R Development Page

autoAnn log file (check_x86_64_linux)

Thu Aug 18 13:50:08 2016: Checking package autoAnn (SVN revision 10) ...
* using log directory ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/autoAnn.Rcheck’
* using R version 3.3.1 Patched (2016-08-17 r71112)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘autoAnn/DESCRIPTION’ ... OK
* this is package ‘autoAnn’ version ‘1.0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Weizhe Liu ’

New submission

The Title field should be in title case, current version then in title case:
‘automatic annotation functions’
‘Automatic Annotation Functions’

The Date field is over a month old.

Size of tarball: 6872720 bytes
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Subdirectory ‘caret’ seems to contain an installed version of the package.
* 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 ‘autoAnn’ can be installed ... [1s/1s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Author field differs from that derived from Authors@R
  Author:    ‘Weizhe Liu [aut, cre], Kidzinski Lukasz [aut]’
  Authors@R: ‘Weizhe Liu Developer [aut, cre], Kidzinski Lukasz Developer [aut]’

Maintainer field differs from that derived from Authors@R
  Maintainer: ‘Weizhe Liu ’
  Authors@R:  ‘Weizhe Liu Developer ’

* checking top-level files ... NOTE
Non-standard files/directories found at top level:
  ‘caret’ ‘openNLP’ ‘qdap’
* checking for left-over files ... OK
* checking index information ... WARNING
Warning in readLines(file) :
  incomplete final line found on 'demo/00Index'
Warning in readLines(file) :
  incomplete final line found on 'demo/00Index'
Demos with missing or empty index information:
  demoCode
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
  qdap/CITATION
Most likely ‘inst/CITATION’ should be used instead.
* 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 use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' calls not declared from:
  ‘NLP’ ‘caret’ ‘openNLP’ ‘qdap’
'library' or 'require' calls in package code:
  ‘NLP’ ‘caret’ ‘openNLP’ ‘qdap’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in 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
featureExtract: no visible global function definition for ‘bracketX’
featureExtract : strcount : : no visible global function
  definition for ‘na.omit’
featureExtract: no visible global function definition for
  ‘Maxent_Sent_Token_Annotator’
featureExtract: no visible global function definition for ‘annotate’
featureExtract : : no visible global function definition for
  ‘which_misspelled’
featurePredict: no visible global function definition for
  ‘trainControl’
featurePredict: no visible global function definition for ‘train’
featurePredict: no visible global function definition for ‘predict’
suggestRelevantWord: no visible global function definition for
  ‘bracketX’
suggestRelevantWord: no visible global function definition for
  ‘rm_stopwords’
Undefined global functions or variables:
  Maxent_Sent_Token_Annotator annotate bracketX na.omit predict
  rm_stopwords train trainControl which_misspelled
Consider adding
  importFrom("stats", "na.omit", "predict")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'autoAnn.Rd':
  \usage lines wider than 90 characters:
     autoAnn(thread_id,title,post_time,post_text,relevant_words,key_words,predicted_feature,method_name,range=NULL)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'suggestRelevantWord':
suggestRelevantWord
  Code: function(dataset)
  Docs: function(post_text)
  Argument names in code not in docs:
    dataset
  Argument names in docs not in code:
    post_text
  Mismatches in argument names:
    Position: 1 Code: dataset Docs: post_text

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... ERROR
Running examples in ‘autoAnn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: featurePredict
> ### Title: featurePredict
> ### Aliases: featurePredict
> ### Keywords: MOOC automatic annotation
> 
> ### ** Examples
> 
> data(iris)
> set.seed(100) 
> trainRow<-sample(1:150,size=100)
> testRow<-setdiff(1:150,trainRow)
> trainSet<-iris[trainRow,]
> testFeature<-iris[testRow,1:4]
> result<-featurePredict(trainSet,as.factor(Species)~.,testFeature,"extraTrees")
Loading required package: caret
Loading required package: lattice
Loading required package: ggplot2
1 package is needed for this model and is not installed. (extraTrees). Would you like to try to install it now?Error in checkInstall(models$library) : 
Calls: featurePredict ... train.formula -> train -> train.default -> checkInstall
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 3 WARNINGs, 7 NOTEs
See
  ‘/mnt/building/build_2016-08-18-12-24/RF_PKG_CHECK/PKGS/autoAnn.Rcheck/00check.log’
for details.

Run time: 25.31 seconds.