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nwfscAgeingError log file (check_x86_64_linux)

Thu Jan 23 00:15:44 2014: Checking package nwfscAgeingError (SVN revision 230) ...
* using log directory ‘/mnt/building/build_2014-01-23-00-12/RF_PKG_CHECK/PKGS/nwfscAgeingError.Rcheck’
* using R version 3.0.2 Patched (2014-01-20 r64850)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘nwfscAgeingError/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nwfscAgeingError’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘James Thorson ’
New submission
* 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 ... WARNING
Found the following executable file:
  inst/executables/agemat.exe
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for hidden files and directories ... OK
* checking for portable file names ... WARNING
Found the following file with a non-portable file name:
  inst/doc/Instructions for use.docx
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘nwfscAgeingError’ can be installed ... [1s/3s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard files found at top level:
  ‘BinaryFiles’ ‘examples’
* 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 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
StepwiseFn: no visible binding for global variable ‘KnotAges’

Found the following calls to attach():
File ‘nwfscAgeingError/R/updateAgeingErrorCode.R’:
  attach(NULL, pos = pos, name = env)
See section ‘Good practice’ in ‘?attach’.
* checking Rd files ... WARNING
prepare_Rd: PlotOutputFn.Rd:27-28: Dropping empty section \details
prepare_Rd: PlotOutputFn.Rd:37-38: Dropping empty section \note
prepare_Rd: PlotOutputFn.Rd:41-42: Dropping empty section \seealso
prepare_Rd: RunFn.Rd:63-64: Dropping empty section \details
prepare_Rd: RunFn.Rd:73-75: Dropping empty section \note
prepare_Rd: RunFn.Rd:79-80: Dropping empty section \seealso
prepare_Rd: SimulatorFn.Rd:46-48: Dropping empty section \details
prepare_Rd: SimulatorFn.Rd:59-61: Dropping empty section \note
prepare_Rd: SimulatorFn.Rd:65-67: Dropping empty section \seealso
prepare_Rd: StepwiseFn.Rd:52-54: Dropping empty section \details
prepare_Rd: StepwiseFn.Rd:55-61: Dropping empty section \value
prepare_Rd: StepwiseFn.Rd:68-70: Dropping empty section \note
prepare_Rd: StepwiseFn.Rd:65-67: Dropping empty section \author
prepare_Rd: StepwiseFn.Rd:74-76: Dropping empty section \seealso
prepare_Rd: cMx.Rd:7-9: Dropping empty section \description
prepare_Rd: cMx.Rd:19-21: Dropping empty section \details
prepare_Rd: cMx.Rd:22-28: Dropping empty section \value
prepare_Rd: cMx.Rd:35-37: Dropping empty section \note
prepare_Rd: cMx.Rd:32-34: Dropping empty section \author
prepare_Rd: cMx.Rd:29-31: Dropping empty section \references
prepare_Rd: cMx.Rd:41-43: Dropping empty section \seealso
checkRd: (5) cMx.Rd:0-59: Must have a \description
nwfscAgeingError-package.Rd: non-ASCII input and no declared encoding
prepare_Rd: rMx.Rd:7-9: Dropping empty section \description
prepare_Rd: rMx.Rd:19-21: Dropping empty section \details
prepare_Rd: rMx.Rd:22-28: Dropping empty section \value
prepare_Rd: rMx.Rd:35-37: Dropping empty section \note
prepare_Rd: rMx.Rd:32-34: Dropping empty section \author
prepare_Rd: rMx.Rd:29-31: Dropping empty section \references
prepare_Rd: rMx.Rd:41-43: Dropping empty section \seealso
checkRd: (5) rMx.Rd:0-65: Must have a \description
problem found in ‘nwfscAgeingError-package.Rd’
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file ‘/mnt/building/build_2014-01-23-00-12/RF_PKG_CHECK/PKGS/nwfscAgeingError.Rcheck/00_pkg_src/nwfscAgeingError/man/RunFn.Rd’:
  \usage lines wider than 90 characters:
     RunFn(Data, SigOpt, BiasOpt, NDataSets, MinAge, MaxAge, RefAge, MinusAge, PlusAge, MaxSd, MaxExpectedAge, SaveFile, EffSampleSize = 0,  ... [TRUNCATED]

Rd file ‘/mnt/building/build_2014-01-23-00-12/RF_PKG_CHECK/PKGS/nwfscAgeingError.Rcheck/00_pkg_src/nwfscAgeingError/man/SimulatorFn.Rd’:
  \usage lines wider than 90 characters:
     SimulatorFn(Nreaders, M, SelexForm, ErrorParams, BiasParams, SelexParams, ReadsMat, RecCv = 0.6, RecAr1 = 0.8, Amax = 100)

Rd file ‘/mnt/building/build_2014-01-23-00-12/RF_PKG_CHECK/PKGS/nwfscAgeingError.Rcheck/00_pkg_src/nwfscAgeingError/man/StepwiseFn.Rd’:
  \usage lines wider than 90 characters:
     StepwiseFn(SearchMat, Data, NDataSets, MinAge, MaxAge, RefAge, MaxSd, MaxExpectedAge, SaveFile, EffSampleSize = 0, Intern = TRUE, Infor ... [TRUNCATED]
  \examples lines wider than 100 characters:
       # One row for each reader + 2 rows for PlusAge (the age where the proportion-at-age begins to decrease exponentially with increasing  ... [TRUNCATED]
       SearchMat = array(NA, dim=c(Nreaders*2+2,7), dimnames=list(c(paste("Error_Reader",1:Nreaders),paste("Bias_Reader",1:Nreaders),"MinusA ... [TRUNCATED]
         SearchMat[9,1:7] = c(StartMinusAge,StartMinusAge-10,StartMinusAge-4,StartMinusAge-1,StartMinusAge+1,StartMinusAge+4,StartMinusAge+1 ... [TRUNCATED]
         SearchMat[10,1:7] = c(StartPlusAge,StartPlusAge-10,StartPlusAge-4,StartPlusAge-1,StartPlusAge+1,StartPlusAge+4,StartPlusAge+10)
         # 1. "Stepwise - Model loop X.txt" -- Shows the AIC/BIC/AICc value for all different combinations of parameters arising from changi ... [TRUNCATED]
         # 2. "Stepwise - Record.txt" -- The Xth row of IcRecord shows the record of the Information Criterion for all trials in loop X, whi ... [TRUNCATED]
       # WARNING: One run of this stepwise model building example can take 8+ hours, and should be run overnight
       StepwiseFn(SearchMat=SearchMat, Data=AgeReads2, NDataSets=1, MinAge=MinAge, MaxAge=MaxAge, RefAge=10, MaxSd=40, MaxExpectedAge=MaxAge ... [TRUNCATED]

Rd file ‘/mnt/building/build_2014-01-23-00-12/RF_PKG_CHECK/PKGS/nwfscAgeingError.Rcheck/00_pkg_src/nwfscAgeingError/man/nwfscAgeingError-package.Rd’:
  \examples lines wider than 100 characters:
       #   ReadsMat is a matrix where each row specifies how many reads (in the first column) have a particular pattern of double reads (in  ... [TRUNCATED]
       #   SelexForm is the selectivity-at-age form (logistic selex-at-age is the only one that is implemented)
       ReadsMat = cbind(NumberOfReads=rep(100,5), Reader1=c(1,1,0,0,1), Reader1_DoubleReads=c(0,1,0,0,0), Reader2=c(0,0,1,1,1), Reader2_Doub ... [TRUNCATED]
         rownames(ReadsMat) = c("Reader1_Only", "Reader1_DoubleReads", "Reader2_Only", "Reader2_DoubleReads", "Reader1_&_Reader2")
       AgeReads = SimulatorFn(Nreaders=Nreaders, M=0.2, SelexForm="Logistic", SelexParams=c(5,0.2), BiasParams=c(1,1,1.1,1.1), ErrorParams=c ... [TRUNCATED]
         AgeReads = ifelse(is.na(AgeReads),-999,AgeReads)  # Change NA to -999 (which the Punt software considers missing data)
         # These rows have no information about reading error, but are potentially informative about latent age-structure
         # It is unknown whether eliminating these rows degrades estimation of error and bias, and is currently recommended to speed up comp ... [TRUNCATED]
         if(!is.na(DupRow)) AgeReads2[DupRow,1] = AgeReads2[DupRow,1] + 1 # Increment number of samples for the previous duplicate
         #Data=AgeReads2; SigOpt=SigOpt; BiasOpt=BiasOpt; NDataSets=1; MinAge=MinAge; MaxAge=MaxAge; RefAge=10; MinusAge=1; PlusAge=30; MaxS ... [TRUNCATED]
       RunFn(Data=AgeReads2, SigOpt=SigOpt, BiasOpt=BiasOpt, NDataSets=1, MinAge=MinAge, MaxAge=MaxAge, RefAge=10, MinusAge=1, PlusAge=30, S ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘updateAgeingErrorCode’
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 'RunFn':
RunFn
  Code: function(Data, SigOpt, KnotAges, BiasOpt, NDataSets, MinAge,
                 MaxAge, RefAge, MinusAge, PlusAge, MaxSd,
                 MaxExpectedAge, SaveFile, EffSampleSize = 0, Intern =
                 TRUE, AdmbFile = NULL, JustWrite = FALSE, CallType =
                 "system")
  Docs: function(Data, SigOpt, BiasOpt, NDataSets, MinAge, MaxAge,
                 RefAge, MinusAge, PlusAge, MaxSd, MaxExpectedAge,
                 SaveFile, EffSampleSize = 0, Intern = TRUE, AdmbFile =
                 NULL, JustWrite = FALSE)
  Argument names in code not in docs:
    KnotAges CallType
  Mismatches in argument names (first 3):
    Position: 3 Code: KnotAges Docs: BiasOpt
    Position: 4 Code: BiasOpt Docs: NDataSets
    Position: 5 Code: NDataSets Docs: MinAge

Codoc mismatches from documentation object 'StepwiseFn':
StepwiseFn
  Code: function(SearchMat, Data, NDataSets, MinAge, MaxAge, RefAge,
                 MaxSd, MaxExpectedAge, SaveFile, EffSampleSize = 0,
                 Intern = TRUE, InformationCriterion = "AIC",
                 SelectAges = TRUE)
  Docs: function(SearchMat, Data, NDataSets, MinAge, MaxAge, RefAge,
                 MaxSd, MaxExpectedAge, SaveFile, EffSampleSize = 0,
                 Intern = TRUE, InformationCriterion = "AIC")
  Argument names in code not in docs:
    SelectAges

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... WARNING
  ‘gs+qpdf’ made some significant size reductions:
     compacted ‘Instructions_for_use.pdf’ from 489Kb to 131Kb
  consider running tools::compactPDF(gs_quality = "ebook") on these files
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... [1s/3s] OK
* checking PDF version of manual ... OK

WARNING: There were 6 warnings.
NOTE: There were 4 notes.
See
  ‘/mnt/building/build_2014-01-23-00-12/RF_PKG_CHECK/PKGS/nwfscAgeingError.Rcheck/00check.log’
for details.

Run time: 89.82 seconds.