Restrict threads to 2

aravind-j · Aug 30, 2023 · e2f7166 · e2f7166
1 parent 4db2646
commit e2f7166
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Showing 27 changed files with 401 additions and 2 deletions.
diff --git a/R/AddProbDup.R b/R/AddProbDup.R
@@ -44,6 +44,16 @@
 #' @return A data frame of the PGR passport database with the probable duplicate
 #'   sets fields added.
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' \dontrun{
 #' 
 #' #' # Load PGR passport database
@@ -87,6 +97,12 @@
 #' GNwithdup <-  AddProbDup(pdup = GNdup, db = GN1000, addto = "I")                  
 #' 
 #' }
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @seealso \code{\link[PGRdup]{DataClean}}, \code{\link[PGRdup]{KWIC}},
 #'   \code{\link[PGRdup]{ProbDup}}
 #' @note When any primary ID/key records in the fuzzy, phonetic or semantic 

diff --git a/R/DisProbDup.R b/R/DisProbDup.R
@@ -43,6 +43,16 @@
 #'   disjoint duplicate sets as an additional element \code{DisjointDupicates}
 #'   according to the choice specified in the argument \code{combine}.
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' \dontrun{
 #'
 #' # Load PGR passport database
@@ -92,6 +102,12 @@
 #' lapply(disGNdup2, nrow)
 #'
 #' }
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @seealso \code{\link[PGRdup]{ProbDup}}
 #' @import igraph
 #' @import data.table

diff --git a/R/KWCounts.R b/R/KWCounts.R
@@ -39,6 +39,16 @@
 #' @note For large number of exceptions and/or large data.frame computation of
 #' keyword counts may take some time.
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' # Load PGR passport database
 #' GN <- GN1000
 #'
@@ -60,6 +70,12 @@
 #' bp <- barplot(table(GNKWCouts$COUNT),
 #'               xlab = "Word count", ylab = "Frequency", col = "#CD5555")
 #' text(bp, 0, table(GNKWCouts$COUNT),cex=1,pos=3)
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @seealso \code{\link[stringi]{stri_count}}
 #' @return A data frame with the keyword counts for each record.
 #' @import data.table

diff --git a/R/KWIC.R b/R/KWIC.R
@@ -61,6 +61,16 @@
 #'
 #' @encoding UTF-8
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' # Load PGR passport database
 #' GN <- GN1000
 #'
@@ -88,6 +98,12 @@
 #' GN[1001,3] <- ""
 #' GNKWIC <- KWIC(GN, GNfields)
 #' }
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @import data.table
 #' @importFrom stringi stri_split_fixed
 #' @export KWIC

diff --git a/R/MergeProbDup.R b/R/MergeProbDup.R
@@ -26,6 +26,16 @@
 #'   and semantic probable duplicate sets.
 #' @seealso \code{\link[PGRdup]{ProbDup}}, \code{\link[PGRdup]{SplitProbDup}}
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' \dontrun{
 #' #' # Load PGR passport database
 #' GN <- GN1000
@@ -71,6 +81,12 @@
 #' GNdupMerged <- MergeProbDup(GNdupSplit[[1]], GNdupSplit[[3]])
 #' 
 #' }
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @import data.table
 #' @importFrom methods is
 #' @export

diff --git a/R/ParseProbDup.R b/R/ParseProbDup.R
@@ -37,6 +37,16 @@
 #'   retrieved columns(fields) the prefix \code{K*} indicates the KWIC index of 
 #'   origin.
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' \dontrun{
 #' 
 #' #' # Load PGR passport database
@@ -80,6 +90,12 @@
 #' GNdupParsed <- ParseProbDup(GNdup)
 #' 
 #' }
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @seealso 
 #'   \code{\link[PGRdup]{ProbDup}},
 #' @import data.table

diff --git a/R/ProbDup.R b/R/ProbDup.R
@@ -152,6 +152,16 @@
 #'   \url{https://journal.r-project.org/archive/2014/RJ-2014-011/index.html}.
 #' @encoding UTF-8
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' \dontrun{
 #'
 #' # Method "a"
@@ -255,6 +265,12 @@
 #' GNdupc
 #'
 #' }
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @seealso \code{\link[PGRdup]{KWIC}}, \code{\link[PGRdup]{DoubleMetaphone}}
 #'   \code{\link[stringdist:stringdist]{stringdistmatrix}},
 #'   \code{\link[utils]{adist}}, \code{\link[PGRdup]{print.ProbDup}}

diff --git a/R/ReconstructProbDup.R b/R/ReconstructProbDup.R
@@ -42,6 +42,16 @@
 #'   phonetic and semantic probable duplicate sets according to the instructions
 #'   specified under clerical review.
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' \dontrun{
 #'
 #' # Load PGR passport database
@@ -107,6 +117,12 @@
 #' lapply(GNdup2, nrow)
 #' 
 #' }
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @seealso \code{\link[PGRdup]{ProbDup}}, \code{\link[PGRdup]{ReviewProbDup}}
 #' @import data.table
 #' @importFrom stringi stri_count_fixed

diff --git a/R/ReviewProbDup.R b/R/ReviewProbDup.R
@@ -94,6 +94,16 @@
 #' @seealso \code{\link[PGRdup]{DataClean}}, \code{\link[PGRdup]{KWIC}},
 #'   \code{\link[PGRdup]{ProbDup}}
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' \dontrun{
 #'
 #' # Load PGR passport database
@@ -147,6 +157,12 @@
 #' write.csv(file="Duplicate sets for review.csv", x=RevGNdup)
 #'
 #' }
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @import data.table
 #' @importFrom methods is
 #' @export

diff --git a/R/SplitProbDup.R b/R/SplitProbDup.R
@@ -28,6 +28,16 @@
 #'   accessions present in each (\code{list1} and \code{list2}).
 #' @seealso \code{\link[PGRdup]{ProbDup}}, \code{\link[PGRdup]{MergeProbDup}}
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' \dontrun{
 #' # Load PGR passport database
 #' GN <- GN1000
@@ -70,6 +80,12 @@
 #' GNdupSplit <- SplitProbDup(GNdup, splitat = c(10, 10, 10))
 #' 
 #' }
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @import data.table
 #' @importFrom methods is
 #' @export

diff --git a/R/ViewProbDup.R b/R/ViewProbDup.R
@@ -79,6 +79,16 @@
 #'   grouped together using \code{\link[gridExtra]{gridExtra-package}}.
 #'   
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' \dontrun{
 #' 
 #' # Method "b and c"
@@ -146,7 +156,13 @@
 #'library(gridExtra)                                                    
 #'grid.arrange(GNdupcView$SummaryGrob)                          
 #' 
-#' }       
+#' }   
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#'     
 #' @seealso \code{\link[PGRdup]{ProbDup}}, \code{\link[PGRdup]{DisProbDup}}, 
 #'   \code{\link[PGRdup]{DataClean}}, \code{\link[ggplot2]{ggplot}}, 
 #'   \code{\link[gridExtra]{gridExtra-package}}

diff --git a/R/read.genesys.R b/R/read.genesys.R
@@ -44,11 +44,27 @@
 #'   to console.
 #' @return A data.frame with the flat file form of the genesys data.
 #' @examples
+#' 
+#' \dontshow{
+#' threads_dt <- data.table::getDTthreads()
+#' threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT")
+#' data.table::setDTthreads(2)
+#' 
+#' data.table::setDTthreads(2)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = 2)
+#' }
+#' 
 #' \dontrun{
 #' # Import the DwC-Germplasm zip archive "genesys-accessions-filtered.zip"
 #' PGRgenesys <- read.genesys("genesys-accessions-filtered.zip",
 #'                            scrub.names.space = TRUE, readme = TRUE)
 #' }
+#' 
+#' \dontshow{
+#' data.table::setDTthreads(threads_dt)
+#' Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP)
+#' }
+#' 
 #' @seealso \code{\link[data.table]{data.table}}
 #' 
 #' @import data.table

diff --git a/man/AddProbDup.Rd b/man/AddProbDup.Rd