R Development Page

mixOmics log file (check_x86_64_linux)

Fri Feb 15 13:04:50 2013: Checking package mixOmics (SVN revision 95) ...
* using log directory ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/mixOmics.Rcheck’
* using R version 2.15.2 Patched (2013-02-13 r61942)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘mixOmics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mixOmics’ version ‘3.0-1’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Kim-Anh Le Cao ’
New submission
Package was archived on CRAN
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking whether package ‘mixOmics’ can be installed ... [3s/8s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function call with ‘PACKAGE’ argument in a base package:
  .C("bincode", ..., PACKAGE = "base")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* checking R code for possible problems ... NOTE
image.estim.regul: warning in axis(4, at = midpoints, label =
  round(midpoints, 3)): partial argument match of 'label' to 'labels'
image.estim.regul: warning in axis(4, at = midpoints[binwidth], label =
  round(midpoints[binwidth], 3)): partial argument match of 'label' to
  'labels'
jet.colors: warning in rgb(ramp(seq(0, 1, length = n)), max = 255):
  partial argument match of 'max' to 'maxColorValue'
plot3dIndiv.ipca: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex): partial argument match of 'text' to
  'texts'
plot3dIndiv.ipca: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex[1]): partial argument match of 'text' to
  'texts'
plot3dIndiv.pca: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex): partial argument match of 'text' to
  'texts'
plot3dIndiv.pca: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex[1]): partial argument match of 'text' to
  'texts'
plot3dIndiv.pls: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex): partial argument match of 'text' to
  'texts'
plot3dIndiv.pls: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex[1]): partial argument match of 'text' to
  'texts'
plot3dIndiv.plsda: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex): partial argument match of 'text' to
  'texts'
plot3dIndiv.plsda: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex[1]): partial argument match of 'text' to
  'texts'
plot3dIndiv.rcc: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex): partial argument match of 'text' to
  'texts'
plot3dIndiv.rcc: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex[1]): partial argument match of 'text' to
  'texts'
plot3dIndiv.sipca: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex): partial argument match of 'text' to
  'texts'
plot3dIndiv.sipca: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex[1]): partial argument match of 'text' to
  'texts'
plot3dIndiv.spca: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex): partial argument match of 'text' to
  'texts'
plot3dIndiv.spca: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex[1]): partial argument match of 'text' to
  'texts'
plot3dIndiv.spls: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex): partial argument match of 'text' to
  'texts'
plot3dIndiv.spls: warning in text3d(x, y, z, text = ind.names, color =
  col, font = font, cex = cex[1]): partial argument match of 'text' to
  'texts'
plot3dIndiv.splsda: warning in text3d(x, y, z, text = ind.names, color
  = col, font = font, cex = cex): partial argument match of 'text' to
  'texts'
plot3dIndiv.splsda: warning in text3d(x, y, z, text = ind.names, color
  = col, font = font, cex = cex[1]): partial argument match of 'text'
  to 'texts'
plot3dVar.ipca: warning in text3d(cord.X[, 1], cord.X[, 2], cord.X[,
  3], text = var.label, color = col, font = font, cex = cex): partial
  argument match of 'text' to 'texts'
plot3dVar.ipca: warning in text3d(1.2, -0.05, 0, text = xlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.ipca: warning in text3d(0, 1.27, 0, text = ylab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.ipca: warning in text3d(0, -0.05, 1.2, text = zlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.pca: warning in text3d(cord.X[, 1], cord.X[, 2], cord.X[, 3],
  text = var.label, color = col, font = font, cex = cex): partial
  argument match of 'text' to 'texts'
plot3dVar.pca: warning in text3d(1.2, -0.05, 0, text = xlab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.pca: warning in text3d(0, 1.27, 0, text = ylab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.pca: warning in text3d(0, -0.05, 1.2, text = zlab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.pls: warning in text3d(cord.X[, 1] + 0.05, cord.X[, 2],
  cord.X[, 3] + 0.05, text = X.label, color = col[[1]], font = font[1],
  cex = cex[1]): partial argument match of 'text' to 'texts'
plot3dVar.pls: warning in text3d(cord.Y[, 1] + 0.05, cord.Y[, 2],
  cord.Y[, 3] + 0.05, text = Y.label, color = col[[2]], font = font[2],
  cex = cex[2]): partial argument match of 'text' to 'texts'
plot3dVar.pls: warning in text3d(1.2, -0.05, 0, text = xlab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.pls: warning in text3d(0, 1.27, 0, text = ylab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.pls: warning in text3d(0, -0.05, 1.2, text = zlab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.plsda: warning in text3d(cord.X[, 1] + 0.05, cord.X[, 2],
  cord.X[, 3] + 0.05, text = var.label, color = col[[1]], font =
  font[1], cex = cex[1]): partial argument match of 'text' to 'texts'
plot3dVar.plsda: warning in text3d(1.2, -0.05, 0, text = xlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.plsda: warning in text3d(0, 1.27, 0, text = ylab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.plsda: warning in text3d(0, -0.05, 1.2, text = zlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.rcc: warning in text3d(cord.X[, 1] + 0.05, cord.X[, 2],
  cord.X[, 3] + 0.05, text = X.label, color = col[[1]], font = font[1],
  cex = cex[1]): partial argument match of 'text' to 'texts'
plot3dVar.rcc: warning in text3d(cord.Y[, 1] + 0.05, cord.Y[, 2],
  cord.Y[, 3] + 0.05, text = Y.label, color = col[[2]], font = font[2],
  cex = cex[2]): partial argument match of 'text' to 'texts'
plot3dVar.rcc: warning in text3d(1.2, -0.05, 0, text = xlab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.rcc: warning in text3d(0, 1.27, 0, text = ylab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.rcc: warning in text3d(0, -0.05, 1.2, text = zlab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.sipca: warning in text3d(cord.X[, 1] + 0.05, cord.X[, 2],
  cord.X[, 3] + 0.05, text = var.label, color = col[[1]], font =
  font[1], cex = cex[1]): partial argument match of 'text' to 'texts'
plot3dVar.sipca: warning in text3d(1.2, -0.05, 0, text = xlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.sipca: warning in text3d(0, 1.27, 0, text = ylab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.sipca: warning in text3d(0, -0.05, 1.2, text = zlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.spca: warning in text3d(cord.X[, 1] + 0.05, cord.X[, 2],
  cord.X[, 3] + 0.05, text = var.label, color = col[[1]], font =
  font[1], cex = cex[1]): partial argument match of 'text' to 'texts'
plot3dVar.spca: warning in text3d(1.2, -0.05, 0, text = xlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.spca: warning in text3d(0, 1.27, 0, text = ylab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.spca: warning in text3d(0, -0.05, 1.2, text = zlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.spls: warning in text3d(cord.X[, 1] + 0.05, cord.X[, 2],
  cord.X[, 3] + 0.05, text = X.label, color = col[[1]], font = font[1],
  cex = cex[1]): partial argument match of 'text' to 'texts'
plot3dVar.spls: warning in text3d(cord.Y[, 1] + 0.05, cord.Y[, 2],
  cord.Y[, 3] + 0.05, text = Y.label, color = col[[2]], font = font[2],
  cex = cex[2]): partial argument match of 'text' to 'texts'
plot3dVar.spls: warning in text3d(1.2, -0.05, 0, text = xlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.spls: warning in text3d(0, 1.27, 0, text = ylab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.spls: warning in text3d(0, -0.05, 1.2, text = zlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.splsda: warning in text3d(cord.X[, 1] + 0.05, cord.X[, 2],
  cord.X[, 3] + 0.05, text = var.label, color = col[[1]], font =
  font[1], cex = cex[1]): partial argument match of 'text' to 'texts'
plot3dVar.splsda: warning in text3d(1.2, -0.05, 0, text = xlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.splsda: warning in text3d(0, 1.27, 0, text = ylab, cex = 0.8,
  color = "black"): partial argument match of 'text' to 'texts'
plot3dVar.splsda: warning in text3d(0, -0.05, 1.2, text = zlab, cex =
  0.8, color = "black"): partial argument match of 'text' to 'texts'
s.match : arrow1: warning in arrows(x0, y0, x1, y1, ang = ang, len =
  len, lty = lty, col = col): partial argument match of 'len' to
  'length'
s.match : arrow1: warning in arrows(x0, y0, x1, y1, ang = ang, len =
  len, lty = lty, col = col): partial argument match of 'ang' to
  'angle'
scatterutil.legend.bw.square: warning in round(br0, dig = 6): partial
  argument match of 'dig' to 'digits'
scatterutil.legend.bw.square: warning in symbols(x0, y0, squares = z0,
  bg = "black", fg = "white", add = TRUE, inch = FALSE): partial
  argument match of 'inch' to 'inches'
scatterutil.legend.bw.square: warning in symbols(x0, y0, squares = z0,
  bg = "white", fg = "black", add = TRUE, inch = FALSE): partial
  argument match of 'inch' to 'inches'
scatterutil.legend.square.grey: warning in round(br0, dig = 6): partial
  argument match of 'dig' to 'digits'
scatterutil.legend.square.grey: warning in symbols(x0, y0, squares = h,
  bg = gray(valgris[i - 1]), add = TRUE, inch = FALSE): partial
  argument match of 'inch' to 'inches'
scatterutil.legend.square.grey: warning in round(cha, dig = 3): partial
  argument match of 'dig' to 'digits'
scatterutil.legendgris: warning in signif(qq, dig = 2): partial
  argument match of 'dig' to 'digits'
Found .Internal calls in the following functions:
  ‘cim.default’ ‘network.default’
with calls to .Internal functions
  ‘locator’

Packages should not call .Internal(): it is not part of the API, for
use only by R itself and subject to change without notice.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... ERROR
Running examples in ‘mixOmics-Ex.R’ failed
The error most likely occurred in:

> ### Name: ipca
> ### Title: Independent Principal Component Analysis
> ### Aliases: ipca
> ### Keywords: algebra
> 
> ### ** Examples
> 
> data(liver.toxicity)
> 
> # implement IPCA on a microarray dataset
> ipca.res <- ipca(liver.toxicity$gene, ncomp = 3, mode="deflation")
> ipca.res

Call:
 ipca(X = liver.toxicity$gene, ncomp = 3, mode = "deflation") 

 IPCA with 3 independent components. 
 You entered data X of dimensions: 64 3116 
 Available components: 
 -------------------- 
 unmixing matrix: see object$unmixing 
 independent principal components: see object$x 
 mxing matrix: see object$mixing 
 kurtosis: see object$kurtosis 
 variable names: see object$names 
 independent loading vectors: see object$loadings 
> 
> # samples representation
> plotIndiv(ipca.res, ind.names = liver.toxicity$treatment[, 4], cex = 0.5, 
+           col = as.numeric(as.factor(liver.toxicity$treatment[, 4])))
> plot3dIndiv(ipca.res, cex = 0.01,
+             col = as.numeric(as.factor(liver.toxicity$treatment[, 4])))

 *** caught segfault ***
address (nil), cause 'unknown'

Traceback:
 1: .C(rgl_bg, success = as.integer(FALSE), idata)
 2: rgl.bg(color = "white", alpha = 1, lit = TRUE, ambient = "#000000",     specular = "#FFFFFF", emission = "#000000", shininess = 50,     smooth = TRUE, front = "filled", back = "lines", size = 3,     lwd = 1, fog = FALSE, point_antialias = FALSE, line_antialias = FALSE,     texture = NULL, textype = "rgb", texmipmap = FALSE, texminfilter = "linear",     texmagfilter = "linear", texenvmap = FALSE, depth_mask = TRUE,     depth_test = "less", sphere = FALSE, fogtype = "none")
 3: do.call("rgl.bg", .fixMaterialArgs(..., Params = new))
 4: bg3d(color = "white")
 5: do.call("bg3d", params$bg)
 6: open3d(windowRect = c(500, 30, 1100, 630))
 7: plot3dIndiv.ipca(ipca.res, cex = 0.01, col = as.numeric(as.factor(liver.toxicity$treatment[,     4])))
 8: plot3dIndiv(ipca.res, cex = 0.01, col = as.numeric(as.factor(liver.toxicity$treatment[,     4])))
aborting ...
Segmentation fault
Run time: 194.93 seconds.