• using R version 2.14.2 RC (2012-02-23 r58468)
• using platform: i686-pc-linux-gnu (32-bit)
• using session charset: UTF-8
• checking for file ‘r4ss/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘r4ss’ version ‘1.16’
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... NOTE
  As from R 2.14.0 all packages need a namespace.
  One will be generated on installation, but it is better to handcraft a
  NAMESPACE file: R CMD build will produce a suitable starting point.
• checking for executable files ... OK
• checking whether package ‘r4ss’ can be installed ... 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 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 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
  DoProjectPlots: no visible binding for global variable ‘.SavedPlots’
  DoProjectPlots: warning in read.table(file = FileName, col.names =
  1:ncols, fill = T, colClass = "character", comment.char = "$", sep =
  ","): partial argument match of 'colClass' to 'colClasses'
  SS_fitbiasramp: warning in legend("topleft", col = c(2, 4), lwd = 3,
  lty = 2:1, inset = 0.01, cex = 0.9, bg = rgb(1, 1, 1, 0.8), box.col =
  NA, leg = c("bias adjust in model", "estimated alternative")):
  partial argument match of 'leg' to 'legend'
  SS_plots: no visible binding for global variable ‘.SavedPlots’
  SS_plots: warning in SSplotTimeseries(replist = replist, subplot =
  isubplot, areas = areas, areacols = areacols, areanames = areanames,
  forecast = doforecast, uncertainty = douncertainty, plot = (5 %in%
  plot), print = (5 %in% print), verbose = verbose, btarg = btarg,
  minbthresh = minbthresh, minyr = minyr, maxyr = maxyr, pwidth =
  pwidth, pheight = pheight, punits = punits, ptsize = ptsize, res =
  res, cex.main = cex.main, plotdir = plotdir): partial argument match
  of 'forecast' to 'forecastplot'
  SS_plots: warning in SSplotTimeseries(replist = replist, subplot =
  isubplot, areas = areas, areacols = areacols, areanames = areanames,
  forecast = doforecast, uncertainty = FALSE, plot = (5 %in% plot),
  print = (5 %in% print), verbose = verbose, btarg = btarg, minbthresh
  = minbthresh, minyr = minyr, maxyr = maxyr, pwidth = pwidth, pheight
  = pheight, punits = punits, ptsize = ptsize, res = res, cex.main =
  cex.main, plotdir = plotdir): partial argument match of 'forecast' to
  'forecastplot'
  SS_plots: warning in SSplotComps(replist = replist, subplot = 3,
  datonly = FALSE, kind = "cond", bub = TRUE, verbose = verbose, fleets
  = fleets, fleetnames = fleetnames, samplesizeplots = samplesizeplots,
  showsampsize = showsampsize, showeffN = showeffN, minnbubble =
  minnbubble, pntscalar = pntscalar, maxrows = maxrows, maxcols =
  maxcols, maxrows2 = maxrows2, maxcols2 = maxcols2, fixdims = fixdims,
  rows = rows, cols = cols, print = (20 %in% print), plot = (20 %in%
  plot), smooth = smooth, plotdir = plotdir, maxneff = maxneff, :
  partial argument match of 'subplot' to 'subplots'
  SS_plots: warning in cex.main = cex.main, scalebins = scalebins, pwidth
  = pwidth, pheight = pheight, punits = punits, ptsize = ptsize, res =
  res, ...): partial argument match of 'subplot' to 'subplots'
  SS_plots: warning in SSplotComps(replist = replist, subplot = 4:5,
  datonly = FALSE, kind = "cond", bub = TRUE, verbose = verbose, fleets
  = fleets, fleetnames = fleetnames, aalbin = aalbin, aalyear =
  aalyear, samplesizeplots = samplesizeplots, showsampsize =
  showsampsize, showeffN = showeffN, minnbubble = minnbubble, pntscalar
  = pntscalar, maxrows = maxrows, maxcols = maxcols, maxrows2 =
  maxrows2, maxcols2 = maxcols2, fixdims = fixdims, rows = rows, cols =
  cols, print = (20 %in% print), plot = (20 %in% plot), smooth =
  smooth, : partial argument match of 'subplot' to 'subplots'
  SS_plots: warning in plotdir = plotdir, maxneff = maxneff, cex.main =
  cex.main, scalebins = scalebins, pwidth = pwidth, pheight = pheight,
  punits = punits, ptsize = ptsize, res = res, ...): partial argument
  match of 'subplot' to 'subplots'
  SS_plots: warning in SSplotComps(replist = replist, subplot = 6,
  datonly = FALSE, kind = "cond", bub = TRUE, verbose = verbose, fleets
  = fleets, fleetnames = fleetnames, aalbin = aalbin, samplesizeplots =
  samplesizeplots, showsampsize = showsampsize, showeffN = showeffN,
  minnbubble = minnbubble, pntscalar = pntscalar, maxrows = maxrows,
  maxcols = maxcols, maxrows2 = maxrows2, maxcols2 = maxcols2, fixdims
  = fixdims, rows = rows, cols = cols, print = (20 %in% print), plot =
  (20 %in% plot), smooth = smooth, plotdir = plotdir, : partial
  argument match of 'subplot' to 'subplots'
  SS_plots: warning in maxneff = maxneff, cex.main = cex.main, scalebins
  = scalebins, pwidth = pwidth, pheight = pheight, punits = punits,
  ptsize = ptsize, res = res, ...): partial argument match of 'subplot'
  to 'subplots'
  SS_plots: warning in SSplotComps(replist = replist, subplot = 8,
  datonly = FALSE, kind = "cond", bub = TRUE, verbose = verbose, fleets
  = fleets, fleetnames = fleetnames, aalbin = aalbin, aalyear =
  aalyear, samplesizeplots = samplesizeplots, showsampsize =
  showsampsize, showeffN = showeffN, minnbubble = minnbubble, pntscalar
  = pntscalar, maxrows = maxrows, maxcols = maxcols, maxrows2 =
  maxrows2, maxcols2 = maxcols2, fixdims = fixdims, rows = rows, cols =
  cols, print = (21 %in% print), plot = (21 %in% plot), smooth =
  smooth, : partial argument match of 'subplot' to 'subplots'
  SS_plots: warning in plotdir = plotdir, maxneff = maxneff, cex.main =
  cex.main, scalebins = FALSE, pwidth = pwidth, pheight = pheight,
  punits = punits, ptsize = ptsize, res = res, ...): partial argument
  match of 'subplot' to 'subplots'
  SS_profile: warning in SS_changepars(dir = dir, ctlfile =
  masterctlfile, newctlfile = newctlfile, linenums = linenum, string =
  string, newvals = profilevec[i], estimate = F, verbose = T): partial
  argument match of 'string' to 'strings'
  SS_profile: warning in read.table("Report.sso", skip =
  grep("LIKELIHOOD", Rep)[2] + 0, nrows = 11, head = T, fill = T):
  partial argument match of 'head' to 'header'
  SS_writeforecast: no visible binding for global variable
  ‘first_selex_yr’
  SS_writeforecast: no visible binding for global variable
  ‘last_selex_yr’
  SS_writeforecast: no visible binding for global variable ‘ErrorStdDev’
  SS_writeforecast: no visible binding for global variable
  ‘RebuilderOutput’
  SS_writeforecast: no visible binding for global variable ‘Ydecl’
  SS_writeforecast: no visible binding for global variable ‘Yinit’
  SSmakesims: no visible global function definition for ‘makectl’
  SSmakesims: no visible binding for global variable ‘maxb’
  SSmakesims: no visible binding for global variable ‘newr’
  SSplotBiology : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSplotCatch : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSplotComparisons : pngfun: warning in png(file = paste(plotdir, file,
  sep = "/"), width = pwidth, height = pheight, units = punits, res =
  res, pointsize = ptsize): partial argument match of 'file' to
  'filename'
  SSplotComparisons: no visible binding for global variable ‘.SavedPlots’
  SSplotComparisons : plotSpawnBio: warning in axis(2, at = yticks, lab =
  format(yticks/yunits), las = 1): partial argument match of 'lab' to
  'labels'
  SSplotComparisons : plotRecruits: warning in axis(2, at = yticks, lab =
  format(yticks/yunits), las = 1): partial argument match of 'lab' to
  'labels'
  SSplotComparisons : plotDensities: warning in axis(1, at = xticks, lab
  = format(xticks/xunits)): partial argument match of 'lab' to 'labels'
  SSplotComps : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSplotComps: multiple local function definitions for ‘tempfun’ with
  different formal arguments
  SSplotData : pngfun: warning in png(file = file, width = pwidth, height
  = pheight, units = punits, res = res, pointsize = ptsize): partial
  argument match of 'file' to 'filename'
  SSplotData : plotdata: warning in axis(4, at = axistable$yval, label =
  fleetnames[axistable$fleet], las = 1): partial argument match of
  'label' to 'labels'
  SSplotDiscard : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSplotIndices : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSplotMnwt : pngfun: warning in png(file = file, width = pwidth, height
  = pheight, units = punits, res = res, pointsize = ptsize): partial
  argument match of 'file' to 'filename'
  SSplotMnwt: warning in png(file = paste(plotdir, "9_bodywtfit",
  fleetname, ".png", sep = ""), width = pwidth, height = pheight, units
  = punits, res = res, pointsize = ptsize): partial argument match of
  'file' to 'filename'
  SSplotMovementMap: no visible global function definition for ‘map’
  SSplotNumbers : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSplotNumbers: multiple local function definitions for ‘tempfun’ with
  different formal arguments
  SSplotPars: warning in read.table(fullpostfile, head = T): partial
  argument match of 'head' to 'header'
  SSplotPars: warning in read.table(fullrepfile, head = F, nrows =
  nrows2, skip = parstart, as.is = T, fill = T, row.names =
  paste(1:nrows2), col.names = 1:60): partial argument match of 'head'
  to 'header'
  SSplotPars: no visible binding for global variable ‘.SavedPlots’
  SSplotRecdevs : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSplotRecdevs : recdevfunc3: warning in axis(side = 4, at = ymax *
  ypts, label = ypts): partial argument match of 'label' to 'labels'
  SSplotRecdist : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSplotRecdist : recdistfun: warning in axis(1, at = areavec, lab =
  areanames): partial argument match of 'lab' to 'labels'
  SSplotRecdist : recdistfun: warning in axis(2, at = seasvec, lab =
  seasnames): partial argument match of 'lab' to 'labels'
  SSplotSPR : pngfun: warning in png(file = file, width = pwidth, height
  = pheight, units = punits, res = res, pointsize = ptsize): partial
  argument match of 'file' to 'filename'
  SSplotSelex : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSplotSpawnrecruit : pngfun: warning in png(file = file, width =
  pwidth, height = pheight, units = punits, res = res, pointsize =
  ptsize): partial argument match of 'file' to 'filename'
  SSplotTags : pngfun: warning in png(file = file, width = pwidth, height
  = pheight, units = punits, res = res, pointsize = ptsize): partial
  argument match of 'file' to 'filename'
  SSplotTimeseries : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSplotYield : pngfun: warning in png(file = file, width = pwidth,
  height = pheight, units = punits, res = res, pointsize = ptsize):
  partial argument match of 'file' to 'filename'
  SSrunsims: no visible global function definition for ‘bootstrap_CAAL’
  mcmc.out: no visible binding for global variable ‘.SavedPlots’
  mcmc.out: no visible global function definition for ‘running’
  mcmc.out: no visible global function definition for ‘hist2d’
  sel.line : sel: no visible binding for global variable ‘nlength’
  selfit : OnSave: warning in get("selfit.tmp", env = selfit.env):
  partial argument match of 'env' to 'envir'
• checking Rd files ... NOTE
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• checking Rd metadata ... OK
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• checking PDF version of manual ... OK