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CALIBERdatamanage log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2018-10-24-19-48/RF_PKG_CHECK/PKGS/CALIBERdatamanage.Rcheck'
* using R version 3.5.1 Patched (2018-09-27 r75383)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'CALIBERdatamanage/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CALIBERdatamanage' version '0.1-14'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Anoop Shah '

New submission

Found the following (possibly) invalid URLs:
  URL: http://cran.r-project.org/web/packages/data.table/index.html
    From: inst/doc/Rdatatable.html
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: http://cran.r-project.org/web/packages/ff/index.html
    From: inst/doc/Rdatatable.html
    Status: 200
    Message: OK
    CRAN URL not in canonical form
  URL: http://research.stowers-institute.org/efg/R/Color/Chart/ColorChart.pdf (moved to http://research.stowers.org/efg/R/Color/Chart/ColorChart.pdf)
    From: man/multiforest.Rd
    Status: 404
    Message: Not Found
  The canonical URL of the CRAN page for a package is 
    https://CRAN.R-project.org/package=pkgname
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'ff' 'ffbase' 'grid' 'foreign' 'data.table' 'xtable'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 'CALIBERdatamanage' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ffbase::[<-.ff' by 'ff::[<-.ff' when loading 'CALIBERdatamanage'
  Warning: replacing previous import 'ffbase::[.ff' by 'ff::[.ff' when loading 'CALIBERdatamanage'
  Warning: replacing previous import 'ffbase::[.ffdf' by 'ff::[.ffdf' when loading 'CALIBERdatamanage'
  Warning: replacing previous import 'ffbase::[<-.ffdf' by 'ff::[<-.ffdf' when loading 'CALIBERdatamanage'
See 'R:/run/building/build_2018-10-24-19-48/RF_PKG_CHECK/PKGS/CALIBERdatamanage.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 use of S3 registration ... OK
* checking 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 ... NOTE
addCodelistToCohort: no visible binding for global variable '.category'
addCodelistToCohort: no visible binding for global variable 'value'
addToCohort: no visible binding for global variable '.eventdate'
addToCohort: no visible binding for global variable 'value'
addToCohort: no visible binding for global variable '.id'
addToCohort: no visible binding for global variable 'indexdate'
addToCohort: no visible binding for global variable 'daysdiff'
addToCohort: no visible binding for global variable 'include'
addToCohort: no visible binding for global variable 'keep'
addToCohort: no visible binding for global variable '.chosen'
addToCohort: no visible binding for global variable 'use'
addToCohort: no visible binding for global variable '.transferChosen'
addToCohort: no visible binding for global variable '.transferDate'
extractCodes: no visible binding for global variable 'category'
extractCodes: no visible global function definition for 'J'
extractCodes: no visible binding for global variable 'shortname'
extractCodes: no visible binding for global variable 'medcode'
extractCodes: no visible binding for global variable 'prodcode'
extractCodes: no visible binding for global variable 'code'
extractCodes: no visible global function definition for 'pvec'
extractCodes: no visible binding for global variable 'icd'
extractCodes: no visible binding for global variable 'opcs'
extractEntity : uselookup: no visible global function definition for
  'J'
extractEntity: no visible binding for global variable 'lookup'
extractEntity: no visible binding for global variable 'description'
extractEntity: no visible binding for global variable 'category'
extractEntity: no visible global function definition for 'J'
extractMedcodes: no visible binding for global variable 'category'
extractMedcodes: no visible global function definition for 'J'
extractMedcodes: no visible binding for global variable 'shortname'
extractMedcodes: no visible binding for global variable 'medcode'
extractMedcodes: no visible binding for global variable 'enttype'
textToDate : doconvertdate: no visible global function definition for
  'pvec'
transferVariables: no visible binding for global variable 'use'
transferVariables: no visible global function definition for 'J'
Undefined global functions or variables:
  .category .chosen .eventdate .id .transferChosen .transferDate J
  category code daysdiff description enttype icd include indexdate keep
  lookup medcode opcs prodcode pvec shortname use value
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  'R:/run/building/build_2018-10-24-19-48/RF_PKG_CHECK/PKGS/CALIBERdatamanage.Rcheck/00check.log'
for details.


Run time: 60.29 seconds.

Additional Logs:   00install.out
Thanks to:
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