diff --git a/R/AddProbDup.R b/R/AddProbDup.R index b4928ad..9a0c214 100644 --- 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 index 2fccae8..5ffd61e 100644 --- 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 index 89166be..d8869f0 100644 --- 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 index 165bcab..8c57807 100644 --- 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 index 9e91a37..324da31 100644 --- 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 index 80b7efc..bc84553 100644 --- 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 index 327584a..d00ce30 100644 --- 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 index e974714..026977e 100644 --- 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 index 41eaf70..f69f6b4 100644 --- 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 index 89944d9..e4a8487 100644 --- 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 index 0173ef6..df0e3cd 100644 --- 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 index 964e43b..a0c8e45 100644 --- 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 index 21cf633..5cabe13 100644 --- a/man/AddProbDup.Rd +++ b/man/AddProbDup.Rd @@ -52,6 +52,16 @@ When any primary ID/key records in the fuzzy, phonetic or semantic on the database \code{db} before running this function. } \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 @@ -95,6 +105,12 @@ GNdup <- ProbDup(kwic1 = GNKWIC, method = "a", excep = exep, fuzzy = TRUE, 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}}, diff --git a/man/DisProbDup.Rd b/man/DisProbDup.Rd index 661a454..564e47d 100644 --- a/man/DisProbDup.Rd +++ b/man/DisProbDup.Rd @@ -37,6 +37,16 @@ as an additional data frame \code{DisjointDuplicates} in an object of class \code{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 @@ -86,6 +96,12 @@ disGNdup2 <- DisProbDup(GNdup, combine = c("F", "P", "S")) lapply(disGNdup2, nrow) } + +\dontshow{ +data.table::setDTthreads(threads_dt) +Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP) +} + } \seealso{ \code{\link[PGRdup]{ProbDup}} diff --git a/man/KWCounts.Rd b/man/KWCounts.Rd index 6de8a99..bd39595 100644 --- a/man/KWCounts.Rd +++ b/man/KWCounts.Rd @@ -39,6 +39,16 @@ 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 @@ GNKWCouts <- KWCounts(GN, GNfields, exep) 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}} diff --git a/man/KWIC.Rd b/man/KWIC.Rd index 4333a0c..f1e3997 100644 --- a/man/KWIC.Rd +++ b/man/KWIC.Rd @@ -42,6 +42,16 @@ Cleaning of the data the input fields(columns) using the suggested before running this function. } \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 @@ -69,6 +79,12 @@ GN[1001:1005,] <- GN[1:5,] GN[1001,3] <- "" GNKWIC <- KWIC(GN, GNfields) } + +\dontshow{ +data.table::setDTthreads(threads_dt) +Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP) +} + } \references{ Kn\enc{ΓΌ}{ue}pffer, H. 1988. "The European Barley Database of the ECP/GR: diff --git a/man/MergeProbDup.Rd b/man/MergeProbDup.Rd index 1571aac..942cc84 100644 --- a/man/MergeProbDup.Rd +++ b/man/MergeProbDup.Rd @@ -20,6 +20,16 @@ An object of class \code{ProbDup} with the merged list of fuzzy, phonetic one. } \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 @@ -65,6 +75,12 @@ GNdupSplit <- SplitProbDup(GNdup, splitat = c(10, 10, 10)) GNdupMerged <- MergeProbDup(GNdupSplit[[1]], GNdupSplit[[3]]) } + +\dontshow{ +data.table::setDTthreads(threads_dt) +Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP) +} + } \seealso{ \code{\link[PGRdup]{ProbDup}}, \code{\link[PGRdup]{SplitProbDup}} diff --git a/man/ParseProbDup.Rd b/man/ParseProbDup.Rd index bfb3ccf..a52369b 100644 --- a/man/ParseProbDup.Rd +++ b/man/ParseProbDup.Rd @@ -31,6 +31,16 @@ A data frame of the long/narrow form of the probable duplicate sets \code{ParseProbDup} converts an object of class \code{ProbDup} to a data frame for export. } \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 @@ -74,6 +84,12 @@ GNdup <- ProbDup(kwic1 = GNKWIC, method = "a", excep = exep, fuzzy = TRUE, GNdupParsed <- ParseProbDup(GNdup) } + +\dontshow{ +data.table::setDTthreads(threads_dt) +Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP) +} + } \seealso{ \code{\link[PGRdup]{ProbDup}}, diff --git a/man/ProbDup.Rd b/man/ProbDup.Rd index 802f6e9..acfa8f8 100644 --- a/man/ProbDup.Rd +++ b/man/ProbDup.Rd @@ -191,6 +191,16 @@ As the number of keywords in the KWIC indexes increases, the memory function, which is made use of here for string matching. } \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" @@ -294,6 +304,12 @@ GNdupc <- ProbDup(kwic1 = GN1KWIC, kwic2 = GN2KWIC, method = "c", GNdupc } + +\dontshow{ +data.table::setDTthreads(threads_dt) +Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP) +} + } \references{ van der Loo, M. P. J. 2014. "The Stringdist Package for diff --git a/man/ReconstructProbDup.Rd b/man/ReconstructProbDup.Rd index 640130a..c9d0441 100644 --- a/man/ReconstructProbDup.Rd +++ b/man/ReconstructProbDup.Rd @@ -35,6 +35,16 @@ identical integers in the column \code{SPLIT} other than the default \code{0} are reassembled into a new set. } \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 @@ -100,6 +110,12 @@ lapply(disGNdup, nrow) 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}} diff --git a/man/ReviewProbDup.Rd b/man/ReviewProbDup.Rd index 8455f1d..6e068a1 100644 --- a/man/ReviewProbDup.Rd +++ b/man/ReviewProbDup.Rd @@ -101,6 +101,16 @@ When any primary ID/key records in the fuzzy, phonetic or semantic which may be safely ignored. } \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 @@ -154,6 +164,12 @@ RevGNdup <- edit(RevGNdup) write.csv(file="Duplicate sets for review.csv", x=RevGNdup) } + +\dontshow{ +data.table::setDTthreads(threads_dt) +Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP) +} + } \seealso{ \code{\link[PGRdup]{DataClean}}, \code{\link[PGRdup]{KWIC}}, diff --git a/man/SplitProbDup.Rd b/man/SplitProbDup.Rd index 168f065..096177b 100644 --- a/man/SplitProbDup.Rd +++ b/man/SplitProbDup.Rd @@ -22,6 +22,16 @@ A list with the the divided objects of class \code{ProbDup} basis of set counts. } \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 @@ -64,6 +74,12 @@ GNdup <- ProbDup(kwic1 = GNKWIC, method = "a", excep = exep, fuzzy = TRUE, GNdupSplit <- SplitProbDup(GNdup, splitat = c(10, 10, 10)) } + +\dontshow{ +data.table::setDTthreads(threads_dt) +Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP) +} + } \seealso{ \code{\link[PGRdup]{ProbDup}}, \code{\link[PGRdup]{MergeProbDup}} diff --git a/man/ViewProbDup.Rd b/man/ViewProbDup.Rd index 133e293..4a16bd3 100644 --- a/man/ViewProbDup.Rd +++ b/man/ViewProbDup.Rd @@ -90,6 +90,16 @@ When any primary ID/key records in the fuzzy, phonetic or semantic 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" @@ -157,7 +167,13 @@ GNdupcView <- ViewProbDup(GNdupc, GN1, GN2, "SourceCountry", "SourceCountry", 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}}, diff --git a/man/read.genesys.Rd b/man/read.genesys.Rd index e5759bf..d4438bf 100644 --- a/man/read.genesys.Rd +++ b/man/read.genesys.Rd @@ -41,11 +41,27 @@ The argument \code{readme} can be used to print the readme file in the archive to console, if required. } \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}} diff --git a/src/PGRdup.so b/src/PGRdup.so index 57eaa09..98f516e 100644 Binary files a/src/PGRdup.so and b/src/PGRdup.so differ diff --git a/vignettes/Introduction.Rmd b/vignettes/Introduction.Rmd index 9960580..b223d0c 100644 --- a/vignettes/Introduction.Rmd +++ b/vignettes/Introduction.Rmd @@ -49,6 +49,15 @@ out_type <- ifelse(identical (out_type, vector(mode = "logical", length = 0)), "latex", out_type) ``` +```{r, echo=FALSE} +# Restrict threads for avoid elapsed threshold error in CRAN check +threads_dt <- data.table::getDTthreads() +threads_OMP <- Sys.getenv("OMP_THREAD_LIMIT") + +data.table::setDTthreads(2) +Sys.setenv(`OMP_THREAD_LIMIT` = 2) +``` + ```{r, results='asis', echo=FALSE} switch(out_type, html = {cat("

1. ICAR-National Bureau of Plant Genetic Resources, New Delhi, India.

@@ -1283,3 +1292,9 @@ sessionInfo() ``` ## References + +```{r, echo=FALSE} +data.table::setDTthreads(threads_dt) +Sys.setenv(`OMP_THREAD_LIMIT` = threads_OMP) +``` + diff --git a/vignettes/Introduction.pdf b/vignettes/Introduction.pdf index 4933c45..2d7a714 100644 Binary files a/vignettes/Introduction.pdf and b/vignettes/Introduction.pdf differ