Running 'add.R' [1s]
  Running 'ade4-functions.R' [1s]
  Running 'adegraphics.R' [1s]
  Running 'nbgraph.R' [3s]
  Running 'panelSpatial.R' [2s]
  Running 'parameter.R' [3s]
  Running 's.arrow.R' [1s]
  Running 's.class.R' [1s]
  Running 's.corcircle.R' [1s]
  Running 's.density.R' [5s]
  Running 's.distri.R' [1s]
  Running 's.image.R' [4s]
  Running 's.label.R' [2s]
  Running 's.logo.R' [2s]
  Running 's.match.R' [2s]
  Running 's.traject.R' [2s]
  Running 's.value.R' [3s]
  Running 's1d.barchart.R' [2s]
  Running 's1d.boxplot.R' [2s]
  Running 's1d.class.R' [1s]
  Running 's1d.density.R' [3s]
  Running 's1d.distri.R' [2s]
  Running 's1d.gauss.R' [1s]
  Running 's1d.hist.R' [2s]
  Running 's1d.label.R' [1s]
  Running 's1d.match.R' [2s]
  Running 'table.image.R' [2s]
  Running 'table.value.R' [1s]
  Running 'triangle.R' [3s]
Running the tests in 'tests/add.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("add.pdf")
  > set.seed(40)
  > 
  > ########################### add.ADEg ##############################
  > 
  > data(granulo, package = "ade4")
  > df <- data.frame(t(apply(granulo$tab, 1, function(x) x / sum(x))))
  > pca <- ade4::dudi.pca(df, scal = FALSE, scan = FALSE)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/ade4-functions.R' failed.
Complete output:
  > ## delete/remove this file when 'scatter' functions will be removed in ade4
  > 
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("ade4-functions.pdf")
  > 
  > ##################### scatter.dudi
  > data(deug, package = "ade4")
  > dd1 <- ade4::dudi.pca(deug$tab, scannf = FALSE, nf = 4)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/adegraphics.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("adegraphics.pdf")
  > 
  > xy <- cbind.data.frame(runif(7), runif(7))
  > g1 <- s.label(xy)
  > 
  > data(olympic, package = "ade4")
  > pca <- ade4::dudi.pca(olympic$tab, scan = FALSE)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/panelSpatial.R' failed.
Complete output:
  > library(ade4)
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  
  Attaching package: 'adegraphics'
  
  The following objects are masked from 'package:ade4':
  
      kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
      s.label, s.logo, s.match, s.traject, s.value, table.value,
      triangle.class
  
  > library(sp)
  > pdf("panelSpatial.pdf")
  > 
  > ## ex1
  > data(mafragh, package = "ade4")
  > dfxy1 <- coordinates(mafragh$Spatial)
  > g1 <- s.label(dfxy1, Sp = mafragh$Spatial, pSp.col = colorRampPalette(c("yellow", "blue"))(97), pgrid.draw = FALSE, plabels.cex = 0)
  > 
  > 
  > ## ex2
  > data(meuse, package = "sp")
  > coordinates(meuse) <- ~ x + y
  > data(meuse.grid, package = "sp")
  > m <- SpatialPixelsDataFrame(points = meuse.grid[c("x", "y")], data = meuse.grid)
  > data(meuse.riv)
  > meuse.sr <- SpatialPolygons(list(Polygons(list(Polygon(meuse.riv)), "meuse.riv")))
  > 
  > scale1 <- list("SpatialPolygonsRescale", offset = c(179900, 329600), scale = 500, fill = c("transparent", "black"), layout.scale.bar())
  > text11 <- list("sp.text", c(179900, 329700), "0")
  > text21 <- list("sp.text", c(180400, 329700), "500 m")
  > arrow1 <- list("SpatialPolygonsRescale", offset = c(178750, 332500), scale = 400, layout.north.arrow())
  > river <- list("sp.polygons", meuse.sr, fill = "lightblue")
  > dfxy2 <- as.data.frame(coordinates(meuse))
  > g2 <- s.value(dfxy2, z = meuse[, 1]$cadmium, sp.layout = list(scale1, text11, text21, arrow1, river), Sp = m)
  > 
  > fac <- meuse@data$ffreq
  > levels(fac)[1] <- "1 in 2 years"
  > levels(fac)[2] <- "1 in 10 years"
  > levels(fac)[3] <- "1 in 50 years"
  > arrow2 <- list("SpatialPolygonsRescale", layout.north.arrow(), offset = c(181750, 330000), scale = 400)
  > scale2 <- list("SpatialPolygonsRescale", layout.scale.bar(), offset =  c(178050, 333600), scale = 500, fill = c("transparent", "black"))
  > text12 <- list("sp.text", c(178050, 333700), "0")
  > text22 <- list("sp.text", c(178550, 333700), "500 m")
  > g3 <- s.class(dfxy2, fac = fac, sp.layout = list(scale2, text12, text22, arrow2, river), starSize = 1, col = c(1, 2, 4), pellipses.col = c(1, 2, 4), 
  +   pellipses.alpha = 0.7, plines.lty = 3, psub.text = "Flooding frequency \n near the Meuse river", psub.pos = c(0.2, 0.88), pgrid.text.cex = 0,
  +   porigin.include = FALSE, Sp = meuse.sr)
  Error in crossprod(x) : "crossprod" is not a BUILTIN function
  Calls: s.class ... prepare -> prepare -> covfacwt -> lapply -> FUN -> covwt
  Execution halted
Running the tests in 'tests/parameter.R' failed.
Complete output:
  > library(ade4)
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  
  Attaching package: 'adegraphics'
  
  The following objects are masked from 'package:ade4':
  
      kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
      s.label, s.logo, s.match, s.traject, s.value, table.value,
      triangle.class
  
  > pdf("parameter.pdf")
  > 
  > adegparold <- adegpar()
  > b1 <- length(adegraphics:::separation(plines = list(col = "blue"), plab.bo.dra = FALSE, plab = list(orien = F))$rest) == 0
  > b2 <- length(adegraphics:::separation(plines = list(col = "blue", lwd = c(1:5)), parr.end = NA, plab.boxes.dr = FALSE)$rest) == 0
  > b3 <- length(adegraphics:::separation(plot.li = list(col = "blue", lwd = c(1:5)), par.end = NA, pl.boxes.draw = FALSE, pattern = 1)$rest) == 2
  > b4 <- length(adegraphics:::separation(plot.li = list(col = "blue", lwd = c(1:5)), par.end = NA, pl.boxes.draw = FALSE, pattern = 0)$rest) == 2
  > b5 <- length(adegraphics:::separation()) == 2
  > b6 <- length(adegraphics:::separation(par.sub.text = list("lineheight" = 5), pattern = 1)$rest) == 0
  > b7 <- names(adegraphics:::separation(toto = "rienavoir!")$rest) == "toto"
  > b8 <- names(adegraphics:::separation(toto = "rienavoir!", pattern = 1)$rest) == "toto"
  > 
  > l1 <- list(parrow = list(col = "blue", lwd = c(1:5), end = NA), plboxes.draw = FALSE, pattern = 1)
  > sep1 <- adegraphics:::separation(l1)  ## no recognition of "pattern" in a list
  > 
  > l2 <- list("parrow.lwd", "plboxes.draw")
  > sep2 <- adegraphics:::separation(l2)
  > 
  > sep3 <- adegraphics:::separation("plboxes" = list("draw" = FALSE, "col"))
  > sep4 <- adegraphics:::separation("plboxes" = list("draw" = FALSE, "col" = 2))
  > sep5 <- adegraphics:::separation(pla.box = list(col = 1:5))
  > sep6 <- adegraphics:::separation(pla.box.col = c(1:5))
  > sep7 <- adegraphics:::separation(pla = list(box.col = 1:5))  ## don't match
  > 
  > 
  > ## adegpar test
  > ad1 <- adegpar()
  > ad2 <- adegpar("paxes.draw")
  > ad3 <- adegpar("paxes.draw", "psub.cex")
  > 
  > ad4 <- adegpar("psub.cex" = 5)
  > ad5 <- adegpar("psub.cex" = 5, paxes.draw = FALSE)
  > ad6 <- adegpar("psub")
  > ad7 <- adegpar("psub.cex", "plabe.boxes")
  > 
  > ad8 <- adegpar(ppoints = list(col = "yellow"), pgrid.space = 4, plines = list(lwd = c(1:5)))
  > ad9 <- adegpar(ppoints = list(col = "red"), pgrid = list(nint = 12), plines = list(lwd = c(1:5)))
  > ad10 <- adegpar("ppoints.col", "pgrid.nint", "plines")
  > 
  > ad11 <- adegpar(paxes = list("x"), pgrid = list("nint", "col"))
  > ad12 <- adegpar(list(pellip = list(col = "red"), grid.nint = 8, plines = list(lwd = c(1:5))))
  > ad13 <- adegpar(paxes = list("x"), pgrid = list("nint", "col"), "plines", "pellipse")
  > 
  > ad14 <- adegpar(plegend.drawKey = FALSE)
  > ad15 <- adegpar(list(paxes = list(col = "white"), pgrid.nint = 6, plines = list(lwd = c(1:5))))
  > ad16 <- adegpar(paxes = list(x = list(draw = TRUE)))
  > 
  > adegpar(adegparold)
  > 
  > ## merging list
  > l3 <- list(plabels = list(boxes = list(col = "white", alpha = 1)), plabels = list(cex = 2), plabels = list(col = "red"))
  > adegraphics:::.mergingList(l3)
  $plabels
  $plabels$boxes
  $plabels$boxes$col
  [1] "white"
  
  $plabels$boxes$alpha
  [1] 1
  
  
  $plabels$cex
  [1] 2
  
  $plabels$col
  [1] "red"
  
  
  > adegraphics:::.mergingList(list(plabels = list(cex = 3)))
  $plabels
  $plabels$cex
  [1] 3
  
  
  > 
  > 
  > ## update parameters in graphics
  > cha <- rep(LETTERS, length.out = 100)
  > xy <- cbind.data.frame(runif(length(cha)), runif(length(cha)))
  > g1 <- s.label(xy, labels = cha, paxes.draw = TRUE, plabels.cex = runif(length(cha), 0.5, 1.5))
  > update(g1, paxes = list(aspect = "fill", draw = TRUE, x = list(draw = FALSE)), 
  +   pgrid = list(col = "black", lwd = 2, lty = 5), 
  +   plabels = list(col = 1:4, alpha = 0.5, cex = 2, boxes = list(border = "blue", col = "antiquewhite", alpha = 0.2, lwd = 2.5, lty = 5))) 
  > 
  > g2 <- s.label(xy, labels = cha)
  > update(g2, paxes.draw = FALSE, pgrid = list(col = "blue", lwd = 2, lty = 5, text = list(pos = "bottomright", cex = 2, col = "green")))
  > update(g2, porigin = list(alpha = 0.5, col = "red", lty = 5 , lwd = 2, origin = c(0.6, 0.1)), pgrid.lwd = 0.5)
  > update(g2, psub = list(text = "parameters", cex = 2, col = "red", position = "topright"))
  > update(g2, plabels.cex = 0, ppoints = list(alpha = 0.4, cex = 2, col = "red", fill = "blue", pch = 21))
  > 
  > 
  > ## from tdr641
  > data(doubs, package = "ade4")
  > dudi1 <- ade4::dudi.pca(doubs$env, scale = T, scannf = F, nf = 3)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/s.arrow.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.arrow.pdf")
  > 
  > ## ex1 : from tdr641
  > data(doubs, package = "ade4") 
  > dudi1 <- ade4::dudi.pca(doubs$env, scale = T, scan = F, nf = 3)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/s.class.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.class.pdf")
  > 
  > xy0 <- cbind.data.frame(x = runif(20, -1, 1), y = runif(20, -1, 6))
  > basic <- s.class(xy0, fac = factor(rep(c("A", "B"), le = 20)), chull = 0, star = 0)
  Error in crossprod(x) : "crossprod" is not a BUILTIN function
  Calls: s.class ... prepare -> prepare -> covfacwt -> lapply -> FUN -> covwt
  Execution halted
Running the tests in 'tests/s.corcircle.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.corcircle.pdf")
  > data(olympic, package = "ade4")
  > 
  > dudi1 <- ade4::dudi.pca(olympic$tab, scan = FALSE) # a normed PCA
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/s.distri.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.distri.pdf")
  > 
  > xy5 <- cbind.data.frame(x = runif(200, -1, 1), y = runif(200, -1, 1))
  > w1 <- as.numeric((xy5$x > 0) & (xy5$y > 0))
  > w2 <- ((xy5$x > 0) & (xy5$y < 0)) * (1 - xy5$y) * xy5$x
  > w3 <- ((xy5$x < 0) & (xy5$y > 0)) * (1 - xy5$x) * xy5$y
  > w4 <- ((xy5$x < 0) & (xy5$y < 0)) * xy5$y * xy5$x
  > distri <- data.frame(a = w1 / sum(w1), b = w2 / sum(w2), c = w3 / sum(w3), d = w4 / sum(w4))
  > g5 <- s.distri(xy5, distri, plabels.boxes = list(col = "white", alpha = 1), plabels.cex = 2, plabels.col = 1:5)
  Error in crossprod(x) : "crossprod" is not a BUILTIN function
  Calls: s.distri -> prepare -> prepare -> lapply -> FUN -> covwt
  Execution halted
Running the tests in 'tests/s.value.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s.value.pdf")
  > 
  > ## ex1
  > xy <- cbind.data.frame(x = runif(50, -1, 1), y = runif(50, 0, 2))
  > z <- rnorm(50)
  > z <- sapply(z, function(X) max(X, -3))
  > z <- sapply(z, function(X) min(X, 3))
  > val1 <- s.value(xy, z, method = "size", symbol = "square", plot = F)
  > val2 <- s.value(xy, z, method = "color", symbol = "square", plot = F)
  > val3 <- s.value(xy, z, method = "size", symbol = "circle", plot = F)
  > val4 <- s.value(xy, z, method = "color", symbol = "circle", plot = F)
  > g1 <- ADEgS(c(val1, val2, val3, val4), positions = layout2position(matrix(c(1, 2, 3, 4), 2, 2)), add = matrix(0, ncol = 4, nrow = 4))
  > g2 <- s.value(xy, z, method = "color", symbol = "square", breaks = c(-3, -1, -0.5, 0, 0.5, 1, 3))
  > g3 <- s.value(xy, z, method = "color", col = colorRampPalette(c("yellow", "blue"))(6))
  > g4 <- s.value(xy, z, method = "size", symbol = "circle", paxes.draw = FALSE)
  > 
  > ## ex2
  > xx <- runif(100) * 100
  > yy <- 1:100 
  > zz <- 1:100
  > breaks <- c(0, 25, 50, 75, 100)
  > g5 <- s.value(data.frame(xx, yy), zz, breaks = breaks, method = "color", paxes.draw = TRUE,  porigin.include = FALSE)
  > g6 <- s.value(data.frame(xx, yy), cbind(zz, rev(zz)), breaks = breaks, method = "color", col = c("blue", "red", "green", "yellow"), paxes.draw = TRUE)
  > g7 <- s.value(data.frame(xx, yy), cbind(zz, rev(zz)), nclass = c(2, 6), method = "color", col = c("blue", "red", "pink", "green", "yellow"), paxes.draw = TRUE)
  > 
  > ## ex3
  > data(rpjdl, package = "ade4")
  > fau.coa <- ade4::dudi.coa(rpjdl$fau, scan = FALSE, nf = 3)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/s1d.barchart.R' failed.
Complete output:
  > library(ade4)
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  
  Attaching package: 'adegraphics'
  
  The following objects are masked from 'package:ade4':
  
      kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
      s.label, s.logo, s.match, s.traject, s.value, table.value,
      triangle.class
  
  > pdf("s1d.barchart.pdf")
  > 
  > ## 1 : reverse and horizontal
  > set.seed(40)
  > x1 <- rnorm(10)
  > g11 <- s1d.barchart(x1)
  > g12 <- s1d.barchart(x1, ppoly.col = "blue")
  > 
  > g21 <- s1d.barchart(x1, p1d.hori = FALSE, p1d.rev = TRUE)
  > g23 <- s1d.barchart(x1, p1d.hori = FALSE, p1d.rev = FALSE)
  > g24 <- s1d.barchart(x1, p1d.hori = TRUE, p1d.rev = TRUE)
  > g24 <- s1d.barchart(x1, p1d.hori = TRUE, p1d.rev = FALSE)
  > 
  > ## 2 : at and sort
  > data(rpjdl, package = "ade4")
  > rpjdl.coa <- ade4::dudi.coa(rpjdl$fau, scannf = FALSE, nf = 4)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/s1d.boxplot.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s1d.boxplot.pdf")
  > 
  > ## ex1
  > x <- c(rnorm(10), rnorm(10))
  > fact <- factor(rep(c("A", "B"), 10))
  > g11 <- s1d.boxplot(x, fact)
  > g12 <- s1d.boxplot(x, fact, col = TRUE)
  > g12 <- s1d.boxplot(x, fact, col = 2:3)
  > g12 <- s1d.boxplot(x, fact, col = TRUE, plines.col = "black")
  > 
  > g2 <- s1d.boxplot(x, fact, ppolygon.border = c("red", "blue"), box.rectangle = list(alpha = 1, fill = "green"))
  > 
  > ## ex2
  > w1 <- rnorm(100, -1)
  > w2 <- rnorm(100)
  > w3 <- rnorm(100, 1)
  > f1 <- gl(3, 100)
  > f2 <- gl(30, 10)
  > g3 <- s1d.boxplot(c(w1, w2, w3), f1)
  > g4 <- s1d.boxplot(c(w1, w2, w3), f2)
  > g5 <- s1d.boxplot(c(w1, w2, w3), f2, p1d.rug.draw = FALSE)
  > 
  > mat <- matrix(0, ncol = 1, nrow = 8)
  > mat[c(2), ] <- 1
  > mat[c(3:8), ] <- 2
  > mat[1, ] <- 3
  > g6 <- ADEgS(c(g3, g4, s1d.label(c(w1, w2, w3), p1d = list(rug = list(tck = 0.8), rev = TRUE), ppoints.cex = 0, plabels.cex = 0, plot = F, pgrid.draw = F)), 
  +   layout = matrix((rev(mat)), ncol = 1))
  > g7 <- s1d.boxplot(c(w1, w2, w3), data.frame(f1, f2))
  > 
  > ## ex3
  > data(banque, package = "ade4")
  > banque.acm <- ade4::dudi.acm(banque, scan = FALSE, nf = 4)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/s1d.class.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s1d.class.pdf")
  > data(meau, package = "ade4")
  > 
  > ## ex1
  > envpca <- ade4::dudi.pca(meau$env, scannf = FALSE)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/s1d.gauss.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s1d.gauss.pdf")
  > 
  > data(meau, package= "ade4")
  > envpca <- ade4::dudi.pca(meau$env, scannf = FALSE)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/s1d.hist.R' failed.
Complete output:
  > library(ade4)
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  
  Attaching package: 'adegraphics'
  
  The following objects are masked from 'package:ade4':
  
      kplotsepan.coa, s.arrow, s.class, s.corcircle, s.distri, s.image,
      s.label, s.logo, s.match, s.traject, s.value, table.value,
      triangle.class
  
  > pdf("s1d.hist.pdf")
  > 
  > set.seed(40)
  > x1 <- rnorm(1000)
  > g11 <- s1d.hist(x1)
  > g12 <- s1d.hist(x1, col = 1:10)
  > g13 <- s1d.hist(x1, col = FALSE, ppoly.col = 1:10)
  > g14 <- s1d.hist(x1, col = TRUE, ppoly.col = "blue")
  > 
  > set.seed(50)
  > x1 <- rnorm(1000)
  > g21 <- s1d.hist(x1) # p1d.hori = TRUE and p1d.reverse = FALSE by default
  > # g22 <- s1d.hist(x1, p1d.hori = TRUE,  p1d.rev = TRUE)
  > g23 <- s1d.hist(x1, p1d.hori = FALSE, p1d.rev = FALSE)
  > # g24 <- s1d.hist(x1, p1d.hori = FALSE, p1d.rev = TRUE)
  > 
  > 
  > # randtest.pcaiv
  > data(rpjdl, package = "ade4")
  > millog <- log(rpjdl$mil + 1)
  > coa1 <- dudi.coa(rpjdl$fau, scann = FALSE)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: dudi.coa -> as.dudi
  Execution halted
Running the tests in 'tests/s1d.label.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("s1d.label.pdf")
  > data(meau, package= "ade4")
  > 
  > envpca <- ade4::dudi.pca(meau$env, scannf = FALSE)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/table.image.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("table.image.pdf")
  > 
  > ## ex1
  > x <- 1:4
  > y <- 1:4
  > df <- data.frame(as.matrix(cbind(x, y)))
  > g1 <- table.image(df, col = 2:4)
  > update(g1, plegend.drawColorKey = TRUE)
  > 
  > ## ex2
  > df <- matrix(0, 10, 10)
  > df[1:3, 1:3] <- 5        
  > g2 <- table.image(df)
  > g3 <- table.image(df, breaks = c(5, 2, 0))
  > 
  > ## ex3
  > data(rpjdl, package = "ade4")
  > X <- data.frame(t(rpjdl$fau))
  > Y <- data.frame(t(rpjdl$mil))
  > coa1 <- ade4::dudi.coa(X, scan = FALSE)
  Error in tcrossprod(df, df) : "tcrossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/table.value.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("table.value.pdf")
  > 
  > 
  > ## ex1
  > data(olympic, package = "ade4")
  > tab1 <- data.frame(scale(olympic$tab))
  > pca <- ade4::dudi.pca(tab1, scann = FALSE)
  Error in crossprod(df, df) : "crossprod" is not a BUILTIN function
  Calls: <Anonymous> -> as.dudi
  Execution halted
Running the tests in 'tests/triangle.R' failed.
Complete output:
  > library(adegraphics)
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  Registered S3 methods overwritten by 'adegraphics':
    method         from
    biplot.dudi    ade4
    kplot.foucart  ade4
    kplot.mcoa     ade4
    kplot.mfa      ade4
    kplot.pta      ade4
    kplot.sepan    ade4
    kplot.statis   ade4
    scatter.coa    ade4
    scatter.dudi   ade4
    scatter.nipals ade4
    scatter.pco    ade4
    score.acm      ade4
    score.mix      ade4
    score.pca      ade4
    screeplot.dudi ade4
  > pdf("triangle.pdf")
  > 
  > ## ex1
  > data(euro123, package = "ade4")
  > 
  > dfxyz1 <- rbind.data.frame(euro123$in78, euro123$in86, euro123$in97)
  > row.names(dfxyz1) <- paste(row.names(euro123$in78), rep(c(1, 2, 3), rep(12, 3)), sep = "")
  > g1 <- triangle.label(dfxyz1, label = row.names(dfxyz1))
  > g2 <- triangle.label(euro123$in86, label = row.names(euro123$in78), plab.cex = 0.8)
  > g3 <- triangle.match(euro123$in78, euro123$in86)
  > g4 <- triangle.label(rbind.data.frame(euro123$in78, euro123$in86), plab.cex = 1, addaxes = TRUE, psub = list(text = "Principal axis", cex = 2, pos = "topright"))
  > g5 <- triangle.label(euro123[[1]], min3 = c(0, 0.2, 0.3), max3 = c(0.5, 0.7, 0.8), plabels.cex = 1, label = row.names(euro123[[1]]), addax = TRUE)
  > g6 <- triangle.label(euro123[[2]], min3 = c(0, 0.2, 0.3), max3 = c(0.5, 0.7, 0.8), label = row.names(euro123[[1]]), addax = TRUE)
  > g7 <- triangle.label(euro123[[3]], min3 = c(0, 0.2, 0.3), max3 = c(0.5, 0.7, 0.8), label = row.names(euro123[[1]]), addax = TRUE)
  > g8 <- triangle.label(rbind.data.frame(euro123[[1]], euro123[[2]], euro123[[3]]))
  > 
  > ## ex2
  > dfxyz2 <- cbind.data.frame(a = runif(100), b = runif(100), c = runif(100, 4, 5))
  > g9 <- triangle.label(dfxyz2)
  > 
  > ## ex3
  > g10 <- triangle.label(dfxyz1)
  > g11 <- triangle.class(dfxyz1, as.factor(rep("G", 36)), star = 0.5, ellips = 1)
  Error in crossprod(x) : "crossprod" is not a BUILTIN function
  Calls: triangle.class ... prepare -> prepare -> covfacwt -> lapply -> FUN -> covwt
  Execution halted