
 \alias{bploop.iterate}
 
 \alias{bprunMPIslave}
+\alias{bprunMPIworker}
 
 \title{Internal Functions for SNOW-style Parallel Evaluation}
 

diff --git a/vignettes/BiocParallel_BatchtoolsParam.Rnw b/vignettes/BiocParallel_BatchtoolsParam.Rnw
@@ -192,7 +192,7 @@ cluster.  For example, one might use instead:
 
 \begin{verbatim}
 echo 'batchtools::doJobCollection("<%= uri %>")' |\
-    ArbitraryRcommand --no-save --slave
+    ArbitraryRcommand --no-save --no-echo
 \end{verbatim}
 
 If such customization is necessary, we suggest making a local copy of