• using R version 2.10.0 alpha (2009-10-01 r49916)
• using session charset: ASCII
• checking for file 'CoCo/DESCRIPTION' ... OK
• looks like 'CoCo' is a package bundle
• this is bundle 'CoCo' version '0.1.7.5'
• checking bundle dependencies ... OK
• checking if this is a source bundle ... OK
• checking for executable files ... OK
• checking whether bundle 'CoCo' can be installed ... OK
• checking 'CoCoObjects' in bundle 'CoCo'
  • checking package directory ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking for file 'DESCRIPTION.in' ... OK
  • checking DESCRIPTION meta-information ... WARNING
    Invalid license file pointers: LICENSE
  • 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 name space can be loaded with stated dependencies ... 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 ... OK
  • checking Rd files ... OK
  • checking Rd metadata ... OK
  • checking Rd cross-references ... WARNING
    Missing link(s) in documentation object './man/CoCoClass-class.Rd':
    '[CoCoOldData]{select.cases}' '[CoCoRaw]{enterTwoList}'
    '[CoCoRaw]{ExcludeMissing}' '[dynamicGraph]{GraphLatticeProto-class}'
    
    Missing link(s) in documentation object './man/CoCoIdClass-class.Rd':
    '[dynamicGraph]{GraphLatticeProto-class}'
    
    Missing link(s) in documentation object './man/CoCoModelClass-class.Rd':
    '[dynamicGraph]{GraphLatticeProto-class}'
    
    Suspect link(s) in documentation object './man/CoCoClass-class.Rd':
    '[CoCoOldData]{set.observations.file}'
    '[CoCoOldData]{set.specification.file}'
    '[CoCoOldData]{read.specification}' '[CoCoOldData]{read.names}'
    '[CoCoOldData]{read.factors}' '[CoCoOldData]{or.reject.cases}'
    '[CoCoOldData]{or.select.cases}' '[CoCoOldData]{read.observations}'
    '[CoCoOldData]{read.table.coco}' '[CoCoOldData]{read.list}'
    '[CoCoOldData]{read.q.list}' '[CoCoRaw]{importCoCo}'
    '[CoCoRaw]{enterQlist}'
    
    See the information in section 'Cross-references' of the 'Writing R
    Extensions' manual.
    
    'Suspect' links are those of the form \link[pkg]{a} where 'a' exists as
    an alias but not as a filename -- such links will not work in R <
    2.10.0, and only in HTML (not PDF) help in current versions.
    
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking examples ... OK
• checking 'CoCoCore' in bundle 'CoCo'
  • checking package directory ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking for file 'DESCRIPTION.in' ... OK
  • checking DESCRIPTION meta-information ... WARNING
    Invalid license file pointers: LICENSE
  • 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 name space can be loaded with stated dependencies ... 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 ... OK
  • checking Rd files ... OK
  • checking Rd metadata ... OK
  • checking Rd cross-references ... WARNING
    Missing link(s) in documentation object './man/call.coco.Rd':
    '[CoCoRaw]{cutpoints}' '[CoCoOldData]{select.cases}'
    
    Missing link(s) in documentation object './man/call.coco.chars.Rd':
    '[CoCoOldData]{excludeMissing}'
    
    Missing link(s) in documentation object './man/coco.simple.model.Rd':
    '[CoCoRaw]{editmodel}'
    
    Suspect link(s) in documentation object './man/call.coco.Rd':
    '[CoCoRaw]{enterQlist}' '[CoCoRaw]{enterTwoLists}'
    '[CoCoOldData]{or.reject.cases}' '[CoCoOldData]{or.select.cases}'
    
    Suspect link(s) in documentation object './man/call.coco.chars.Rd':
    '[CoCoOldData]{read.q.list}' '[CoCoRaw]{ehForceReject}'
    '[CoCoOldData]{set.observations.file}'
    '[CoCoOldData]{set.specification.file}' '[CoCoRaw]{importCoCo}'
    '[CoCoRaw]{makeBase}'
    
    Suspect link(s) in documentation object './man/call.coco.simple.Rd':
    '[CoCoOldData]{read.factors}' '[CoCoOldData]{read.list}'
    '[CoCoOldData]{read.names}' '[CoCoOldData]{read.observations}'
    '[CoCoOldData]{read.specification}' '[CoCoOldData]{read.table.coco}'
    '[CoCoRaw]{forward}'
    
    Suspect link(s) in documentation object './man/coco.start.Rd':
    '[CoCoCore]{coco.resume}'
    
    See the information in section 'Cross-references' of the 'Writing R
    Extensions' manual.
    
    'Suspect' links are those of the form \link[pkg]{a} where 'a' exists as
    an alias but not as a filename -- such links will not work in R <
    2.10.0, and only in HTML (not PDF) help in current versions.
    
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking line endings in C/C++/Fortran sources/headers ... OK
  • checking line endings in Makefiles ... OK
  • checking for portable compilation flags in Makevars ... OK
  • checking for portable use of $BLAS_LIBS ... OK
  • checking examples ... OK
• checking 'CoCoRaw' in bundle 'CoCo'
  • checking package directory ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking for file 'DESCRIPTION.in' ... OK
  • checking DESCRIPTION meta-information ... WARNING
    Invalid license file pointers: LICENSE
  • 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 name space can be loaded with stated dependencies ... 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 ... OK
  • checking Rd files ... OK
  • checking Rd metadata ... OK
  • checking Rd cross-references ... WARNING
    Suspect link(s) in documentation object './man/exportCoCo.Rd':
    '[CoCoObjects]{makeCurrentCoCo}'
    
    See the information in section 'Cross-references' of the 'Writing R
    Extensions' manual.
    
    'Suspect' links are those of the form \link[pkg]{a} where 'a' exists as
    an alias but not as a filename -- such links will not work in R <
    2.10.0, and only in HTML (not PDF) help in current versions.
    
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking examples ... OK
• checking 'CoCoOldData' in bundle 'CoCo'
  • checking package directory ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking for file 'DESCRIPTION.in' ... OK
  • checking DESCRIPTION meta-information ... WARNING
    Invalid license file pointers: LICENSE
  • 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 name space can be loaded with stated dependencies ... 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 ... OK
  • checking Rd files ... OK
  • checking Rd metadata ... OK
  • checking Rd cross-references ... WARNING
    Missing link(s) in documentation object './man/cutpoints.Rd':
    '[CoCoRaw]{read.data}'
    
    Missing link(s) in documentation object './man/read.data.Rd':
    '[CoCoRaw]{set.data.file}'
    
    Missing link(s) in documentation object './man/redefine.factor.Rd':
    '[CoCoRaw]{read.data}'
    
    Missing link(s) in documentation object './man/reject.cases.Rd':
    '[CoCoRaw]{read.data}'
    
    Missing link(s) in documentation object './man/set.data.file.Rd':
    '[CoCoRaw]{read.data}'
    
    Missing link(s) in documentation object './man/skip.missing.Rd':
    '[CoCoRaw]{read.data}'
    
    See the information in section 'Cross-references' of the 'Writing R
    Extensions' manual.
    
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking examples ... NONE
• checking 'CoCoGraph' in bundle 'CoCo'
  • checking package directory ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking for file 'DESCRIPTION.in' ... OK
  • checking DESCRIPTION meta-information ... WARNING
    Invalid license file pointers: LICENSE
  • 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 name space can be loaded with stated dependencies ... 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 ... OK
  • checking Rd files ... OK
  • checking Rd metadata ... OK
  • checking Rd cross-references ... WARNING
    Suspect link(s) in documentation object './man/CoCoGraph-internal.Rd':
    '[dynamicGraph]{dg}' '[dynamicGraph]{modifyModel}'
    '[dynamicGraph]{testEdge}'
    
    See the information in section 'Cross-references' of the 'Writing R
    Extensions' manual.
    
    'Suspect' links are those of the form \link[pkg]{a} where 'a' exists as
    an alias but not as a filename -- such links will not work in R <
    2.10.0, and only in HTML (not PDF) help in current versions.
    
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking examples ... NONE
• checking 'CoCo' in bundle 'CoCo'
  • checking package directory ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking for file 'DESCRIPTION.in' ... OK
  • checking DESCRIPTION meta-information ... WARNING
    Invalid license file pointers: LICENSE
  • 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 name space can be loaded with stated dependencies ... 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 ... OK
  • checking Rd files ... OK
  • checking Rd metadata ... OK
  • checking Rd cross-references ... WARNING
    Unknown package(s) 'quitCoCo' in Rd xrefs
    Suspect link(s) in documentation object './man/CoCo-internal.Rd':
    '[dynamicGraph]{dg}'
    
    Suspect link(s) in documentation object './man/CoCo-package.Rd':
    '[dynamicGraph]{dg}' '[CoCoCg]{CoCoCg}'
    
    See the information in section 'Cross-references' of the 'Writing R
    Extensions' manual.
    
    'Suspect' links are those of the form \link[pkg]{a} where 'a' exists as
    an alias but not as a filename -- such links will not work in R <
    2.10.0, and only in HTML (not PDF) help in current versions.
    
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking data for non-ASCII characters ... OK
  • checking examples ... OK
• checking 'CoCoCg' in bundle 'CoCo'
  • checking package directory ... OK
  • checking for portable file names ... OK
  • checking for sufficient/correct file permissions ... OK
  • checking for file 'DESCRIPTION.in' ... OK
  • checking DESCRIPTION meta-information ... WARNING
    Invalid license file pointers: LICENSE
  • 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 name space can be loaded with stated dependencies ... 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 ... OK
  • checking Rd files ... OK
  • checking Rd metadata ... OK
  • checking Rd cross-references ... WARNING
    Unknown package(s) 'quitCoCo' in Rd xrefs
    Suspect link(s) in documentation object './man/CoCoCg-package.Rd':
    '[CoCo]{CoCo}'
    
    See the information in section 'Cross-references' of the 'Writing R
    Extensions' manual.
    
    'Suspect' links are those of the form \link[pkg]{a} where 'a' exists as
    an alias but not as a filename -- such links will not work in R <
    2.10.0, and only in HTML (not PDF) help in current versions.
    
  • checking for missing documentation entries ... OK
  • checking for code/documentation mismatches ... OK
  • checking Rd \usage sections ... OK
  • checking data for non-ASCII characters ... OK
  • checking line endings in C/C++/Fortran sources/headers ... OK
  • checking line endings in Makefiles ... OK
  • checking for portable compilation flags in Makevars ... OK
  • checking for portable use of $BLAS_LIBS ... OK
  • checking examples ... OK
• elapsed time (check, wall clock): 9:54