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nwfscSurveyCode log file (check_x86_64_linux)

Fri Sep 13 20:59:35 2013: Checking package nwfscSurveyCode (SVN revision 110) ...
* using log directory ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck’
* using R version 3.0.1 Patched (2013-09-11 r63910)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘nwfscSurveyCode/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘nwfscSurveyCode’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Allan Hicks ’
New submission
Non-FOSS package license (What license is it under?)
* 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 ‘nwfscSurveyCode’ can be installed ... [1s/2s] WARNING
Found the following significant warnings:
  Warning: /mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/StrataAreas.fn.Rd:29: unknown macro '\begin'
  Warning: /mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/StrataAreas.fn.Rd:39: unknown macro '\end'
  Warning: /mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/StrataFactors.fn.Rd:29: unknown macro '\begin'
  Warning: /mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/StrataFactors.fn.Rd:39: unknown macro '\end'
  Warning: /mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SurveyAgeAtLen.EWC.fn.Rd:70: unknown macro '\begin'
  Warning: /mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SurveyAgeAtLen.EWC.fn.Rd:80: unknown macro '\end'
  Warning: /mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SurveyLFs.EWC.fn.Rd:58: unknown macro '\begin'
  Warning: /mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SurveyLFs.EWC.fn.Rd:68: unknown macro '\end'
  Warning: /mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/nwfscSurveyCode-package.Rd:27: All text must be in a section
See ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... WARNING
Non-standard license specification:
  What license is it under?
Standardizable: FALSE
* 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 dependencies in R code ... WARNING
‘library’ or ‘require’ call not declared from: ‘RODBC’
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
plotBioStrata.fn: warning in axis(1, at = x, label =
  as.character(bio$Stratum), padj = 0, las = 2, cex.axis = 0.5):
  partial argument match of 'label' to 'labels'
plotFreqDataStrata.fn: warning in axis(1, at = x, label = xlabels, padj
  = 0, las = 2, cex.axis = 0.5): partial argument match of 'label' to
  'labels'
readDataFromExcel.fn: no visible global function definition for
  ‘odbcConnectExcel’
readDataFromExcel.fn: no visible global function definition for
  ‘sqlFetch’
readDataFromExcel.fn: no visible global function definition for
  ‘sqlFetchMore’

Found the following calls to attach():
File ‘nwfscSurveyCode/R/updateSurveyCode.R’:
  attach(NULL, pos = pos, name = env)
See section ‘Good practice’ in ‘?attach’.
* checking Rd files ... WARNING
prepare_Rd: DesignBasedEstBiomass.EWC.fn.Rd:58-60: Dropping empty section \note
prepare_Rd: DesignBasedEstBiomass.EWC.fn.Rd:52-54: Dropping empty section \references
prepare_Rd: GetAges.fn.Rd:48-50: Dropping empty section \details
prepare_Rd: GetAges.fn.Rd:51-57: Dropping empty section \value
prepare_Rd: GetAges.fn.Rd:64-66: Dropping empty section \note
prepare_Rd: GetAges.fn.Rd:61-63: Dropping empty section \author
prepare_Rd: GetAges.fn.Rd:58-60: Dropping empty section \references
prepare_Rd: GetAges.fn.Rd:70-72: Dropping empty section \seealso
prepare_Rd: GetAges.fn.Rd:73-88: Dropping empty section \examples
prepare_Rd: GetAgesExcel.fn.Rd:49-51: Dropping empty section \details
prepare_Rd: GetAgesExcel.fn.Rd:52-58: Dropping empty section \value
prepare_Rd: GetAgesExcel.fn.Rd:65-67: Dropping empty section \note
prepare_Rd: GetAgesExcel.fn.Rd:62-64: Dropping empty section \author
prepare_Rd: GetAgesExcel.fn.Rd:59-61: Dropping empty section \references
prepare_Rd: GetAgesExcel.fn.Rd:71-73: Dropping empty section \seealso
prepare_Rd: GetAgesExcel.fn.Rd:74-89: Dropping empty section \examples
prepare_Rd: GetLFs.fn.Rd:52-54: Dropping empty section \details
prepare_Rd: GetLFs.fn.Rd:55-61: Dropping empty section \value
prepare_Rd: GetLFs.fn.Rd:68-70: Dropping empty section \note
prepare_Rd: GetLFs.fn.Rd:65-67: Dropping empty section \author
prepare_Rd: GetLFs.fn.Rd:62-64: Dropping empty section \references
prepare_Rd: GetLFs.fn.Rd:74-76: Dropping empty section \seealso
prepare_Rd: GetLFs.fn.Rd:77-93: Dropping empty section \examples
prepare_Rd: GetLFsFromExcel.fn.Rd:52-54: Dropping empty section \details
prepare_Rd: GetLFsFromExcel.fn.Rd:55-61: Dropping empty section \value
prepare_Rd: GetLFsFromExcel.fn.Rd:68-70: Dropping empty section \note
prepare_Rd: GetLFsFromExcel.fn.Rd:65-67: Dropping empty section \author
prepare_Rd: GetLFsFromExcel.fn.Rd:62-64: Dropping empty section \references
prepare_Rd: GetLFsFromExcel.fn.Rd:74-76: Dropping empty section \seealso
prepare_Rd: GetLFsFromExcel.fn.Rd:77-93: Dropping empty section \examples
prepare_Rd: GetTotalBiomass.fn.Rd:32-34: Dropping empty section \details
prepare_Rd: GetTotalBiomass.fn.Rd:35-41: Dropping empty section \value
prepare_Rd: GetTotalBiomass.fn.Rd:48-50: Dropping empty section \note
prepare_Rd: GetTotalBiomass.fn.Rd:45-47: Dropping empty section \author
prepare_Rd: GetTotalBiomass.fn.Rd:42-44: Dropping empty section \references
prepare_Rd: GetTotalBiomass.fn.Rd:54-56: Dropping empty section \seealso
prepare_Rd: GetTotalBiomass.fn.Rd:57-69: Dropping empty section \examples
prepare_Rd: GetTotalBiomassExcel.fn.Rd:34-36: Dropping empty section \details
prepare_Rd: GetTotalBiomassExcel.fn.Rd:37-43: Dropping empty section \value
prepare_Rd: GetTotalBiomassExcel.fn.Rd:50-52: Dropping empty section \note
prepare_Rd: GetTotalBiomassExcel.fn.Rd:47-49: Dropping empty section \author
prepare_Rd: GetTotalBiomassExcel.fn.Rd:44-46: Dropping empty section \references
prepare_Rd: GetTotalBiomassExcel.fn.Rd:56-58: Dropping empty section \seealso
prepare_Rd: GetTotalBiomassExcel.fn.Rd:59-71: Dropping empty section \examples
prepare_Rd: ReadInBiomass.EWC.fn.Rd:35-37: Dropping empty section \details
prepare_Rd: ReadInBiomass.EWC.fn.Rd:47-49: Dropping empty section \note
prepare_Rd: ReadInBiomass.EWC.fn.Rd:41-43: Dropping empty section \references
prepare_Rd: ReadInBiomass.EWC.fn.Rd:53-55: Dropping empty section \seealso
prepare_Rd: ReadInBiomass.EWC.fn.Rd:56-58: Dropping empty section \examples
prepare_Rd: ReadInLengths.EWC.fn.Rd:31-33: Dropping empty section \details
prepare_Rd: ReadInLengths.EWC.fn.Rd:43-45: Dropping empty section \note
prepare_Rd: ReadInLengths.EWC.fn.Rd:37-39: Dropping empty section \references
prepare_Rd: ReadInLengths.EWC.fn.Rd:49-51: Dropping empty section \seealso
prepare_Rd: ReadInLengths.EWC.fn.Rd:52-54: Dropping empty section \examples
prepare_Rd: SA3.Rd:23-25: Dropping empty section \details
prepare_Rd: SA3.Rd:29-31: Dropping empty section \references
prepare_Rd: SS3AgeAtLen.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: SS3AgeAtLen.fn.Rd:46-48: Dropping empty section \details
prepare_Rd: SS3AgeAtLen.fn.Rd:49-55: Dropping empty section \value
prepare_Rd: SS3AgeAtLen.fn.Rd:62-64: Dropping empty section \note
prepare_Rd: SS3AgeAtLen.fn.Rd:59-61: Dropping empty section \author
prepare_Rd: SS3AgeAtLen.fn.Rd:56-58: Dropping empty section \references
prepare_Rd: SS3AgeAtLen.fn.Rd:68-70: Dropping empty section \seealso
prepare_Rd: SS3AgeAtLen.fn.Rd:71-80: Dropping empty section \examples
checkRd: (5) SS3AgeAtLen.fn.Rd:0-85: Must have a \description
prepare_Rd: SS3Biomass.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: SS3Biomass.fn.Rd:28-30: Dropping empty section \details
prepare_Rd: SS3Biomass.fn.Rd:31-37: Dropping empty section \value
prepare_Rd: SS3Biomass.fn.Rd:44-46: Dropping empty section \note
prepare_Rd: SS3Biomass.fn.Rd:41-43: Dropping empty section \author
prepare_Rd: SS3Biomass.fn.Rd:38-40: Dropping empty section \references
prepare_Rd: SS3Biomass.fn.Rd:50-52: Dropping empty section \seealso
prepare_Rd: SS3Biomass.fn.Rd:53-60: Dropping empty section \examples
checkRd: (5) SS3Biomass.fn.Rd:0-65: Must have a \description
prepare_Rd: SS3LF.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: SS3LF.fn.Rd:46-48: Dropping empty section \details
prepare_Rd: SS3LF.fn.Rd:49-55: Dropping empty section \value
prepare_Rd: SS3LF.fn.Rd:62-64: Dropping empty section \note
prepare_Rd: SS3LF.fn.Rd:59-61: Dropping empty section \author
prepare_Rd: SS3LF.fn.Rd:56-58: Dropping empty section \references
prepare_Rd: SS3LF.fn.Rd:68-70: Dropping empty section \seealso
prepare_Rd: SS3LF.fn.Rd:71-80: Dropping empty section \examples
checkRd: (5) SS3LF.fn.Rd:0-85: Must have a \description
prepare_Rd: SS3LFstrata.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: SS3LFstrata.fn.Rd:43-45: Dropping empty section \details
prepare_Rd: SS3LFstrata.fn.Rd:46-52: Dropping empty section \value
prepare_Rd: SS3LFstrata.fn.Rd:59-61: Dropping empty section \note
prepare_Rd: SS3LFstrata.fn.Rd:56-58: Dropping empty section \author
prepare_Rd: SS3LFstrata.fn.Rd:53-55: Dropping empty section \references
prepare_Rd: SS3LFstrata.fn.Rd:65-67: Dropping empty section \seealso
prepare_Rd: SS3LFstrata.fn.Rd:68-76: Dropping empty section \examples
checkRd: (5) SS3LFstrata.fn.Rd:0-81: Must have a \description
prepare_Rd: StrataAreas.fn.Rd:29: unknown macro '\begin'
prepare_Rd: StrataAreas.fn.Rd:39: unknown macro '\end'
prepare_Rd: StrataAreas.fn.Rd:52-54: Dropping empty section \note
prepare_Rd: StrataAreas.fn.Rd:46-48: Dropping empty section \references
prepare_Rd: StrataAreas.fn.Rd:58-60: Dropping empty section \seealso
prepare_Rd: StrataAreas.fn.Rd:61-63: Dropping empty section \examples
prepare_Rd: StrataFactors.fn.Rd:29: unknown macro '\begin'
prepare_Rd: StrataFactors.fn.Rd:39: unknown macro '\end'
prepare_Rd: StrataFactors.fn.Rd:52-54: Dropping empty section \note
prepare_Rd: StrataFactors.fn.Rd:46-48: Dropping empty section \references
prepare_Rd: StrataFactors.fn.Rd:58-60: Dropping empty section \seealso
prepare_Rd: StrataFactors.fn.Rd:61-62: Dropping empty section \examples
prepare_Rd: SurveyAgeAtLen.EWC.fn.Rd:70: unknown macro '\begin'
prepare_Rd: SurveyAgeAtLen.EWC.fn.Rd:80: unknown macro '\end'
prepare_Rd: SurveyAgeAtLen.EWC.fn.Rd:100-102: Dropping empty section \note
prepare_Rd: SurveyAgeAtLen.EWC.fn.Rd:94-96: Dropping empty section \references
prepare_Rd: SurveyAgeAtLen.EWC.fn.Rd:106-108: Dropping empty section \seealso
prepare_Rd: SurveyAgeAtLen.EWC.fn.Rd:109-110: Dropping empty section \examples
prepare_Rd: SurveyLFs.EWC.fn.Rd:58: unknown macro '\begin'
prepare_Rd: SurveyLFs.EWC.fn.Rd:68: unknown macro '\end'
prepare_Rd: SurveyLFs.EWC.fn.Rd:91-93: Dropping empty section \note
prepare_Rd: SurveyLFs.EWC.fn.Rd:85-87: Dropping empty section \references
prepare_Rd: SurveyLFs.EWC.fn.Rd:97-99: Dropping empty section \seealso
prepare_Rd: createStrataDF.fn.Rd:44-47: Dropping empty section \value
prepare_Rd: createStrataDF.fn.Rd:54-56: Dropping empty section \note
prepare_Rd: createStrataDF.fn.Rd:48-50: Dropping empty section \references
prepare_Rd: createStrataDF.fn.Rd:63-68: Dropping empty section \examples
prepare_Rd: nwfscSurveyCode-package.Rd:27: All text must be in a section
prepare_Rd: nwfscSurveyCode-package.Rd:33-34: Dropping empty section \examples
prepare_Rd: plotBio.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: plotBio.fn.Rd:40-42: Dropping empty section \details
prepare_Rd: plotBio.fn.Rd:43-49: Dropping empty section \value
prepare_Rd: plotBio.fn.Rd:56-58: Dropping empty section \note
prepare_Rd: plotBio.fn.Rd:53-55: Dropping empty section \author
prepare_Rd: plotBio.fn.Rd:50-52: Dropping empty section \references
prepare_Rd: plotBio.fn.Rd:62-64: Dropping empty section \seealso
prepare_Rd: plotBio.fn.Rd:65-73: Dropping empty section \examples
checkRd: (5) plotBio.fn.Rd:0-78: Must have a \description
prepare_Rd: plotBioStrata.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: plotBioStrata.fn.Rd:40-42: Dropping empty section \details
prepare_Rd: plotBioStrata.fn.Rd:43-49: Dropping empty section \value
prepare_Rd: plotBioStrata.fn.Rd:56-58: Dropping empty section \note
prepare_Rd: plotBioStrata.fn.Rd:53-55: Dropping empty section \author
prepare_Rd: plotBioStrata.fn.Rd:50-52: Dropping empty section \references
prepare_Rd: plotBioStrata.fn.Rd:62-64: Dropping empty section \seealso
prepare_Rd: plotBioStrata.fn.Rd:65-73: Dropping empty section \examples
checkRd: (5) plotBioStrata.fn.Rd:0-78: Must have a \description
prepare_Rd: plotFreqData.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: plotFreqData.fn.Rd:37-39: Dropping empty section \details
prepare_Rd: plotFreqData.fn.Rd:40-46: Dropping empty section \value
prepare_Rd: plotFreqData.fn.Rd:53-55: Dropping empty section \note
prepare_Rd: plotFreqData.fn.Rd:50-52: Dropping empty section \author
prepare_Rd: plotFreqData.fn.Rd:47-49: Dropping empty section \references
prepare_Rd: plotFreqData.fn.Rd:59-61: Dropping empty section \seealso
prepare_Rd: plotFreqData.fn.Rd:62-70: Dropping empty section \examples
checkRd: (5) plotFreqData.fn.Rd:0-75: Must have a \description
prepare_Rd: plotFreqDataStrata.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: plotFreqDataStrata.fn.Rd:34-36: Dropping empty section \details
prepare_Rd: plotFreqDataStrata.fn.Rd:37-43: Dropping empty section \value
prepare_Rd: plotFreqDataStrata.fn.Rd:50-52: Dropping empty section \note
prepare_Rd: plotFreqDataStrata.fn.Rd:47-49: Dropping empty section \author
prepare_Rd: plotFreqDataStrata.fn.Rd:44-46: Dropping empty section \references
prepare_Rd: plotFreqDataStrata.fn.Rd:56-58: Dropping empty section \seealso
prepare_Rd: plotFreqDataStrata.fn.Rd:59-67: Dropping empty section \examples
checkRd: (5) plotFreqDataStrata.fn.Rd:0-72: Must have a \description
prepare_Rd: plotLFs.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: plotLFs.fn.Rd:34-36: Dropping empty section \details
prepare_Rd: plotLFs.fn.Rd:37-43: Dropping empty section \value
prepare_Rd: plotLFs.fn.Rd:50-52: Dropping empty section \note
prepare_Rd: plotLFs.fn.Rd:47-49: Dropping empty section \author
prepare_Rd: plotLFs.fn.Rd:44-46: Dropping empty section \references
prepare_Rd: plotLFs.fn.Rd:56-58: Dropping empty section \seealso
prepare_Rd: plotLFs.fn.Rd:59-67: Dropping empty section \examples
checkRd: (5) plotLFs.fn.Rd:0-72: Must have a \description
prepare_Rd: plotSexRatio.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: plotSexRatio.fn.Rd:29-31: Dropping empty section \details
prepare_Rd: plotSexRatio.fn.Rd:32-38: Dropping empty section \value
prepare_Rd: plotSexRatio.fn.Rd:45-47: Dropping empty section \note
prepare_Rd: plotSexRatio.fn.Rd:39-41: Dropping empty section \references
prepare_Rd: plotSexRatio.fn.Rd:51-53: Dropping empty section \seealso
prepare_Rd: plotSexRatio.fn.Rd:54-61: Dropping empty section \examples
checkRd: (5) plotSexRatio.fn.Rd:0-66: Must have a \description
prepare_Rd: readDataFromExcel.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: readDataFromExcel.fn.Rd:25-27: Dropping empty section \details
prepare_Rd: readDataFromExcel.fn.Rd:28-34: Dropping empty section \value
prepare_Rd: readDataFromExcel.fn.Rd:41-43: Dropping empty section \note
prepare_Rd: readDataFromExcel.fn.Rd:38-40: Dropping empty section \author
prepare_Rd: readDataFromExcel.fn.Rd:35-37: Dropping empty section \references
prepare_Rd: readDataFromExcel.fn.Rd:47-49: Dropping empty section \seealso
prepare_Rd: readDataFromExcel.fn.Rd:50-57: Dropping empty section \examples
checkRd: (5) readDataFromExcel.fn.Rd:0-62: Must have a \description
prepare_Rd: readInAgeComps.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: readInAgeComps.fn.Rd:28-30: Dropping empty section \details
prepare_Rd: readInAgeComps.fn.Rd:31-37: Dropping empty section \value
prepare_Rd: readInAgeComps.fn.Rd:44-46: Dropping empty section \note
prepare_Rd: readInAgeComps.fn.Rd:41-43: Dropping empty section \author
prepare_Rd: readInAgeComps.fn.Rd:38-40: Dropping empty section \references
prepare_Rd: readInAgeComps.fn.Rd:50-52: Dropping empty section \seealso
prepare_Rd: readInAgeComps.fn.Rd:53-63: Dropping empty section \examples
checkRd: (5) readInAgeComps.fn.Rd:0-68: Must have a \description
prepare_Rd: readInBiomass.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: readInBiomass.fn.Rd:28-30: Dropping empty section \details
prepare_Rd: readInBiomass.fn.Rd:31-37: Dropping empty section \value
prepare_Rd: readInBiomass.fn.Rd:44-46: Dropping empty section \note
prepare_Rd: readInBiomass.fn.Rd:41-43: Dropping empty section \author
prepare_Rd: readInBiomass.fn.Rd:38-40: Dropping empty section \references
prepare_Rd: readInBiomass.fn.Rd:50-52: Dropping empty section \seealso
prepare_Rd: readInBiomass.fn.Rd:53-65: Dropping empty section \examples
checkRd: (5) readInBiomass.fn.Rd:0-70: Must have a \description
prepare_Rd: readInExcelAgeComps.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: readInExcelAgeComps.fn.Rd:25-27: Dropping empty section \details
prepare_Rd: readInExcelAgeComps.fn.Rd:28-34: Dropping empty section \value
prepare_Rd: readInExcelAgeComps.fn.Rd:41-43: Dropping empty section \note
prepare_Rd: readInExcelAgeComps.fn.Rd:38-40: Dropping empty section \author
prepare_Rd: readInExcelAgeComps.fn.Rd:35-37: Dropping empty section \references
prepare_Rd: readInExcelAgeComps.fn.Rd:47-49: Dropping empty section \seealso
prepare_Rd: readInExcelAgeComps.fn.Rd:50-57: Dropping empty section \examples
checkRd: (5) readInExcelAgeComps.fn.Rd:0-62: Must have a \description
prepare_Rd: readInExcelBiomass.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: readInExcelBiomass.fn.Rd:28-30: Dropping empty section \details
prepare_Rd: readInExcelBiomass.fn.Rd:31-37: Dropping empty section \value
prepare_Rd: readInExcelBiomass.fn.Rd:44-46: Dropping empty section \note
prepare_Rd: readInExcelBiomass.fn.Rd:41-43: Dropping empty section \author
prepare_Rd: readInExcelBiomass.fn.Rd:38-40: Dropping empty section \references
prepare_Rd: readInExcelBiomass.fn.Rd:50-52: Dropping empty section \seealso
prepare_Rd: readInExcelBiomass.fn.Rd:53-60: Dropping empty section \examples
checkRd: (5) readInExcelBiomass.fn.Rd:0-65: Must have a \description
prepare_Rd: readInExcelLengthComps.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: readInExcelLengthComps.fn.Rd:25-27: Dropping empty section \details
prepare_Rd: readInExcelLengthComps.fn.Rd:28-34: Dropping empty section \value
prepare_Rd: readInExcelLengthComps.fn.Rd:41-43: Dropping empty section \note
prepare_Rd: readInExcelLengthComps.fn.Rd:38-40: Dropping empty section \author
prepare_Rd: readInExcelLengthComps.fn.Rd:35-37: Dropping empty section \references
prepare_Rd: readInExcelLengthComps.fn.Rd:47-49: Dropping empty section \seealso
prepare_Rd: readInExcelLengthComps.fn.Rd:50-57: Dropping empty section \examples
checkRd: (5) readInExcelLengthComps.fn.Rd:0-62: Must have a \description
prepare_Rd: readInLengthComps.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: readInLengthComps.fn.Rd:28-30: Dropping empty section \details
prepare_Rd: readInLengthComps.fn.Rd:31-37: Dropping empty section \value
prepare_Rd: readInLengthComps.fn.Rd:44-46: Dropping empty section \note
prepare_Rd: readInLengthComps.fn.Rd:41-43: Dropping empty section \author
prepare_Rd: readInLengthComps.fn.Rd:38-40: Dropping empty section \references
prepare_Rd: readInLengthComps.fn.Rd:50-52: Dropping empty section \seealso
prepare_Rd: readInLengthComps.fn.Rd:53-63: Dropping empty section \examples
checkRd: (5) readInLengthComps.fn.Rd:0-68: Must have a \description
prepare_Rd: strataBiomass.fn.Rd:7-9: Dropping empty section \description
prepare_Rd: strataBiomass.fn.Rd:31-33: Dropping empty section \details
prepare_Rd: strataBiomass.fn.Rd:34-40: Dropping empty section \value
prepare_Rd: strataBiomass.fn.Rd:47-49: Dropping empty section \note
prepare_Rd: strataBiomass.fn.Rd:44-46: Dropping empty section \author
prepare_Rd: strataBiomass.fn.Rd:41-43: Dropping empty section \references
prepare_Rd: strataBiomass.fn.Rd:53-55: Dropping empty section \seealso
prepare_Rd: strataBiomass.fn.Rd:56-64: Dropping empty section \examples
checkRd: (5) strataBiomass.fn.Rd:0-69: Must have a \description
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/DesignBasedEstBiomass.EWC.fn.Rd’:
  \examples lines wider than 100 characters:
      xB$catchPerArea[is.na(xB$catchPerArea)&!is.na(xB$areaFished)] <- 0                                  #the tows with no observation of t ... [TRUNCATED]
      biomass <- DesignBasedEstBiomass.EWC.fn(xB,strat.vars=c("BOTTOM_DEPTH","START_LATITUDE"),strat.df=strata.AKslope)

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/GetAges.fn.Rd’:
  \usage lines wider than 90 characters:
     GetAges.fn(file, headerRow, lgthBins = 1, ageBins = 1, nSamps = "EnterNsamps", fleet = "EnterFleet", season = 1, partition = 0, ageerr  ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/GetAgesExcel.fn.Rd’:
  \usage lines wider than 90 characters:
     GetAgesExcel.fn(file, sheet = "AgeComps", headerRow, lgthBins = 1, ageBins = 1, nSamps = "EnterNsamps", fleet = "EnterFleet", season =  ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/GetLFs.fn.Rd’:
  \usage lines wider than 90 characters:
     GetLFs.fn(file, headerRow, lgthBins = 1, gender = 3, nSamps = "EnterNsamps", fleet = "EnterFleet", season = 1, partition = 0, NAs2zero  ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/GetLFsFromExcel.fn.Rd’:
  \usage lines wider than 90 characters:
     GetLFsFromExcel.fn(file, sheet = "LengthComps", headerRow, lgthBins = 1, gender = 3, nSamps = "EnterNsamps", fleet = "EnterFleet", seas ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/GetTotalBiomassExcel.fn.Rd’:
  \usage lines wider than 90 characters:
     GetTotalBiomassExcel.fn(file, sheet = "BiomassAbundance", headerRow, fleet = "EnterFleet", season = 1, outputMedian = T)

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SS3AgeAtLen.fn.Rd’:
  \usage lines wider than 90 characters:
     SS3AgeAtLen.fn(ages, lgthBins = 1, ageBins = 1, fleet = "EnterFleet", season = 1, partition = 0, ageerr = "EnterAgeErr", raw = T, sexRa ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SS3LF.fn.Rd’:
  \usage lines wider than 90 characters:
     SS3LF.fn(len, lgthBins = 1, gender = 3, nSamps = "EnterNsamps", fleet = "EnterFleet", season = 1, partition = 0, NAs2zero = T, sexRatio ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SS3LFstrata.fn.Rd’:
  \usage lines wider than 90 characters:
     SS3LFstrata.fn(len, Strata = "Year", lgthBins = 1, gender = 3, nSamps = "EnterNsamps", fleet = "EnterFleet", season = 1, partition = 0, ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SurveyAgeAtLen.EWC.fn.Rd’:
  \usage lines wider than 90 characters:
     SurveyAgeAtLen.EWC.fn(datAL, datTows, strat.vars = NULL, strat.df = NULL, femaleMale = c(2, 1), lgthBins = 1, ageBins = 1, SS3out = F,  ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SurveyLFs.EWC.fn.Rd’:
  \usage lines wider than 90 characters:
     SurveyLFs.EWC.fn(datL, datTows, strat.vars = NULL, strat.df = NULL, femaleMale = c(2, 1), lgthBins = 1, SS3out = F, meanRatioMethod = T ... [TRUNCATED]
  \examples lines wider than 100 characters:
          LFs <- SurveyLFs.EWC.fn(xL,xB,strat.vars=c("BOTTOM_DEPTH","START_LATITUDE"),strat.df=strata.AKslope,femaleMale=c(2,1),lgthBins=seq ... [TRUNCATED]
          SurveyLFs.EWC.fn(xL,xB,strat.vars=c("BOTTOM_DEPTH","START_LATITUDE"),strat.df=strata.AKslope,femaleMale=c(2,1),lgthBins=c(80,600), ... [TRUNCATED]
          SurveyLFs.EWC.fn(xL,xB,strat.vars=c("BOTTOM_DEPTH","START_LATITUDE"),strat.df=strata.AKslope,femaleMale=c(2,1),lgthBins=seq(10,80, ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/plotBio.fn.Rd’:
  \usage lines wider than 90 characters:
     plotBio.fn(bio, CI = 0.95, scalar = 1e+06, gap = 0.03, ylab = "Biomass (‘000 mt)", xlab = "Year", ylim = NULL, ...)

Rd file ’/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/plotBioStrata.fn.Rd‘:
  \usage lines wider than 90 characters:
     plotBioStrata.fn(bio, CI = 0.95, scalar = 1e+06, gap = 0.03, ylab = "Biomass (’000 mt)", xlab = "Stratum", ylim = NULL, ...)

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/readInAgeComps.fn.Rd’:
  \usage lines wider than 90 characters:
     readInAgeComps.fn(file, headerRow = 7, sep = ",", colNames = c("SpeciesCode", "Species", "Year", "Project", "AreaName", "MinStratumDept ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/readInBiomass.fn.Rd’:
  \usage lines wider than 90 characters:
     readInBiomass.fn(filename, headerRow = 1, sep = ",", colNames = c("Species", "ScientificName", "SpeciesCode", "Year", "Project", "Strat ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/readInLengthComps.fn.Rd’:
  \usage lines wider than 90 characters:
     readInLengthComps.fn(file, headerRow = 7, sep = ",", colNames = c("SpeciesCode", "ScientificName", "Species", "Year", "Project", "AreaS ... [TRUNCATED]

Rd file ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/strataBiomass.fn.Rd’:
  \usage lines wider than 90 characters:
     strataBiomass.fn(bio, theStrata = "Year", fleet = "EnterFleet", season = 1, outputMedian = T)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Missing link or links in documentation object ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/DesignBasedEstBiomass.EWC.fn.Rd’:
  ‘StratAreas.fn’

Missing link or links in documentation object ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/StrataFactors.fn.Rd’:
  ‘StratAreas.fn’

Missing link or links in documentation object ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SurveyAgeAtLen.EWC.fn.Rd’:
  ‘StratAreas.fn’

Missing link or links in documentation object ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/SurveyLFs.EWC.fn.Rd’:
  ‘StratAreas.fn’

Missing link or links in documentation object ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00_pkg_src/nwfscSurveyCode/man/createStrataDF.fn.Rd’:
  ‘StratAreas.fn’

See the information in section ‘Cross-references’ of the ‘Writing R
Extensions’ manual.

* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘updateSurveyCode’
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 'plotFreqData.fn':
plotFreqData.fn
  Code: function(dat, inch = 0.15, ylab = "Bins", xlab = "Year",
                 zero2NAs = T, main = NULL, xlim = NULL, ...)
  Docs: function(dat, inch = 0.15, ylab = "Bins", xlab = "Year",
                 zero2NAs = T, ...)
  Argument names in code not in docs:
    main xlim
  Mismatches in argument names:
    Position: 6 Code: main Docs: ...

* checking Rd \usage sections ... WARNING
Documented arguments not in \usage in documentation object 'plotFreqData.fn':
  ‘main’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... [0s/1s] OK
* checking PDF version of manual ... OK

WARNING: There were 8 warnings.
NOTE: There were 3 notes.
See
  ‘/mnt/building/build_2013-09-13-08-12/RF_PKG_CHECK/PKGS/nwfscSurveyCode.Rcheck/00check.log’
for details.

Run time: 38.29 seconds.