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r4ss log file (check_x86_64_linux)

Thu May 16 20:24:22 2013: Checking package r4ss (SVN revision 26) ...
* using log directory ‘/mnt/building/build_2013-05-16-20-03/RF_PKG_CHECK/PKGS/r4ss.Rcheck’
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘r4ss/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘r4ss’ version ‘1.20’
* checking CRAN incoming feasibility ... WARNING
Maintainer: ‘Ian Taylor ’
Insufficient package version (submitted: 1.20, existing: 1.20)
* 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘r4ss’ can be installed ... [4s/9s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... WARNING
‘library’ or ‘require’ call not declared from: ‘pso’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SS_fitbiasramp : optimfun: no visible global function definition for
  ‘psoptim’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘PinerPlot’ ‘SSplotRetroRecruits’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'SS_changepars':
SS_changepars
  Code: function(dir = "C:/myfiles/mymodels/myrun/", ctlfile =
                 "control.ss_new", newctlfile = "control_modified.ss",
                 linenums = NULL, strings = NULL, newvals = NULL,
                 estimate = FALSE, verbose = TRUE, repeat_vals = FALSE)
  Docs: function(dir = "C:/myfiles/mymodels/myrun/", ctlfile =
                 "control.ss_new", newctlfile = "control_modified.ss",
                 linenums = NULL, strings = NULL, newvals = NULL,
                 estimate = FALSE, verbose = TRUE)
  Argument names in code not in docs:
    repeat_vals

Codoc mismatches from documentation object 'SS_doRetro':
SS_doRetro
  Code: function(masterdir, oldsubdir, newsubdir = "retrospectives",
                 subdirstart = "retro", years = 0:-5, overwrite = TRUE,
                 extras = "-nox", intern = FALSE, CallType = "system")
  Docs: function(masterdir, oldsubdir, newsubdir = "retrospectives",
                 subdirstart = "retro", years = 0:-5, overwrite = TRUE,
                 extras = "-nox", intern = FALSE)
  Argument names in code not in docs:
    CallType

Codoc mismatches from documentation object 'SS_fitbiasramp':
SS_fitbiasramp
  Code: function(replist, verbose = FALSE, startvalues = NULL, method =
                 "BFGS", twoplots = TRUE, transform = FALSE, plot =
                 TRUE, print = FALSE, plotdir = "default", oldctl =
                 NULL, newctl = NULL, altmethod = "nlminb", pwidth = 7,
                 pheight = 7, punits = "in", ptsize = 12, res = 300,
                 cex.main = 1)
  Docs: function(replist, verbose = FALSE, startvalues = NULL, method =
                 "BFGS", twoplots = TRUE, transform = FALSE, plot =
                 TRUE, print = FALSE, plotdir = "default", oldctl =
                 NULL, newctl = NULL, nlminb = TRUE, pwidth = 7,
                 pheight = 7, punits = "in", ptsize = 12, res = 300,
                 cex.main = 1)
  Argument names in code not in docs:
    altmethod
  Argument names in docs not in code:
    nlminb
  Mismatches in argument names:
    Position: 12 Code: altmethod Docs: nlminb

Codoc mismatches from documentation object 'SS_plots':
SS_plots
  Code: function(replist = NULL, plot = 1:24, print = NULL, pdf =
                 FALSE, png = FALSE, html = png, printfolder = "plots",
                 dir = "default", fleets = "all", areas = "all",
                 fleetnames = "default", fleetcols = "default",
                 fleetlty = 1, fleetpch = 1, lwd = 1, areacols =
                 "default", areanames = "default", verbose = TRUE,
                 uncertainty = TRUE, forecastplot = FALSE, datplot =
                 FALSE, Natageplot = TRUE, samplesizeplots = TRUE,
                 compresidplots = TRUE, sprtarg = "default", btarg =
                 "default", minbthresh = "default", pntscalar = NULL,
                 bub.scale.pearson = 1.5, bub.scale.dat = 3,
                 pntscalar.nums = 2.6, minnbubble = 8, aalyear = -1,
                 aalbin = -1, aalresids = FALSE, maxneff = 5000,
                 cohortlines = c(), smooth = TRUE, showsampsize = TRUE,
                 showeffN = TRUE, sampsizeline = FALSE, effNline =
                 FALSE, showlegend = TRUE, pwidth = 7, pheight = 7,
                 punits = "in", ptsize = 12, res = 300, cex.main = 1,
                 selexlines = 1:6, rows = 1, cols = 1, maxrows = 6,
                 maxcols = 6, maxrows2 = 2, maxcols2 = 4, andrerows =
                 3, tagrows = 3, tagcols = 3, fixdims = TRUE, new =
                 TRUE, SSplotDatMargin = 8, filenotes = NULL,
                 catchasnumbers = NULL, catchbars = TRUE, legendloc =
                 "topleft", minyr = NULL, maxyr = NULL, scalebins =
                 FALSE, scalebubbles = FALSE, tslabels = NULL,
                 catlabels = NULL, ...)
  Docs: function(replist = NULL, plot = 1:24, print = NULL, pdf =
                 FALSE, png = FALSE, html = png, printfolder = "plots",
                 dir = "default", fleets = "all", areas = "all",
                 fleetnames = "default", fleetcols = "default",
                 fleetlty = 1, fleetpch = 1, lwd = 1, areacols =
                 "default", areanames = "default", verbose = TRUE,
                 uncertainty = TRUE, forecastplot = FALSE, datplot =
                 FALSE, Natageplot = TRUE, samplesizeplots = TRUE,
                 compresidplots = TRUE, sprtarg = "default", btarg =
                 "default", minbthresh = "default", pntscalar = NULL,
                 bub.scale.pearson = 1.5, bub.scale.dat = 3,
                 pntscalar.nums = 2.6, minnbubble = 8, aalyear = -1,
                 aalbin = -1, aalresids = FALSE, maxneff = 5000,
                 cohortlines = c(), smooth = TRUE, showsampsize = TRUE,
                 showeffN = TRUE, showlegend = TRUE, pwidth = 7,
                 pheight = 7, punits = "in", ptsize = 12, res = 300,
                 cex.main = 1, selexlines = 1:5, rows = 1, cols = 1,
                 maxrows = 6, maxcols = 6, maxrows2 = 2, maxcols2 = 4,
                 tagrows = 3, tagcols = 3, fixdims = TRUE, new = TRUE,
                 SSplotDatMargin = 8, filenotes = NULL, catchasnumbers
                 = NULL, catchbars = TRUE, legendloc = "topleft", minyr
                 = NULL, maxyr = NULL, scalebins = FALSE, scalebubbles
                 = FALSE, ...)
  Argument names in code not in docs:
    sampsizeline effNline andrerows tslabels catlabels
  Mismatches in argument names (first 3):
    Position: 41 Code: sampsizeline Docs: showlegend
    Position: 42 Code: effNline Docs: pwidth
    Position: 43 Code: showlegend Docs: pheight
  Mismatches in argument default values:
    Name: 'selexlines' Code: 1:6 Docs: 1:5

Codoc mismatches from documentation object 'SS_profile':
SS_profile
  Code: function(dir = "C:/myfiles/mymodels/myrun/", masterctlfile =
                 "control.ss_new", newctlfile = "control_modified.ss",
                 linenum = NULL, string = NULL, profilevec = NULL,
                 usepar = FALSE, globalpar = FALSE, parfile = NULL,
                 parlinenum = NULL, parstring = NULL, dircopy = TRUE,
                 exe.delete = FALSE, model = "ss3", extras = "-nox",
                 systemcmd = FALSE, saveoutput = TRUE, overwrite =
                 TRUE, verbose = TRUE)
  Docs: function(dir = "C:/myfiles/mymodels/myrun/", masterctlfile =
                 "control.ss_new", newctlfile = "control_modified.ss",
                 linenum = NULL, string = NULL, profilevec = NULL,
                 usepar = TRUE, dircopy = TRUE, exe.delete = FALSE,
                 model = "ss3", extras = "-nox", systemcmd = FALSE,
                 saveoutput = TRUE, overwrite = TRUE, verbose = TRUE)
  Argument names in code not in docs:
    globalpar parfile parlinenum parstring
  Mismatches in argument names (first 3):
    Position: 8 Code: globalpar Docs: dircopy
    Position: 9 Code: parfile Docs: exe.delete
    Position: 10 Code: parlinenum Docs: model
  Mismatches in argument default values:
    Name: 'usepar' Code: FALSE Docs: TRUE

Codoc mismatches from documentation object 'SSplotCatch':
SSplotCatch
  Code: function(replist, subplots = 1:15, add = FALSE, areas = 1, plot
                 = TRUE, print = FALSE, type = "l", fleetlty = 1,
                 fleetpch = 1, fleetcols = "default", fleetnames =
                 "default", lwd = 3, areacols = "default", areanames =
                 "default", minyr = NULL, maxyr = NULL, annualcatch =
                 TRUE, forecastplot = TRUE, plotdir = "default",
                 showlegend = TRUE, legendloc = "topleft", xlab =
                 "Year", labels = NULL, catchasnumbers = NULL,
                 catchbars = TRUE, pwidth = 7, pheight = 7, punits =
                 "in", res = 300, ptsize = 12, cex.main = 1, verbose =
                 TRUE)
  Docs: function(replist, subplots = 1:15, add = FALSE, areas = 1, plot
                 = TRUE, print = FALSE, type = "l", fleetlty = 1,
                 fleetpch = 1, fleetcols = "default", fleetnames =
                 "default", lwd = 3, areacols = "default", areanames =
                 "default", minyr = NULL, maxyr = NULL, annualcatch =
                 TRUE, forecastplot = TRUE, plotdir = "default",
                 showlegend = TRUE, legendloc = "topleft", xlab =
                 "Year", labels = c("Harvest rate/Year", "Continuous
                 F", "Landings", "Total catch", "Predicted Discards",
                 "Discard fraction", "(mt)", "(numbers x1000)",
                 "Observed and expected", "aggregated across seasons"),
                 catchasnumbers = NULL, catchbars = TRUE, pwidth = 7,
                 pheight = 7, punits = "in", res = 300, ptsize = 12,
                 cex.main = 1, verbose = TRUE)
  Mismatches in argument default values:
    Name: 'labels'
    Code: NULL
    Docs: c("Harvest rate/Year", "Continuous F", "Landings", "Total catch", 
          "Predicted Discards", "Discard fraction", "(mt)", "(numbers x1000)", 
          "Observed and expected", "aggregated across seasons")

Codoc mismatches from documentation object 'SSplotComparisons':
SSplotComparisons
  Code: function(summaryoutput, subplots = 1:20, plot = TRUE, print =
                 FALSE, png = print, pdf = FALSE, models = "all",
                 endyrvec = "default", indexfleets = NULL,
                 indexUncertainty = FALSE, indexQlabel = TRUE,
                 indexQdigits = 4, indexSEvec = "default",
                 indexPlotEach = FALSE, labels = c("Year", "Spawning
                 biomass (mt)", "Spawning depletion", "Age-0 recruits
                 (1,000s)", "Recruitment deviations", "Index", "Log
                 index", "SPR ratio", "Density", "Management target",
                 "Minimum stock size threshold", "Spawning output
                 (eggs)"), col = "default", shadecol = "default", pch =
                 "default", lty = 1, lwd = 2, spacepoints = 10,
                 staggerpoints = 1, xlim = "default", ylimAdj = 1, xaxs
                 = "r", yaxs = "r", type = "o", uncertainty = TRUE,
                 shadealpha = 0.1, legend = TRUE, legendlabels =
                 "default", legendloc = "topright", legendorder =
                 "default", legendncol = 1, btarg = 0.4, minbthresh =
                 0.25, sprtarg = 1, pwidth = 7, pheight = 7, punits =
                 "in", res = 300, ptsize = 12, cex.main = 1, plotdir =
                 NULL, densitynames = c("SPB_Virgin", "R0"),
                 densityxlabs = "default", densityscalex = 1,
                 densityscaley = 1, densityadjust = 1, densitysymbols =
                 TRUE, densitytails = TRUE, fix0 = TRUE, new = TRUE,
                 add = FALSE, par = list(mar = c(5, 4, 1, 1) + 0.1),
                 verbose = TRUE, mcmcVec = "default")
  Docs: function(summaryoutput, subplots = 1:20, plot = TRUE, print =
                 FALSE, png = print, pdf = FALSE, models = "all",
                 endyrvec = "default", indexfleets = NULL,
                 indexUncertainty = FALSE, indexQlabel = TRUE,
                 indexQdigits = 4, indexSEvec = "default",
                 indexPlotEach = FALSE, labels = c("Year", "Spawning
                 biomass (mt)", "Spawning depletion", "Age-0 recruits
                 (1,000s)", "Recruitment deviations", "Index", "Log
                 index", "SPR ratio", "Density", "Management target",
                 "Minimum stock size threshold"), col = "default",
                 shadecol = "default", pch = "default", lty = 1, lwd =
                 2, spacepoints = 10, staggerpoints = 1, xlim =
                 "default", ylimAdj = 1, xaxs = "r", yaxs = "r", type =
                 "o", uncertainty = TRUE, shadealpha = 0.1, legend =
                 TRUE, legendlabels = "default", legendloc =
                 "topright", legendorder = "default", legendncol = 1,
                 btarg = 0.4, minbthresh = 0.25, sprtarg = 1, pwidth =
                 7, pheight = 7, punits = "in", res = 300, ptsize = 12,
                 cex.main = 1, plotdir = NULL, densitynames =
                 c("SPB_Virgin", "R0"), densityxlabs = "default",
                 densityscalex = 1, densityscaley = 1, densityadjust =
                 1, densitysymbols = TRUE, densitytails = TRUE, fix0 =
                 TRUE, new = TRUE, add = FALSE, par = list(mar = c(5,
                 4, 1, 1) + 0.1), verbose = TRUE, mcmcVec = "default")
  Mismatches in argument default values:
    Name: 'labels'
    Code: c("Year", "Spawning biomass (mt)", "Spawning depletion", "Age-0 recruits (1,000s)", 
          "Recruitment deviations", "Index", "Log index", "SPR ratio", 
          "Density", "Management target", "Minimum stock size threshold", 
          "Spawning output (eggs)")
    Docs: c("Year", "Spawning biomass (mt)", "Spawning depletion", "Age-0 recruits (1,000s)", 
          "Recruitment deviations", "Index", "Log index", "SPR ratio", 
          "Density", "Management target", "Minimum stock size threshold")

Codoc mismatches from documentation object 'SSplotComps':
SSplotComps
  Code: function(replist, subplots = 1:12, kind = "LEN", sizemethod =
                 1, aalyear = -1, aalbin = -1, plot = TRUE, print =
                 FALSE, fleets = "all", fleetnames = "default", sexes =
                 "all", datonly = FALSE, samplesizeplots = TRUE,
                 compresidplots = TRUE, bub = FALSE, showsampsize =
                 TRUE, showeffN = TRUE, sampsizeline = FALSE, effNline
                 = FALSE, minnbubble = 8, pntscalar = NULL,
                 scalebubbles = FALSE, cexZ1 = 1.5, bublegend = TRUE,
                 blue = rgb(0, 0, 1, 0.7), pwidth = 7, pheight = 7,
                 punits = "in", ptsize = 12, res = 300, plotdir =
                 "default", cex.main = 1, linepos = 1, fitbar = FALSE,
                 do.sqrt = TRUE, smooth = TRUE, cohortlines = c(),
                 labels = c("Length (cm)", "Age (yr)", "Year",
                 "Observed sample size", "Effective sample size",
                 "Proportion", "cm", "Frequency", "Weight", "Length",
                 "(mt)", "(numbers x1000)", "Stdev (Age) (yr)",
                 "Andre's conditional AAL plot, "), printmkt = TRUE,
                 printsex = TRUE, maxrows = 6, maxcols = 6, maxrows2 =
                 2, maxcols2 = 4, rows = 1, cols = 1, andrerows = 3,
                 fixdims = TRUE, fixdims2 = FALSE, maxneff = 5000,
                 verbose = TRUE, scalebins = FALSE, addMeans = TRUE,
                 ...)
  Docs: function(replist, subplots = 1:12, kind = "LEN", sizemethod =
                 1, aalyear = -1, aalbin = -1, plot = TRUE, print =
                 FALSE, fleets = "all", fleetnames = "default", sexes =
                 "all", datonly = FALSE, samplesizeplots = TRUE,
                 compresidplots = TRUE, bub = FALSE, showsampsize =
                 TRUE, showeffN = TRUE, minnbubble = 8, pntscalar =
                 NULL, scalebubbles = FALSE, bub.scale.pearson = 1.5,
                 bub.scale.dat = 3, pwidth = 7, pheight = 7, punits =
                 "in", ptsize = 12, res = 300, plotdir = "default",
                 cex.main = 1, linepos = 1, fitbar = FALSE, do.sqrt =
                 TRUE, smooth = TRUE, cohortlines = c(), labels =
                 c("Length (cm)", "Age (yr)", "Year", "Observed sample
                 size", "Effective sample size", "Proportion", "cm",
                 "Frequency", "Weight", "Length", "(mt)", "(numbers
                 x1000)", "Stdev (Age) (yr)", "Andre's conditional AAL
                 plot, "), printmkt = TRUE, printsex = TRUE, maxrows =
                 6, maxcols = 6, maxrows2 = 2, maxcols2 = 4, rows = 1,
                 cols = 1, fixdims = TRUE, fixdims2 = FALSE, maxneff =
                 5000, verbose = TRUE, scalebins = FALSE, addMeans =
                 TRUE, ...)
  Argument names in code not in docs:
    sampsizeline effNline cexZ1 bublegend blue andrerows
  Argument names in docs not in code:
    bub.scale.pearson bub.scale.dat
  Mismatches in argument names (first 3):
    Position: 18 Code: sampsizeline Docs: minnbubble
    Position: 19 Code: effNline Docs: pntscalar
    Position: 20 Code: minnbubble Docs: scalebubbles

Codoc mismatches from documentation object 'SSplotIndices':
SSplotIndices
  Code: function(replist, subplots = 1:9, plot = TRUE, print = FALSE,
                 fleets = "all", fleetnames = "default", smooth = TRUE,
                 add = FALSE, datplot = FALSE, labels = c("Year",
                 "Index", "Observed index", "Expected index", "Log
                 index", "Log observed index", "Log expected index",
                 "Standardized index", "Catchability (Q)",
                 "Time-varying catchability", "Vulnerable biomass",
                 "Catchability vs. vulnerable biomass"), col1 =
                 "default", col2 = "default", col3 = "blue", col4 =
                 "red", pch1 = 21, pch2 = 16, cex = 1, bg = "white",
                 legend = TRUE, legendloc = "topright", seasnames =
                 NULL, pwidth = 7, pheight = 7, punits = "in", res =
                 300, ptsize = 12, cex.main = 1, addmain = TRUE,
                 plotdir = "default", minyr = NULL, maxyr = NULL,
                 verbose = TRUE)
  Docs: function(replist, subplots = 1:9, plot = TRUE, print = FALSE,
                 fleets = "all", fleetnames = "default", smooth = TRUE,
                 add = FALSE, datplot = FALSE, labels = c("Year",
                 "Index", "Observed index", "Expected index", "Log
                 index", "Log observed index", "Log expected index",
                 "Standardized index", "Catchability (Q)",
                 "Time-varying catchability", "Vulnerable biomass",
                 "Catchability vs. vulnerable biomass"), col1 =
                 "default", col2 = "default", col3 = "blue", col4 =
                 "red", pch1 = 1, pch2 = 16, cex = 1, legend = TRUE,
                 legendloc = "topright", seasnames = NULL, pwidth = 7,
                 pheight = 7, punits = "in", res = 300, ptsize = 12,
                 cex.main = 1, addmain = TRUE, plotdir = "default",
                 minyr = NULL, maxyr = NULL, verbose = TRUE)
  Argument names in code not in docs:
    bg
  Mismatches in argument names (first 3):
    Position: 18 Code: bg Docs: legend
    Position: 19 Code: legend Docs: legendloc
    Position: 20 Code: legendloc Docs: seasnames
  Mismatches in argument default values:
    Name: 'pch1' Code: 21 Docs: 1

Codoc mismatches from documentation object 'SSplotNumbers':
SSplotNumbers
  Code: function(replist, subplots = 1:9, plot = TRUE, print = FALSE,
                 areas = "all", areanames = "default", areacols =
                 "default", pntscalar = 2.6, bublegend = TRUE, period =
                 c("B", "M"), add = FALSE, labels = c("Year", "Age",
                 "True age (yr)", "SD of observed age (yr)", "Mean
                 observed age (yr)", "Mean age (yr)", "mean age in the
                 population", "Ageing imprecision", "Numbers at age at
                 equilibrium", "Equilibrium age distribution", "Sex
                 ratio of numbers at age (males/females)", "Length",
                 "Mean length (cm)", "mean length (cm) in the
                 population", "expected numbers at age", "Beginning of
                 year", "Middle of year", "expected numbers at length",
                 "Sex ratio of numbers at length (males/females)", "Sex
                 ratio of numbers at length (females/males)"), pwidth =
                 7, pheight = 7, punits = "in", res = 300, ptsize = 12,
                 cex.main = 1, plotdir = "default", verbose = TRUE)
  Docs: function(replist, subplots = 1:9, plot = TRUE, print = FALSE,
                 areas = "all", areanames = "default", areacols =
                 "default", pntscalar = 2.6, period = c("B", "M"), add
                 = FALSE, labels = c("Year", "Age", "True age (yr)",
                 "SD of observed age (yr)", "Mean observed age (yr)",
                 "Mean age (yr)", "mean age in the population", "Ageing
                 imprecision", "Numbers at age at equilibrium",
                 "Equilibrium age distribution", "Sex ratio of numbers
                 at age (males/females)", "Length", "Mean length (cm)",
                 "mean length (cm) in the population", "expected
                 numbers at age", "Beginning of year", "Middle of
                 year", "expected numbers at length", "Sex ratio of
                 numbers at length (males/females)", "Sex ratio of
                 numbers at length (females/males)"), pwidth = 7,
                 pheight = 7, punits = "in", res = 300, ptsize = 12,
                 cex.main = 1, plotdir = "default", verbose = TRUE)
  Argument names in code not in docs:
    bublegend
  Mismatches in argument names (first 3):
    Position: 9 Code: bublegend Docs: period
    Position: 10 Code: period Docs: add
    Position: 11 Code: add Docs: labels

Codoc mismatches from documentation object 'SSplotSelex':
SSplotSelex
  Code: function(replist, infotable = NULL, fleets = "all", fleetnames
                 = "default", sizefactors = c("Lsel"), agefactors =
                 c("Asel", "Asel2"), years = "endyr", season = 1, sexes
                 = "all", selexlines = 1:6, subplot = 1:25,
                 skipAgeSelex10 = TRUE, plot = TRUE, print = FALSE, add
                 = FALSE, labels = c("Length (cm)", "Age (yr)", "Year",
                 "Selectivity", "Retention", "Discard mortality"), col1
                 = "red", col2 = "blue", lwd = 2, fleetcols =
                 "default", fleetpch = "default", fleetlty = "default",
                 spacepoints = 5, staggerpoints = 1, legendloc =
                 "bottomright", pwidth = 7, pheight = 7, punits = "in",
                 res = 300, ptsize = 12, cex.main = 1, plotdir =
                 "default", verbose = TRUE)
  Docs: function(replist, infotable = NULL, fleets = "all", fleetnames
                 = "default", sizefactors = c("Lsel"), agefactors =
                 c("Asel"), years = "endyr", season = 1, sexes = "all",
                 selexlines = 1:5, subplot = 1:25, skipAgeSelex10 =
                 TRUE, plot = TRUE, print = FALSE, add = FALSE, labels
                 = c("Length (cm)", "Age (yr)", "Year", "Selectivity",
                 "Retention", "Discard mortality"), col1 = "red", col2
                 = "blue", lwd = 2, fleetcols = "default", fleetpch =
                 "default", fleetlty = "default", spacepoints = 5,
                 staggerpoints = 1, legendloc = "bottomright", pwidth =
                 7, pheight = 7, punits = "in", res = 300, ptsize = 12,
                 cex.main = 1, plotdir = "default", verbose = TRUE)
  Mismatches in argument default values:
    Name: 'agefactors' Code: c("Asel", "Asel2") Docs: c("Asel")
    Name: 'selexlines' Code: 1:6 Docs: 1:5

Codoc mismatches from documentation object 'SSplotTags':
SSplotTags
  Code: function(replist = replist, subplots = 1:8, latency = 0, rows =
                 1, cols = 1, tagrows = 3, tagcols = 3, plot = TRUE,
                 print = FALSE, pntscalar = 2.6, minnbubble = 8, pwidth
                 = 7, pheight = 7, punits = "in", ptsize = 12, res =
                 300, cex.main = 1, col1 = rgb(0, 0, 1, 0.7), col2 =
                 "red", col3 = "grey95", col4 = "grey70", labels =
                 c("Year", "Frequency", "Tag Group", "Fit to tag
                 recaptures by tag group", "Tag recaptures aggregated
                 across tag groups", "Observed tag recaptures by year
                 and tag group", "Residuals for tag recaptures:
                 (obs-exp)/sqrt(exp)", "Observed and expected tag
                 recaptures by year and tag group"), plotdir =
                 "default", verbose = TRUE)
  Docs: function(replist = replist, subplots = 1:8, latency = 0, rows =
                 1, cols = 1, tagrows = 3, tagcols = 3, plot = TRUE,
                 print = FALSE, pntscalar = 2.6, minnbubble = 8, pwidth
                 = 7, pheight = 7, punits = "in", ptsize = 12, res =
                 300, cex.main = 1, col1 = "blue", col2 = "red", col3 =
                 "grey95", col4 = "grey70", labels = c("Year",
                 "Frequency", "Tag Group", "Fit to tag recaptures by
                 tag group", "Tag recaptures aggregated across tag
                 groups", "Observed tag recaptures by year and tag
                 group", "Residuals for tag recaptures:
                 (obs-exp)/sqrt(exp)", "Observed and expected tag
                 recaptures by year and tag group"), plotdir =
                 "default", verbose = TRUE)
  Mismatches in argument default values:
    Name: 'col1' Code: rgb(0, 0, 1, 0.7) Docs: "blue"

Codoc mismatches from documentation object 'SSplotTimeseries':
SSplotTimeseries
  Code: function(replist, subplot, add = FALSE, areas = "all", areacols
                 = "default", areanames = "default", forecastplot =
                 TRUE, uncertainty = TRUE, bioscale = "default", minyr
                 = NULL, maxyr = NULL, plot = TRUE, print = FALSE,
                 plotdir = "default", verbose = TRUE, btarg =
                 "default", minbthresh = "default", xlab = "Year",
                 labels = NULL, pwidth = 7, pheight = 7, punits = "in",
                 res = 300, ptsize = 12, cex.main = 1)
  Docs: function(replist, subplot, add = FALSE, areas = "all", areacols
                 = "default", areanames = "default", forecastplot =
                 TRUE, uncertainty = TRUE, bioscale = "default", minyr
                 = NULL, maxyr = NULL, plot = TRUE, print = FALSE,
                 plotdir = "default", verbose = TRUE, btarg =
                 "default", minbthresh = "default", xlab = "Year",
                 labels = c("Total biomass (mt)", "Total biomass (mt)
                 at beginning of season", "Summary biomass (mt)",
                 "Summary biomass (mt) at beginning of season",
                 "Spawning biomass (mt)", "Spawning depletion",
                 "Spawning output (eggs)", "Age-0 recruits (1,000s)",
                 "Fraction of total Age-0 recruits", "Management
                 target", "Minimum stock size threshold"), pwidth = 7,
                 pheight = 7, punits = "in", res = 300, ptsize = 12,
                 cex.main = 1)
  Mismatches in argument default values:
    Name: 'labels'
    Code: NULL
    Docs: c("Total biomass (mt)", "Total biomass (mt) at beginning of season", 
          "Summary biomass (mt)", "Summary biomass (mt) at beginning of season", 
          "Spawning biomass (mt)", "Spawning depletion", "Spawning output (eggs)", 
          "Age-0 recruits (1,000s)", "Fraction of total Age-0 recruits", 
          "Management target", "Minimum stock size threshold")

Codoc mismatches from documentation object 'SSsummarize':
SSsummarize
  Code: function(biglist, keyvec = NULL, numvec = NULL, sizeselfactor =
                 "Lsel", ageselfactor = "Asel", selfleet = NULL, selyr
                 = "startyr", selgender = 1, SpawnOutputUnits = NULL,
                 lowerCI = 0.025, upperCI = 0.975)
  Docs: function(biglist, keyvec = NULL, numvec = NULL, sizeselfactor =
                 "Lsel", ageselfactor = "Asel", selfleet = NULL, selyr
                 = "startyr", selgender = 1, lowerCI = 0.025, upperCI =
                 0.975)
  Argument names in code not in docs:
    SpawnOutputUnits
  Mismatches in argument names:
    Position: 9 Code: SpawnOutputUnits Docs: lowerCI
    Position: 10 Code: lowerCI Docs: upperCI

Codoc mismatches from documentation object 'bubble3':
bubble3
  Code: function(x, y, z, col = 1, cexZ1 = 5, maxsize = NULL, do.sqrt =
                 TRUE, legend = TRUE, legendloc = "top", legend.z =
                 "default", legend.yadj = 1.1, main = "", cex.main = 1,
                 xlab = "", ylab = "", minnbubble = 8, xlim = NULL,
                 ylim = NULL, axis1 = TRUE, xlimextra = 1, add = FALSE,
                 las = 1, allopen = TRUE)
  Docs: function(x, y, z, col = 1, cexZ1 = 5, maxsize = NULL, do.sqrt =
                 TRUE, legend = TRUE, legend.z = "default", legend.yadj
                 = 1.1, main = "", cex.main = 1, xlab = "", ylab = "",
                 minnbubble = 8, xlim = NULL, ylim = NULL, axis1 =
                 TRUE, xlimextra = 1, add = FALSE, las = 1, allopen =
                 TRUE)
  Argument names in code not in docs:
    legendloc
  Mismatches in argument names (first 3):
    Position: 9 Code: legendloc Docs: legend.z
    Position: 10 Code: legend.z Docs: legend.yadj
    Position: 11 Code: legend.yadj Docs: main

Codoc mismatches from documentation object 'make_multifig':
make_multifig
  Code: function(ptsx, ptsy, yr, linesx = 0, linesy = 0, ptsSD = 0,
                 sampsize = 0, effN = 0, showsampsize = TRUE, showeffN
                 = TRUE, sampsizeround = 1, maxrows = 6, maxcols = 6,
                 rows = 1, cols = 1, fixdims = TRUE, main = "",
                 cex.main = 1, xlab = "", ylab = "", size = 1, cexZ1 =
                 1.5, bublegend = TRUE, maxsize = NULL, do.sqrt = TRUE,
                 minnbubble = 8, allopen = TRUE, horiz_lab = "default",
                 xbuffer = c(0.1, 0.1), ybuffer = c(0, 0.15), ymin0 =
                 TRUE, axis1 = "default", axis2 = "default", linepos =
                 1, type = "o", bars = FALSE, barwidth = "default",
                 ptscex = 1, ptscol = 1, ptscol2 = 1, linescol = 2, lty
                 = 1, lwd = 1, pch = 1, nlegends = 3, legtext =
                 list("yr", "sampsize", "effN"), legx = "default", legy
                 = "default", legadjx = "default", legadjy = "default",
                 legsize = c(1.2, 1), legfont = c(2, 1), sampsizeline =
                 FALSE, effNline = FALSE, sampsizemean = NULL, effNmean
                 = NULL, ipage = 0, scalebins = FALSE)
  Docs: function(ptsx, ptsy, yr, linesx = 0, linesy = 0, ptsSD = 0,
                 sampsize = 0, effN = 0, showsampsize = TRUE, showeffN
                 = TRUE, sampsizeround = 1, maxrows = 6, maxcols = 6,
                 rows = 1, cols = 1, fixdims = TRUE, main = "",
                 cex.main = 1, xlab = "", ylab = "", size = 1, maxsize
                 = 3, do.sqrt = TRUE, minnbubble = 8, allopen = TRUE,
                 horiz_lab = "default", xbuffer = c(0.1, 0.1), ybuffer
                 = c(0, 0.15), ymin0 = TRUE, axis1 = "default", axis2 =
                 "default", linepos = 1, type = "o", bars = FALSE,
                 barwidth = "default", ptscex = 1, ptscol = 1, ptscol2
                 = 1, linescol = 2, lty = 1, lwd = 1, pch = 1, nlegends
                 = 3, legtext = list("yr", "sampsize", "effN"), legx =
                 "default", legy = "default", legadjx = "default",
                 legadjy = "default", legsize = c(1.2, 1), legfont =
                 c(2, 1), ipage = 0, scalebins = FALSE)
  Argument names in code not in docs:
    cexZ1 bublegend sampsizeline effNline sampsizemean effNmean
  Mismatches in argument names (first 3):
    Position: 22 Code: cexZ1 Docs: maxsize
    Position: 23 Code: bublegend Docs: do.sqrt
    Position: 24 Code: maxsize Docs: minnbubble
  Mismatches in argument default values:
    Name: 'maxsize' Code: NULL Docs: 3

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... [3s/3s] OK
* checking PDF version of manual ... OK

WARNING: There were 4 warnings.
NOTE: There was 1 note.
See
  ‘/mnt/building/build_2013-05-16-20-03/RF_PKG_CHECK/PKGS/r4ss.Rcheck/00check.log’
for details.

Run time: 157.27 seconds.