R Development Page

CALIBERcodelists log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2020-02-27-17-06/RF_PKG_CHECK/PKGS/CALIBERcodelists.Rcheck'
* using R version 3.6.2 Patched (2020-01-13 r77668)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'CALIBERcodelists/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CALIBERcodelists' version '0.2-11'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Anoop Shah '

New submission

Suggests or Enhances not in mainstream repositories:
  CALIBERlookups

Found the following (possibly) invalid URLs:
  URL: http://www.cms.gov/Medicare/Coding/ICD10/2013-ICD-10-CM-and-GEMs.html (moved to https://www.cms.gov/Medicare/Coding/ICD10/2013-ICD-10-CM-and-GEMs)
    From: man/GEM.Rd
    Status: 404
    Message: Not Found
  URL: https://www.uktcregistration.nss.cfh.nhs.uk/trud3/
    From: man/loadDicts.Rd
    Status: Error
    Message: libcurl error code 6:
      	Could not resolve host: www.uktcregistration.nss.cfh.nhs.uk

The Title field should be in title case. Current version is:
'Generate ICD10, Read and OPCS codelists'
In title case that is:
'Generate ICD10, Read and OPCS Codelists'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: 'CALIBERlookups'
* 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 serialization versions ... OK
* checking whether package 'CALIBERcodelists' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... 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 use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... WARNING
export:
  function(x, ...)
export.codelist:
  function(x, filename, categories, contractIfICD10, contractIfICD9)

export:
  function(x, ...)
export.codelist:
  function(x, filename, categories, contractIfICD10, contractIfICD9)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addCategory: no visible binding for global variable 'category'
assigncat: no visible binding for global variable 'CALIBER_DICT'
assigncat: no visible binding for global variable 'category'
assigncat: no visible binding for global variable 'dict'
assigncat: no visible binding for global variable 'code'
assigncat: no visible binding for global variable 'change'
assignmetadata: no visible binding for global variable 'Source'
assignmetadata: no visible binding for global variable 'dict'
assignmetadata: no visible binding for global variable 'item'
assignmetadata: no visible binding for global variable 'value'
browseCodelist: no visible binding for global variable 'code'
browseCodelist: no visible binding for global variable 'category'
browseCodelist: no visible binding for global variable 'readcode'
browseCodelist: no visible binding for global variable 'medcode'
browseCodelist: no visible binding for global variable 'new_cat'
browseDICT: no visible binding for global variable 'CALIBER_DICT'
browseDICT: no visible binding for global variable 'dict'
browseDICT: no visible binding for global variable 'medcode'
browseDICT: no visible binding for global variable 'code'
browseDICT: no visible binding for global variable 'term'
browseDICT: no visible binding for global variable 'events'
browseDICT: no visible binding for global variable 'category'
browseDICT: no visible binding for global variable 'new_cat'
browseLoad: no visible binding for global variable 'value'
browseLoad: no visible binding for global variable 'code'
browseSelection: no visible binding for global variable 'CALIBER_DICT'
browseSelection: no visible binding for global variable 'dict'
browseSelection: no visible binding for global variable 'category'
browseSelectionNotDICT: no visible binding for global variable
  'CALIBER_DICT'
browseSelectionNotDICT: no visible binding for global variable 'dict'
browseSelectionNotDICT: no visible binding for global variable
  'medcode'
browseSelectionNotDICT: no visible binding for global variable 'code'
browseSelectionNotDICT: no visible binding for global variable 'term'
browseSelectionNotDICT: no visible binding for global variable 'events'
browseSelectionNotDICT: no visible binding for global variable
  'include'
browseSelectionNotDICT: no visible global function definition for
  'show'
codelistToDict: no visible binding for global variable 'dict'
codelistToDict: no visible binding for global variable 'category'
codelistToDict: no visible binding for global variable 'code'
codelistToDict: no visible binding for global variable 'CALIBER_DICT'
codelistToDict: no visible binding for global variable 'shortname'
codelistToDict: no visible binding for global variable 'description'
codelistToDict: no visible binding for global variable 'item'
codelistToDict: no visible binding for global variable 'value'
codelistToSelection: no visible binding for global variable 'dict'
codelistToSelection: no visible binding for global variable 'code'
codelistToSelection: no visible binding for global variable
  'CALIBER_DICT'
codelistToSelection: no visible binding for global variable 'select'
codematch: no visible binding for global variable 'CALIBER_DICT'
codematch: no visible binding for global variable 'dict'
codematch: no visible binding for global variable 'code'
codematch: no visible binding for global variable 'value'
codematch: no visible binding for global variable 'CALIBER_DICTMAPS'
codematch: no visible binding for global variable 'map_stat'
codematch: no visible binding for global variable 'medcode'
codematch: no visible binding for global variable 'CALIBER_GEM'
codematch: no visible binding for global variable 'icd9'
codematch: no visible global function definition for 'J'
codematch: no visible binding for global variable 'use'
codematch: no visible binding for global variable 'from9to10'
codematch: no visible binding for global variable 'icd10'
codematch: no visible binding for global variable 'item'
compare: no visible binding for global variable 'medcode'
compare: no visible binding for global variable 'code'
compare: no visible binding for global variable 'category'
compare: no visible binding for global variable 'term'
compare: no visible binding for global variable 'prodcode'
compare: no visible binding for global variable 'term_old'
compare: no visible binding for global variable 'cat_old'
compare: no visible binding for global variable 'code_old'
compare: no visible binding for global variable 'same'
compare: no visible binding for global variable 'old'
compare: no visible binding for global variable 'new'
compare: no visible binding for global variable 'description'
compare: no visible binding for global variable 'shortname'
compare: no visible binding for global variable 'old_shortname'
compare: no visible binding for global variable 'new_shortname'
compare: no visible binding for global variable 'old_description'
compare: no visible binding for global variable 'new_description'
compare: no visible binding for global variable 'same_shortname'
compare: no visible binding for global variable 'same_description'
contractCodelist: no visible binding for global variable 'Source'
contractCodelist: no visible binding for global variable 'dict'
contractCodelist: no visible binding for global variable 'code'
contractCodelist: no visible binding for global variable 'category'
contractCodelist : : no visible binding for global variable
  'category'
contractCodelist : : no visible binding for global variable
  'code'
contractCodelist : : no visible binding for global variable
  'CALIBER_DICT'
contractCodelist : : no visible binding for global variable
  'term'
contractICD : : no visible binding for global variable
  'CALIBER_DICT'
contractICD : : no visible binding for global variable
  'dict'
contractICD : : no visible binding for global variable
  'code'
contractICD : checkCodes: no visible binding for global variable
  'CALIBER_DICT'
contractICD : checkCodes: no visible binding for global variable 'dict'
contractICD : checkCodes: no visible binding for global variable 'code'
convertCodelist: no visible binding for global variable 'dict'
convertCodelist: no visible binding for global variable 'Source'
convertCodelist : : no visible binding for global variable
  'category'
convertCodelist : : no visible binding for global variable
  'medcode'
convertCodelist : : no visible binding for global variable
  'code'
convertCodelist : : no visible binding for global variable
  'CALIBER_GEM'
convertCodelist : : no visible binding for global variable
  'icd9'
convertCodelist : : no visible binding for global variable
  'use'
convertCodelist : : no visible binding for global variable
  'from9to10'
convertCodelist : : no visible binding for global variable
  'icd10'
convertMedcodes: no visible binding for global variable
  'CALIBER_DICTMAPS'
convertMedcodes: no visible binding for global variable 'dict'
convertMedcodes: no visible binding for global variable 'map_stat'
convertMedcodes: no visible binding for global variable 'medcode'
convertMedcodes: no visible binding for global variable 'code'
convertToMedcodes: no visible binding for global variable
  'CALIBER_DICTMAPS'
convertToMedcodes: no visible binding for global variable 'dict'
convertToMedcodes: no visible binding for global variable 'map_stat'
convertToMedcodes: no visible binding for global variable 'code'
convertToMedcodes: no visible binding for global variable 'medcode'
decode: no visible binding for global variable 'dict'
decode: no visible binding for global variable 'medcode'
decode: no visible binding for global variable 'CALIBER_DICT'
decode: no visible binding for global variable 'term'
decode: no visible binding for global variable 'code'
dictToCodelist: no visible binding for global variable 'CALIBER_DICT'
dictToCodelist: no visible binding for global variable 'dict'
dictToCodelist: no visible binding for global variable 'category'
dictToCodelist: no visible binding for global variable 'code'
dictToCodelist: no visible binding for global variable 'term'
dictToCodelist: no visible binding for global variable 'medcode'
dictToCodelist: no visible binding for global variable 'events'
dictis: no visible binding for global variable 'CALIBER_DICT'
emptySelection: no visible binding for global variable 'CALIBER_DICT'
expandCodelist: no visible binding for global variable 'dict'
expandCodelist: no visible binding for global variable 'Source'
expandCodelist: no visible binding for global variable 'code'
expandCodelist: no visible binding for global variable 'category'
expandCodelist: no visible binding for global variable 'CALIBER_DICT'
expandCodelist : : no visible binding for global variable
  'category'
expandCodelist : : no visible binding for global variable
  'code'
expandCodelist : : no visible binding for global variable
  'CALIBER_DICT'
expandCodelist : : no visible binding for global variable
  'term'
expandCodelist: no visible binding for global variable 'hierarchy'
expandICD : : no visible binding for global variable
  'CALIBER_DICT'
expandICD : : no visible binding for global variable 'dict'
expandICD : : no visible binding for global variable 'code'
explode: no visible binding for global variable 'CALIBER_DICT'
explode: no visible binding for global variable 'dict'
explode: no visible binding for global variable 'code'
explode: no visible binding for global variable 'partcode'
explode: no visible binding for global variable 'sel2match'
explode: no visible binding for global variable 'sel'
explode: no visible binding for global variable 'events'
export.codelist: no visible binding for global variable 'category'
export.codelist: no visible binding for global variable 'dict'
export.codelist: no visible binding for global variable 'Source'
export.codelist: no visible binding for global variable 'icd_code'
export.codelist: no visible binding for global variable 'icd9_code'
export.codelist: no visible binding for global variable 'readcode'
export.codelist: no visible binding for global variable 'opcs_code'
export.codelist: no visible binding for global variable 'prodcode'
exportall: no visible binding for global variable 'item'
exportall: no visible binding for global variable 'value'
exportall: no visible binding for global variable 'dict'
exportall: no visible binding for global variable 'Source'
extractMetadataFromColumn: no visible binding for global variable
  'category'
extractMetadataFromMETA: no visible binding for global variable 'item'
extractMetadataFromMETA: no visible binding for global variable 'value'
extractMetadataFromMETA: no visible binding for global variable 'dict'
extractMetadataFromMETA: no visible binding for global variable
  'Source'
findICDhead : : no visible binding for global variable
  'CALIBER_DICT'
findICDhead : : no visible binding for global variable
  'dict'
findICDhead : : no visible binding for global variable
  'code'
findICDhead : : no visible binding for global variable
  'term'
getCatLabels: no visible global function definition for 'J'
getCatLabels: no visible binding for global variable 'shortname'
getCatLabels: no visible binding for global variable 'category'
getSourceDict: no visible binding for global variable 'Source'
getSourceDict: no visible binding for global variable 'dict'
getdictionary: no visible binding for global variable 'item'
getdictionary: no visible binding for global variable 'value'
htmlCodelistTable: no visible binding for global variable 'code'
htmlCodelistTable: no visible binding for global variable 'category'
htmlCodelistTable: no visible binding for global variable 'term'
htmlCodelistTable: no visible binding for global variable 'events'
htmlCodelistTable: no visible binding for global variable 'item'
htmlCodelistTable: no visible binding for global variable 'value'
htmlCodelistTable: no visible binding for global variable 'Source'
htmlCodelistTable: no visible binding for global variable 'hierarchy'
htmlCodelistTable: no visible binding for global variable 'rawcode'
iAssignCat: no visible binding for global variable 'category'
iAssignCat: no visible binding for global variable 'shortname'
iAssignCat: no visible binding for global variable 'description'
iBrowseEditSelection: no visible binding for global variable
  'CALIBER_DICT'
iBrowseEditSelection: no visible binding for global variable 'dict'
iBrowseEditSelection: no visible binding for global variable 'code'
iCodelistMenu: no visible binding for global variable 'code'
iCodelistMenu: no visible binding for global variable 'old_cat'
iCodelistMenu: no visible binding for global variable 'category'
iCreateCodelistMenu: no visible binding for global variable
  'CALIBER_DICT'
iCreateCodelistMenu: no visible binding for global variable 'dict'
iCreateCodelistMenu: no visible binding for global variable 'category'
iCreateCodelistMenu: no visible binding for global variable 'value'
importCSVcodelist: no visible global function definition for 'show'
isContractedCodelist: no visible binding for global variable 'dict'
isContractedCodelist: no visible binding for global variable 'Source'
isExpandedCodelist: no visible binding for global variable 'dict'
isExpandedCodelist: no visible binding for global variable 'Source'
loadDICT: no visible binding for global variable 'CALIBER_DICT'
loadDICT: no visible binding for global variable 'dict'
loadDICT: no visible binding for global variable 'code'
loadDICTMAPS: no visible binding for global variable 'CALIBER_DICTMAPS'
loadICDMAPS: no visible binding for global variable 'CALIBER_GEM'
medcodeToReadCode: no visible binding for global variable
  'CALIBER_DICT'
medcodeToReadCode: no visible binding for global variable 'dict'
medcodeToReadCode: no visible binding for global variable 'medcode'
medcodeToReadCode: no visible binding for global variable 'code'
medcodeToReadCode: no visible binding for global variable '.order'
medcodeis: no visible binding for global variable 'CALIBER_DICT'
merge.codelist: no visible binding for global variable 'category'
merge.codelist: no visible binding for global variable 'hierarchy'
merge.codelist: no visible binding for global variable 'medcode'
merge.codelist: no visible binding for global variable 'code'
printCodelist: no visible binding for global variable 'category'
printCodelist: no visible binding for global variable 'code'
printSelection: no visible binding for global variable 'CALIBER_DICT'
printSelection: no visible binding for global variable 'dict'
printSelection: no visible binding for global variable 'medcode'
printSelection: no visible binding for global variable 'code'
printSelection: no visible binding for global variable 'term'
printSelection: no visible binding for global variable 'events'
printTerms: no visible binding for global variable 'term'
printTerms: no visible global function definition for 'show'
process: no visible binding for global variable 'value'
process: no visible binding for global variable 'item'
removeUnusedCategories: no visible binding for global variable
  'CALIBER_DICT'
removeUnusedCategories: no visible binding for global variable 'dict'
removeUnusedCategories: no visible binding for global variable
  'category'
retrieveCategories: no visible binding for global variable 'category'
retrieveCategoriesFromMETA: no visible binding for global variable
  'item'
retrieveCategoriesFromMETA: no visible binding for global variable
  'value'
retrieveCategoriesFromMETA: no visible binding for global variable
  'category'
retrieveCategoriesFromMETA: no visible binding for global variable
  'CALIBER_DICT'
saveCategories: no visible binding for global variable 'shortname'
saveCategories: no visible binding for global variable 'description'
saveCategories: no visible binding for global variable 'category'
saveCategoriesToMETA: no visible binding for global variable 'item'
saveCategoriesToMETA: no visible binding for global variable 'value'
selection: no visible binding for global variable 'CALIBER_DICT'
selectionToCodelist: no visible binding for global variable
  'CALIBER_DICT'
selectionToCodelist: no visible binding for global variable 'dict'
selectionToCodelist: no visible binding for global variable 'code'
selectionToCodelist: no visible binding for global variable 'term'
selectionToCodelist: no visible binding for global variable 'medcode'
selectionToCodelist: no visible binding for global variable 'events'
setDictKey: no visible binding for global variable 'CALIBER_DICT'
setDictKey: no visible binding for global variable 'dict'
setDictKey: no visible binding for global variable 'code'
setMetadata: no visible binding for global variable 'dict'
setdictionary: no visible binding for global variable 'item'
setdictionary: no visible binding for global variable 'value'
setdictionary: no visible binding for global variable 'CALIBER_DICT'
setdictionary: no visible binding for global variable 'category'
showhtml: no visible binding for global variable 'value'
showhtml: no visible binding for global variable 'CALIBER_DICT'
showhtml: no visible binding for global variable 'category'
showhtml: no visible binding for global variable 'shortname'
showhtml: no visible binding for global variable 'description'
showhtml: no visible binding for global variable 'nterms'
showhtml: no visible binding for global variable 'item'
showhtml : : no visible binding for global variable
  'CALIBER_DICT'
showhtml : : no visible binding for global variable
  'category'
showhtml : : no visible binding for global variable
  'description'
tableToCodelist: no visible binding for global variable 'medcode'
tableToCodelist: no visible binding for global variable 'termlc'
tableToCodelist: no visible binding for global variable 'category'
tableToCodelist: no visible binding for global variable 'shortname'
tableToCodelist: no visible binding for global variable 'description'
tableToCodelist: no visible global function definition for 'J'
tableToCodelist: no visible binding for global variable 'dict'
tableToCodelist: no visible binding for global variable 'Source'
tableToCodelist: no visible binding for global variable 'code'
tableToCodelist: no visible binding for global variable 'CALIBER_DICT'
tableToCodelist: no visible binding for global variable 'term'
tableToCodelist: no visible binding for global variable '.corrCode'
tableToCodelist: no visible binding for global variable '.corrTerm'
termhas: no visible binding for global variable 'CALIBER_DICT'
textToDate : doconvertdate: no visible global function definition for
  'pvec'
Undefined global functions or variables:
  .corrCode .corrTerm .order CALIBER_DICT CALIBER_DICTMAPS CALIBER_GEM
  J Source cat_old category change code code_old description dict
  events from9to10 hierarchy icd10 icd9 icd9_code icd_code include item
  map_stat medcode new new_cat new_description new_shortname nterms old
  old_cat old_description old_shortname opcs_code partcode prodcode
  pvec rawcode readcode same same_description same_shortname sel
  sel2match select shortname show term term_old termlc use value
Consider adding
  importFrom("methods", "new", "show")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').

Found the following assignments to the global environment:
File 'CALIBERcodelists/R/exploreCodes.R':
  assign(newCodelistName, temp, envir = .GlobalEnv)
  assign(newCodelistName, temp, envir = .GlobalEnv)
  assign(codelistName, temp, envir = .GlobalEnv)
  assign(newCodelistName, as.codelist(thedict), envir = .GlobalEnv)
  assign(newSelectionName, eval(parse(text = selectionText)), envir = .GlobalEnv)
File 'CALIBERcodelists/R/loading.R':
  assign("CALIBER_DICT", SAMPLE_DICT, envir = .GlobalEnv)
  assign("CALIBER_DICTMAPS", SAMPLE_DICTMAPS, envir = .GlobalEnv)
  assign("CALIBER_GEM", SAMPLE_GEM, envir = .GlobalEnv)

Found the following calls to data() loading into the global environment:
File 'CALIBERcodelists/R/loading.R':
  data("CALIBER_DICT", envir = .GlobalEnv)
  data("CALIBER_DICTMAPS", envir = .GlobalEnv)
  data("CALIBER_GEM", envir = .GlobalEnv)
See section 'Good practice' in '?data'.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking R/sysdata.rda ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'R:/run/building/build_2020-02-27-17-06/RF_PKG_CHECK/PKGS/CALIBERcodelists.Rcheck/00check.log'
for details.


Run time: 85.89 seconds.