R Development Page

ruleR log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2014-10-27-15-04/RF_PKG_CHECK/PKGS/ruleR.Rcheck'
* using R version 3.1.2 Patched (2014-11-05 r66943)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'ruleR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'ruleR' version '0.1'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Philipp Doebler '
New submission
Vignette sources in 'inst/doc' with no 'vignettes' directory:
  'ruleR.Rnw'
A 'vignettes' directory is required as from R 3.1.0
* checking package namespace information ... OK
* checking package dependencies ... NOTE
  No repository set, so cyclic dependency check skipped
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'ruleR' can be installed ... WARNING
Found the following significant warnings:
  Warning: undefined slot classes in definition of "SingleRule": previousRule(class "SingleRule")
See 'R:/run/building/build_2014-10-27-15-04/RF_PKG_CHECK/PKGS/ruleR.Rcheck/00install.out' for details.
* 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 dependencies in R code ... NOTE
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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 ... OK
* checking Rd files ... NOTE
prepare_Rd: AddConstSingleRule-class.Rd:37-39: Dropping empty section \note
prepare_Rd: AddConstSingleRule-class.Rd:31-33: Dropping empty section \references
prepare_Rd: AddDoubleRule-class.Rd:37-39: Dropping empty section \note
prepare_Rd: AddDoubleRule-class.Rd:31-33: Dropping empty section \references
prepare_Rd: DictionaryRule-class.Rd:32-34: Dropping empty section \note
prepare_Rd: DictionaryRule-class.Rd:29-31: Dropping empty section \author
prepare_Rd: DictionaryRule-class.Rd:26-28: Dropping empty section \references
prepare_Rd: DictionaryRule-class.Rd:42-45: Dropping empty section \examples
prepare_Rd: DigSumSingleRule-class.Rd:36-38: Dropping empty section \note
prepare_Rd: DigSumSingleRule-class.Rd:33-35: Dropping empty section \author
prepare_Rd: DigSumSingleRule-class.Rd:30-32: Dropping empty section \references
prepare_Rd: DoubleRule-class.Rd:13-15: Dropping empty section 'Objects from the Class'
prepare_Rd: DoubleRule-class.Rd:35-37: Dropping empty section \note
prepare_Rd: DoubleRule-class.Rd:32-34: Dropping empty section \author
prepare_Rd: DoubleRule-class.Rd:29-31: Dropping empty section \references
prepare_Rd: DoubleRule-class.Rd:49-51: Dropping empty section \examples
prepare_Rd: IdenSingleRule-class.Rd:35-37: Dropping empty section \note
prepare_Rd: IdenSingleRule-class.Rd:32-34: Dropping empty section \author
prepare_Rd: IdenSingleRule-class.Rd:29-31: Dropping empty section \references
prepare_Rd: MultConstSingleRule-class.Rd:36-38: Dropping empty section \note
prepare_Rd: MultConstSingleRule-class.Rd:33-35: Dropping empty section \author
prepare_Rd: MultConstSingleRule-class.Rd:30-32: Dropping empty section \references
prepare_Rd: MultDoubleRule-class.Rd:38-40: Dropping empty section \note
prepare_Rd: MultDoubleRule-class.Rd:35-37: Dropping empty section \author
prepare_Rd: MultDoubleRule-class.Rd:32-34: Dropping empty section \references
prepare_Rd: Rule-class.Rd:20-22: Dropping empty section \note
prepare_Rd: Rule-class.Rd:17-19: Dropping empty section \author
prepare_Rd: Rule-class.Rd:14-16: Dropping empty section \references
prepare_Rd: Rule-class.Rd:26-29: Dropping empty section \seealso
prepare_Rd: SingleRule-class.Rd:37-39: Dropping empty section \note
prepare_Rd: SingleRule-class.Rd:34-36: Dropping empty section \author
prepare_Rd: SingleRule-class.Rd:31-33: Dropping empty section \references
prepare_Rd: SingleRule-class.Rd:43-46: Dropping empty section \seealso
prepare_Rd: b.Rd:15-17: Dropping empty section \details
prepare_Rd: b.Rd:18-20: Dropping empty section \source
prepare_Rd: b.Rd:21-23: Dropping empty section \references
prepare_Rd: b.Rd:24-26: Dropping empty section \examples
prepare_Rd: basicDictionary.Rd:12-14: Dropping empty section \format
prepare_Rd: basicDictionary.Rd:15-17: Dropping empty section \details
prepare_Rd: basicDictionary.Rd:18-20: Dropping empty section \source
prepare_Rd: basicDictionary.Rd:21-23: Dropping empty section \references
prepare_Rd: basicDictionary.Rd:24-26: Dropping empty section \examples
prepare_Rd: calculate.Rd:35-37: Dropping empty section \note
prepare_Rd: calculate.Rd:32-34: Dropping empty section \author
prepare_Rd: calculate.Rd:29-31: Dropping empty section \references
prepare_Rd: calculateSpecific.Rd:42-44: Dropping empty section \note
prepare_Rd: calculateSpecific.Rd:39-41: Dropping empty section \author
prepare_Rd: calculateSpecific.Rd:36-38: Dropping empty section \references
prepare_Rd: calculateSpecific.Rd:48-50: Dropping empty section \seealso
prepare_Rd: check.Rd:36-38: Dropping empty section \note
prepare_Rd: check.Rd:33-35: Dropping empty section \author
prepare_Rd: check.Rd:30-32: Dropping empty section \references
prepare_Rd: conCheck.Rd:36-38: Dropping empty section \note
prepare_Rd: conCheck.Rd:33-35: Dropping empty section \author
prepare_Rd: conCheck.Rd:30-32: Dropping empty section \references
prepare_Rd: conCheck.Rd:42-44: Dropping empty section \seealso
prepare_Rd: conCheck.Rd:45-47: Dropping empty section \examples
prepare_Rd: createDR.Rd:44-46: Dropping empty section \note
prepare_Rd: createDR.Rd:41-43: Dropping empty section \author
prepare_Rd: createDR.Rd:38-40: Dropping empty section \references
prepare_Rd: createDictRule.Rd:28-30: Dropping empty section \details
prepare_Rd: createDictRule.Rd:31-37: Dropping empty section \value
prepare_Rd: createDictRule.Rd:44-46: Dropping empty section \note
prepare_Rd: createDictRule.Rd:41-43: Dropping empty section \author
prepare_Rd: createDictRule.Rd:38-40: Dropping empty section \references
prepare_Rd: createDictRule.Rd:50-52: Dropping empty section \seealso
prepare_Rd: createSR.Rd:28-30: Dropping empty section \details
prepare_Rd: createSR.Rd:31-37: Dropping empty section \value
prepare_Rd: createSR.Rd:44-46: Dropping empty section \note
prepare_Rd: createSR.Rd:41-43: Dropping empty section \author
prepare_Rd: createSR.Rd:38-40: Dropping empty section \references
prepare_Rd: createSR.Rd:50-52: Dropping empty section \seealso
prepare_Rd: createTest.Rd:58-60: Dropping empty section \note
prepare_Rd: createTest.Rd:55-57: Dropping empty section \author
prepare_Rd: createTest.Rd:52-54: Dropping empty section \references
prepare_Rd: digits.Rd:20-22: Dropping empty section \details
prepare_Rd: digits.Rd:37-39: Dropping empty section \note
prepare_Rd: digits.Rd:34-36: Dropping empty section \author
prepare_Rd: doubleRules.Rd:37-39: Dropping empty section \details
prepare_Rd: doubleRules.Rd:40-42: Dropping empty section \source
prepare_Rd: doubleRules.Rd:43-45: Dropping empty section \references
prepare_Rd: duplicate.Rd:38-40: Dropping empty section \note
prepare_Rd: duplicate.Rd:35-37: Dropping empty section \author
prepare_Rd: duplicate.Rd:32-34: Dropping empty section \references
prepare_Rd: duplicate.Rd:44-46: Dropping empty section \seealso
prepare_Rd: generateRule.Rd:25-27: Dropping empty section \details
prepare_Rd: generateRule.Rd:28-34: Dropping empty section \value
prepare_Rd: generateRule.Rd:41-43: Dropping empty section \note
prepare_Rd: generateRule.Rd:38-40: Dropping empty section \author
prepare_Rd: generateRule.Rd:35-37: Dropping empty section \references
prepare_Rd: generateRule.Rd:47-49: Dropping empty section \seealso
prepare_Rd: generateRule.Rd:50-51: Dropping empty section \examples
prepare_Rd: generate_cv.Rd:19-21: Dropping empty section \details
prepare_Rd: generate_cv.Rd:22-28: Dropping empty section \value
prepare_Rd: generate_cv.Rd:35-37: Dropping empty section \note
prepare_Rd: generate_cv.Rd:32-34: Dropping empty section \author
prepare_Rd: generate_cv.Rd:29-31: Dropping empty section \references
prepare_Rd: generate_cv.Rd:41-43: Dropping empty section \seealso
prepare_Rd: generate_cv.Rd:44-45: Dropping empty section \examples
prepare_Rd: nest.Rd:25-27: Dropping empty section \details
prepare_Rd: nest.Rd:28-34: Dropping empty section \value
prepare_Rd: nest.Rd:41-43: Dropping empty section \note
prepare_Rd: nest.Rd:38-40: Dropping empty section \author
prepare_Rd: nest.Rd:35-37: Dropping empty section \references
prepare_Rd: nest.Rd:47-49: Dropping empty section \seealso
prepare_Rd: nest.Rd:50-51: Dropping empty section \examples
prepare_Rd: print.DoubleRule.Rd:19-21: Dropping empty section \details
prepare_Rd: print.DoubleRule.Rd:22-28: Dropping empty section \value
prepare_Rd: print.DoubleRule.Rd:35-37: Dropping empty section \note
prepare_Rd: print.DoubleRule.Rd:32-34: Dropping empty section \author
prepare_Rd: print.DoubleRule.Rd:29-31: Dropping empty section \references
prepare_Rd: print.Rule.Rd:19-21: Dropping empty section \details
prepare_Rd: print.Rule.Rd:22-28: Dropping empty section \value
prepare_Rd: print.Rule.Rd:35-37: Dropping empty section \note
prepare_Rd: print.Rule.Rd:32-34: Dropping empty section \author
prepare_Rd: print.Rule.Rd:29-31: Dropping empty section \references
prepare_Rd: ruleR-package.Rd:41-43: Dropping empty section \references
prepare_Rd: sequenceR.Rd:31-33: Dropping empty section \details
prepare_Rd: sequenceR.Rd:47-49: Dropping empty section \note
prepare_Rd: sequenceR.Rd:44-46: Dropping empty section \author
prepare_Rd: sequenceR.Rd:41-43: Dropping empty section \references
prepare_Rd: singleRules.Rd:19-21: Dropping empty section \details
prepare_Rd: singleRules.Rd:22-24: Dropping empty section \source
prepare_Rd: singleRules.Rd:25-27: Dropping empty section \references
prepare_Rd: split_dict.Rd:22-24: Dropping empty section \details
prepare_Rd: split_dict.Rd:25-31: Dropping empty section \value
prepare_Rd: split_dict.Rd:38-40: Dropping empty section \note
prepare_Rd: split_dict.Rd:35-37: Dropping empty section \author
prepare_Rd: split_dict.Rd:32-34: Dropping empty section \references
prepare_Rd: split_dict.Rd:44-46: Dropping empty section \seealso
prepare_Rd: split_dict.Rd:47-48: Dropping empty section \examples
prepare_Rd: val.Rd:44-46: Dropping empty section \details
prepare_Rd: val.Rd:47-53: Dropping empty section \value
prepare_Rd: val.Rd:60-62: Dropping empty section \note
prepare_Rd: val.Rd:57-59: Dropping empty section \author
prepare_Rd: val.Rd:54-56: Dropping empty section \references
prepare_Rd: val.Rd:66-68: Dropping empty section \seealso
prepare_Rd: vecORnull-class.Rd:20-22: Dropping empty section \note
prepare_Rd: vecORnull-class.Rd:17-19: Dropping empty section \author
prepare_Rd: vecORnull-class.Rd:14-16: Dropping empty section \references
prepare_Rd: vecORnull-class.Rd:26-29: Dropping empty section \seealso
prepare_Rd: writing_double.Rd:19-21: Dropping empty section \details
prepare_Rd: writing_double.Rd:22-28: Dropping empty section \value
prepare_Rd: writing_double.Rd:35-37: Dropping empty section \note
prepare_Rd: writing_double.Rd:32-34: Dropping empty section \author
prepare_Rd: writing_double.Rd:29-31: Dropping empty section \references
prepare_Rd: writing_double.Rd:41-43: Dropping empty section \seealso
prepare_Rd: writing_single.Rd:18-20: Dropping empty section \details
prepare_Rd: writing_single.Rd:21-27: Dropping empty section \value
prepare_Rd: writing_single.Rd:34-36: Dropping empty section \note
prepare_Rd: writing_single.Rd:31-33: Dropping empty section \author
prepare_Rd: writing_single.Rd:28-30: Dropping empty section \references
prepare_Rd: writing_single.Rd:40-42: Dropping empty section \seealso
prepare_Rd: ws.Rd:19-21: Dropping empty section \details
prepare_Rd: ws.Rd:22-28: Dropping empty section \value
prepare_Rd: ws.Rd:35-37: Dropping empty section \note
prepare_Rd: ws.Rd:32-34: Dropping empty section \author
prepare_Rd: ws.Rd:29-31: Dropping empty section \references
prepare_Rd: ws.Rd:41-43: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'MultConstSingleRule-class.Rd':
  \examples lines wider than 100 characters:
     m<-new("MultConstSingleRule",constantVal=4,previousRule=new("IdenSingleRule")) #or m<-createSR(a1=3,cv1=4,n=0)

Rd file 'createDR.Rd':
  \examples lines wider than 100 characters:
     #altrnatively 'm<-createDR(a=1,fr=new("IdenSingleRule"),sr=new("IdenSingleRule"),ns=new("IdenSingleRule"))'

Rd file 'createTest.Rd':
  \examples lines wider than 100 characters:
     #rules 1 and 2 can be used to create first numeric sequence, rules 2 and 3 to create second numeric sequence ...

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'generateRule.Rd':
  'DictionaryRule'

Missing link or links in documentation object 'split_dict.Rd':
  'DictionaryRule'

Missing link or links in documentation object 'writing_double.Rd':
  'extract_double_comment'

Missing link or links in documentation object 'writing_single.Rd':
  'extract_single_comment' 'extract_double_comment'

Missing link or links in documentation object 'ws.Rd':
  'extract_single_comment' 'extract_double_comment'

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

* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  'IntertwinedRule'
Undocumented S4 methods:
  generic 'calculate' and siglist 'DoubleRule,numeric,numeric'
  generic 'calculate' and siglist 'SingleRule,numeric,ANY'
  generic 'print' and siglist 'DoubleRule'
  generic 'print' and siglist 'IntertwinedRule'
  generic 'print' and siglist 'SingleRule'
  generic 'sequenceR' and siglist 'vector,DoubleRule,numeric'
  generic 'sequenceR' and siglist 'vector,IntertwinedRule,numeric'
  generic 'sequenceR' and siglist 'vector,SingleRule,numeric'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Functions or methods with usage in documentation object 'print.DoubleRule' but not in code:
  print.DoubleRule

Functions or methods with usage in documentation object 'writing_double' but not in code:
  writing_double

Functions or methods with usage in documentation object 'writing_single' but not in code:
  writing_single

Functions or methods with usage in documentation object 'ws' but not in code:
  ws

Codoc mismatches from documentation object 'print.Rule':
print
  Code: function(x, ...)
  Docs: function(x)
  Argument names in code not in docs:
    ...

S4 class codoc mismatches from documentation object 'AddDoubleRule-class':
Slots for class 'AddDoubleRule'
  Code: .S3Class description firstRule nextSingle secondRule
  Inherited: firstRule secondRule nextSingle .S3Class
  Docs: .S3Class firstRule nextSingle secondRule

S4 class codoc mismatches from documentation object 'MultDoubleRule-class':
Slots for class 'MultDoubleRule'
  Code: .S3Class description firstRule nextSingle secondRule
  Inherited: firstRule secondRule nextSingle .S3Class
  Docs: .S3Class firstRule nextSingle secondRule

S4 class codoc mismatches from documentation object 'SingleRule-class':
Slots for class 'SingleRule'
  Code: .S3Class description previousRule
  Docs: .S3Class previousRule

* checking Rd \usage sections ... WARNING
Objects in \usage without \alias in documentation object 'print.Rule':
  'print'

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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'ruleR.Rnw'
A 'vignettes' directory is required as from R 3.1.0
and these will not be indexed nor checked
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

WARNING: There were 5 warnings.
NOTE: There were 6 notes.
See
  'R:/run/building/build_2014-10-27-15-04/RF_PKG_CHECK/PKGS/ruleR.Rcheck/00check.log'
for details.

Run time: 35.78 seconds.