* using log directory 'd:/Rcompile/CRANpkg/local/2.12/r4ss.Rcheck'
* using R version 2.12.2 (2011-02-25)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 whether package 'r4ss' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... 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'
SS_plots: no visible binding for global variable '.SavedPlots'
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'
SSplotComparisons: no visible binding for global variable '.SavedPlots'
SSplotComps: multiple local function definitions for 'tempfun' with
  different formal arguments
SSplotMovementMap: no visible global function definition for 'map'
SSplotNumbers: multiple local function definitions for 'tempfun' with
  different formal arguments
SSplotPars: no visible binding for global variable '.SavedPlots'
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'
Found possibly global 'T' or 'F' in the following functions:
  DoProjectPlots IOTCmove SS_fitbiasramp SS_output SS_parlines
  SS_profile SS_readforecast SS_readstarter SS_splitdat SS_writectl
  SS_writestarter SSmakesims SSplotCatch SSplotData
  SSplotMCMC_ExtraSelex SSplotMovementMap SSplotMovementRates
  SSplotPars SSplotRecdist SSplotSelex SSrunsims mcmc.nuisance mcmc.out
  mountains movepars stackpoly update_r4ss_files
* checking Rd files ... NOTE
prepare_Rd: IOTCmove.Rd:37-39: Dropping empty section \details
prepare_Rd: IOTCmove.Rd:40-46: Dropping empty section \value
prepare_Rd: IOTCmove.Rd:53-54: Dropping empty section \note
prepare_Rd: IOTCmove.Rd:47-49: Dropping empty section \references
prepare_Rd: IOTCmove.Rd:58-60: Dropping empty section \seealso
prepare_Rd: IOTCmove.Rd:61-65: Dropping empty section \examples
prepare_Rd: SS_makedatlist.Rd:153-155: Dropping empty section \details
prepare_Rd: SS_makedatlist.Rd:156-162: Dropping empty section \value
prepare_Rd: SS_makedatlist.Rd:169-171: Dropping empty section \note
prepare_Rd: SS_makedatlist.Rd:163-165: Dropping empty section \references
prepare_Rd: SS_makedatlist.Rd:178-179: Dropping empty section \examples
prepare_Rd: SS_plots.Rd:178-180: Dropping empty section \details
prepare_Rd: SS_plots.Rd:181-187: Dropping empty section \value
prepare_Rd: SS_plots.Rd:196-198: Dropping empty section \note
prepare_Rd: SS_plots.Rd:212-213: Dropping empty section \examples
prepare_Rd: SS_readctl.Rd:25-31: Dropping empty section \value
prepare_Rd: SS_readctl.Rd:38-40: Dropping empty section \note
prepare_Rd: SS_readctl.Rd:35-37: Dropping empty section \author
prepare_Rd: SS_readctl.Rd:32-34: Dropping empty section \references
prepare_Rd: SS_readctl.Rd:50-51: Dropping empty section \examples
prepare_Rd: SS_readdat.Rd:31-33: Dropping empty section \details
prepare_Rd: SS_readdat.Rd:34-40: Dropping empty section \value
prepare_Rd: SS_readdat.Rd:47-49: Dropping empty section \note
prepare_Rd: SS_readdat.Rd:41-43: Dropping empty section \references
prepare_Rd: SS_readdat.Rd:59-60: Dropping empty section \examples
prepare_Rd: SS_readforecast.Rd:26-28: Dropping empty section \details
prepare_Rd: SS_readforecast.Rd:29-35: Dropping empty section \value
prepare_Rd: SS_readforecast.Rd:42-44: Dropping empty section \note
prepare_Rd: SS_readforecast.Rd:36-38: Dropping empty section \references
prepare_Rd: SS_readforecast.Rd:54-55: Dropping empty section \examples
prepare_Rd: SS_readstarter.Rd:22-24: Dropping empty section \details
prepare_Rd: SS_readstarter.Rd:25-31: Dropping empty section \value
prepare_Rd: SS_readstarter.Rd:38-40: Dropping empty section \note
prepare_Rd: SS_readstarter.Rd:32-34: Dropping empty section \references
prepare_Rd: SS_readstarter.Rd:50-51: Dropping empty section \examples
prepare_Rd: SS_writectl.Rd:29-31: Dropping empty section \details
prepare_Rd: SS_writectl.Rd:32-38: Dropping empty section \value
prepare_Rd: SS_writectl.Rd:45-47: Dropping empty section \note
prepare_Rd: SS_writectl.Rd:39-41: Dropping empty section \references
prepare_Rd: SS_writectl.Rd:57-58: Dropping empty section \examples
prepare_Rd: SS_writedat.Rd:29-31: Dropping empty section \details
prepare_Rd: SS_writedat.Rd:32-38: Dropping empty section \value
prepare_Rd: SS_writedat.Rd:45-47: Dropping empty section \note
prepare_Rd: SS_writedat.Rd:42-44: Dropping empty section \author
prepare_Rd: SS_writedat.Rd:39-41: Dropping empty section \references
prepare_Rd: SS_writedat.Rd:51-53: Dropping empty section \seealso
prepare_Rd: SS_writedat.Rd:54-55: Dropping empty section \examples
prepare_Rd: SS_writeforecast.Rd:39-41: Dropping empty section \details
prepare_Rd: SS_writeforecast.Rd:42-48: Dropping empty section \value
prepare_Rd: SS_writeforecast.Rd:55-57: Dropping empty section \note
prepare_Rd: SS_writeforecast.Rd:49-51: Dropping empty section \references
prepare_Rd: SS_writeforecast.Rd:67-68: Dropping empty section \examples
prepare_Rd: SS_writestarter.Rd:33-35: Dropping empty section \details
prepare_Rd: SS_writestarter.Rd:36-42: Dropping empty section \value
prepare_Rd: SS_writestarter.Rd:49-51: Dropping empty section \note
prepare_Rd: SS_writestarter.Rd:43-45: Dropping empty section \references
prepare_Rd: SS_writestarter.Rd:55-57: Dropping empty section \seealso
prepare_Rd: SS_writestarter.Rd:58-59: Dropping empty section \examples
prepare_Rd: SSgetMCMC.Rd:61-63: Dropping empty section \details
prepare_Rd: SSgetMCMC.Rd:64-70: Dropping empty section \value
prepare_Rd: SSgetMCMC.Rd:77-79: Dropping empty section \note
prepare_Rd: SSgetMCMC.Rd:71-73: Dropping empty section \references
prepare_Rd: SSgetMCMC.Rd:86-87: Dropping empty section \examples
prepare_Rd: SSgetoutput.Rd:56-58: Dropping empty section \details
prepare_Rd: SSgetoutput.Rd:59-65: Dropping empty section \value
prepare_Rd: SSgetoutput.Rd:72-74: Dropping empty section \note
prepare_Rd: SSgetoutput.Rd:66-68: Dropping empty section \references
prepare_Rd: SSgetoutput.Rd:83-84: Dropping empty section \examples
prepare_Rd: SSmakesims.Rd:43-44: Dropping empty section \references
prepare_Rd: SSplotBiology.Rd:91-93: Dropping empty section \details
prepare_Rd: SSplotBiology.Rd:94-100: Dropping empty section \value
prepare_Rd: SSplotBiology.Rd:107-109: Dropping empty section \note
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prepare_Rd: SSplotBiology.Rd:116-117: Dropping empty section \examples
prepare_Rd: SSplotCatch.Rd:123-125: Dropping empty section \details
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prepare_Rd: SSplotCatch.Rd:139-141: Dropping empty section \note
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prepare_Rd: SSplotCatch.Rd:148-149: Dropping empty section \examples
prepare_Rd: SSplotComparisons.Rd:229-231: Dropping empty section \details
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prepare_Rd: SSplotComparisons.Rd:255-256: Dropping empty section \examples
prepare_Rd: SSplotComps.Rd:206-208: Dropping empty section \details
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prepare_Rd: SSplotIndices.Rd:133-135: Dropping empty section \details
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prepare_Rd: SSplotMCMC_ExtraSelex.Rd:41-43: Dropping empty section \details
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prepare_Rd: SSplotMCMC_ExtraSelex.Rd:66-67: Dropping empty section \examples
prepare_Rd: SSplotMnwt.Rd:75-77: Dropping empty section \details
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prepare_Rd: SSplotMnwt.Rd:97-99: Dropping empty section \seealso
prepare_Rd: SSplotMnwt.Rd:100-101: Dropping empty section \examples
prepare_Rd: SSplotMovementMap.Rd:63-65: Dropping empty section \details
prepare_Rd: SSplotMovementMap.Rd:66-72: Dropping empty section \value
prepare_Rd: SSplotMovementMap.Rd:73-75: Dropping empty section \references
prepare_Rd: SSplotMovementMap.Rd:86-88: Dropping empty section \seealso
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prepare_Rd: SSplotMovementRates.Rd:48-50: Dropping empty section \details
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prepare_Rd: SSplotMovementRates.Rd:64-65: Dropping empty section \note
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prepare_Rd: SSplotNumbers.Rd:105-107: Dropping empty section \details
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prepare_Rd: SSplotNumbers.Rd:121-123: Dropping empty section \note
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prepare_Rd: SSplotNumbers.Rd:127-129: Dropping empty section \seealso
prepare_Rd: SSplotNumbers.Rd:130-131: Dropping empty section \examples
prepare_Rd: SSplotRecdevs.Rd:90-92: Dropping empty section \details
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prepare_Rd: SSplotRecdevs.Rd:106-108: Dropping empty section \note
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prepare_Rd: SSplotRecdist.Rd:70-72: Dropping empty section \details
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prepare_Rd: SSplotRecdist.Rd:86-88: Dropping empty section \note
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prepare_Rd: SSplotSPR.Rd:86-88: Dropping empty section \details
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prepare_Rd: SSplotSelex.Rd:92-94: Dropping empty section \details
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prepare_Rd: SSplotSelex.Rd:108-110: Dropping empty section \note
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prepare_Rd: SSplotSelex.Rd:117-118: Dropping empty section \examples
prepare_Rd: SSplotSpawnrecruit.Rd:105-107: Dropping empty section \details
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prepare_Rd: SSplotTags.Rd:97-99: Dropping empty section \details
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prepare_Rd: SSplotTimeseries.Rd:113-115: Dropping empty section \details
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prepare_Rd: SSplotYield.Rd:74-76: Dropping empty section \details
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prepare_Rd: SSrunsims.Rd:125-127: Dropping empty section \details
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prepare_Rd: SSrunsims.Rd:141-143: Dropping empty section \note
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prepare_Rd: SSrunsims.Rd:135-137: Dropping empty section \references
prepare_Rd: SSrunsims.Rd:151-152: Dropping empty section \examples
prepare_Rd: SSsummarize.Rd:54-56: Dropping empty section \details
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prepare_Rd: SStableComparisons.Rd:73-75: Dropping empty section \details
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prepare_Rd: addSSsummarize.Rd:125-127: Dropping empty section \references
prepare_Rd: bubble3.Rd:68-70: Dropping empty section \details
prepare_Rd: bubble3.Rd:71-77: Dropping empty section \value
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prepare_Rd: make_multifig.Rd:200-202: Dropping empty section \details
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prepare_Rd: mcmc.nuisance.Rd:69-71: Dropping empty section \details
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prepare_Rd: mcmc.out.Rd:84-86: Dropping empty section \details
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prepare_Rd: rich.colors.short.Rd:24-26: Dropping empty section \details
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prepare_Rd: stackpoly.Rd:64-66: Dropping empty section \details
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prepare_Rd: stackpoly.Rd:89-90: Dropping empty section \examples
* 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 examples ... OK
* checking PDF version of manual ... OK