• using R Under development (unstable) (2012-08-14 r60253)
• using platform: x86_64-unknown-linux-gnu (64-bit)
• using session charset: UTF-8
• checking for file ‘QTLNetworkR/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘QTLNetworkR’ version ‘0.1-7’
• 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 ‘QTLNetworkR’ can be installed ... OK
• checking installed package size ... NOTE
  installed size is 9.2Mb
• 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 index information ... OK
• checking package subdirectories ... NOTE
  Found the following CITATION file(s) in a non-standard place:
  CITATION
  Most likely ‘inst/CITATION’ should be used instead.
• 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 ... OK
• checking R code for possible problems ... NOTE
  File ‘QTLNetworkR/R/zzz.R’:
  .onLoad calls:
  cat("\nUse 'QTLNetworkR()' to restart the programe.\n", fill = TRUE)
  
  Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
  See section ‘Good practice’ in ?.onAttach.
  
  QTLNetworkR: warning in ggroup(horizontal = FALSE, cont = win, expand =
  TRUE): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gtoolbar(tb, cont = gp): partial argument match
  of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("Map File...", cont = lyout, handler =
  function(h, ...) {: partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in std <- gfile(text = "Select Map File...",
  filter = list(`Map files` = list(patterns = c("*.map")), `All files`
  = list(patterns = c("*")))): partial argument match of 'cont' to
  'container'
  QTLNetworkR: warning in if (std != "") {: partial argument match of
  'cont' to 'container'
  QTLNetworkR: warning in if (length(grep("\\", std, fixed = TRUE)) > 0)
  {: partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in mystr <- strsplit(std, split = "\\", fixed =
  T)[[1]]: partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in mystr.lth <- mystr[length(mystr)]: partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in mydir <- substr(std, 1, stop = (nchar(std) -
  nchar(mystr.lth) - 1)): partial argument match of 'cont' to
  'container'
  QTLNetworkR: warning in setwd(mydir): partial argument match of 'cont'
  to 'container'
  QTLNetworkR: warning in }: partial argument match of 'cont' to
  'container'
  QTLNetworkR: warning in else if (length(grep("/", std, fixed = TRUE)) >
  0) {: partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in mystr <- strsplit(std, split = "/", fixed =
  T)[[1]]: partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in x <- read.table(std, fill = T, colClasses =
  "character"): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in y <- 1:as.numeric(x[grep("_c|Chromosome", x[,
  1]), 2]): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in assign("mapfile", x, envir = .qtlnetworkr):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in assign("chromosome", y, envir = .qtlnetworkr):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$map) <- std: partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in }: partial argument match of 'cont' to
  'container'
  QTLNetworkR: warning in }): partial argument match of 'cont' to
  'container'
  QTLNetworkR: warning in gedit(text = "", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("QNK File...", cont = lyout, handler =
  function(h, ...) {: partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in std <- gfile("Select QNK File...", filter =
  list(`QNK files` = list(patterns = c("*.qnk")), `All files` =
  list(patterns = c("*")))): partial argument match of 'cont' to
  'container'
  QTLNetworkR: warning in x <- read.table(std, fill = T, colClasses =
  "character", col.names = paste("col", 1:max(count.fields(std)))):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in y <- length(grep("_trait", x[, 1])): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in z <- x[grep("^_trait$", x[, 1]), 3]: partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in assign("qnkfile", x, envir = .qtlnetworkr):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in assign("traitlth", y, envir = .qtlnetworkr):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in assign("traitname", z, envir = .qtlnetworkr):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$qnk) <- std: partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gnotebook(cont = gp): partial argument match of
  'cont' to 'container'
  QTLNetworkR: warning in ggroup(horizontal = FALSE, cont = nb, label =
  "MI"): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in ggroup(horizontal = FALSE, cont = nb, label =
  "QTL"): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in ggroup(horizontal = FALSE, cont = nb, label =
  "QE"): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in ggroup(horizontal = FALSE, cont = nb, label =
  "MII"): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in ggroup(horizontal = FALSE, cont = nb, label =
  "Epistasis"): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in ggroup(horizontal = FALSE, cont = nb, label =
  "QTLNetwork"): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("Trait...", cont = lyout, handler =
  function(h, ...) {: partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in if (!is.na(get("traitname", envir =
  .qtlnetworkr)[1])) {: partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in std <- myselect.list(list = get("traitname",
  envir = .qtlnetworkr), multiple = TRUE): partial argument match of
  'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$trait) <- toString(std): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$QTLtrait) <- toString(std):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$Effectrait) <- toString(std):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$twodtrait) <- toString(std[1]):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$epitrait) <- toString(std[1]):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$QTLNtrait) <- toString(std):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$color) <-
  toString(cl[1:length(std)]): partial argument match of 'cont' to
  'container'
  QTLNetworkR: warning in svalue(widgets$QTLcolor) <-
  toString(cl[1:length(std)]): partial argument match of 'cont' to
  'container'
  QTLNetworkR: warning in gedit("", cont = lyout): partial argument match
  of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("Color...", cont = lyout, handler =
  function(h, ...) {: partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in if (svalue(widgets$trait) != "") {: partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in std <- myselect.list(list = cl, multiple =
  TRUE, title = "Same number with trait"): partial argument match of
  'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$color) <- toString(std): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("Chromosome...", cont = lyout, handler
  = function(h, ...) {: partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in std <- myselect.list(list = c("all",
  as.character(get("chromosome", envir = .qtlnetworkr))), multiple =
  TRUE, title = "Select chromosomes..."): partial argument match of
  'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$chr) <- toString(std): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gedit("all", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("Threshold", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gcombobox(c("mean", "each"), cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("Clean", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gcombobox(c("FALSE", "TRUE"), cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("LineType", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("Xlabel", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gcombobox(c("Chromosome", "ChromosomeLength"),
  cont = lyout): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("XlabelRot", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gedit("0", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("XlabelFont", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gcombobox(c("1", "2", "3", "4"), cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("XlabelFontSize", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gedit("1", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("YlabelFont", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("YlabelFontSize", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("NotationFont", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("NotationFontSize", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("LineWidth", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in std <- myselect.list(list = cl, multiple =
  TRUE, title = "Same number with trait"): partial argument match of
  'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$QTLcolor) <- toString(std):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$QTLchr) <- toString(std):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gcombobox(c("Chromosome", "chromosomeLength"),
  cont = lyout): partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$twodtrait) <- toString(std):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in svalue(widgets$epitrait) <- toString(std):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("MinYLabel", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("MaxYLabel", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("SymbolSize", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("EnvTextPos", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gedit("3", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("EnvTextFont", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("EnvTextFontSize", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in std <- myselect.list(list = get("traitname",
  envir = .qtlnetworkr), multiple = FALSE): partial argument match of
  'cont' to 'container'
  QTLNetworkR: warning in gbutton("ColorkeyFont", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("ColorkeyFontSize", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("ThresholdFont", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("ThresholdFontSize", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("LeftBottomFont", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("LeftBottomFontSize", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in allow <- AllowTrait(): partial argument match
  of 'cont' to 'container'
  QTLNetworkR: warning in std <- myselect.list(list = get("traitname",
  envir = .qtlnetworkr)[allow], multiple = FALSE): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("Blank", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gedit("10", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("RightTopFont", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("RightTopFontSize", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gedit("0.6", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("chromosome", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gedit("chr", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("ChromosomeWidth", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gedit("15", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("EpistasisLineWidth", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("Text", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gedit("Yes", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("TextPosition", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("ChromosomeFont", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("ChromosomeFontSize", cont = lyout):
  partial argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("TextFont", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("TextFontSize", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("SpaceAD", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gbutton("ParallelDis", cont = lyout): partial
  argument match of 'cont' to 'container'
  QTLNetworkR: warning in gedit("4", cont = lyout): partial argument
  match of 'cont' to 'container'
  QTLNetworkR : myselect.list : helper: warning in gtable(list, multiple
  = multiple, con = x1, expand = TRUE): partial argument match of 'con'
  to 'container'
  QTLNetworkR : myselect.list : helper : <anonymous>: warning in
  assign("selected", value, env = h$action$env): partial argument match
  of 'env' to 'envir'
  QTLNetworkR : MIPlot: warning in grid.layout(nrow = 2, height =
  unit(c(ceiling(length(traitVal)/5) + 1, 1), c("lines", "null"))):
  partial argument match of 'height' to 'heights'
  QTLNetworkR : QTLPlot: warning in grid.layout(nrow = 2, height =
  unit(c(ceiling(length(traitVal)/5) + 1, 1), c("lines", "null"))):
  partial argument match of 'height' to 'heights'
  QTLNetworkR : QTLNetworkPlot: warning in grid.layout(nrow = 2, height =
  unit(c(1, 9), c("null", "null"))): partial argument match of 'height'
  to 'heights'
• 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 R/sysdata.rda ... OK
• checking examples ... OK
• checking PDF version of manual ... OK
  NOTE: There were 3 notes.
  See
  ‘/data/blackswan/ripley/R/packages/tests-devel/QTLNetworkR.Rcheck/00check.log’
  for details.