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CALIBERdatamanage log file (check_x86_64_linux)

Wed Jan 31 19:05:50 2018: Checking package CALIBERdatamanage (SVN revision 59) ...
* using log directory ‘/srv/rf/building/build_2018-01-31-19-04/RF_PKG_CHECK/PKGS/CALIBERdatamanage.Rcheck’
* using R version 3.4.3 Patched (2018-01-29 r74185)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* 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 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 ‘CALIBERdatamanage’ can be installed ... [2s/2s] 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 ‘/srv/rf/building/build_2018-01-31-19-04/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 ... WARNING
subset:
  function(x, ...)
subset.cohort:
  function(x, subset, select)

subset:
  function(x, ...)
subset.cohort:
  function(x, subset, select)

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 ... [9s/9s] NOTE
addCategoryToCohort: no visible global function definition for
  ‘capture.output’
addCodelistToCohort: no visible binding for global variable ‘.category’
addCodelistToCohort: no visible global function definition for
  ‘capture.output’
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’
addToCohort: no visible global function definition for ‘capture.output’
exportTable: no visible global function definition for ‘capture.output’
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’
formathr: no visible global function definition for ‘pt’
formathr: no visible global function definition for ‘qt’
getzipfilename: no visible global function definition for ‘unzip’
importFFDF: no visible global function definition for ‘read.csv’
importFFDF: no visible global function definition for ‘capture.output’
importTemplate: no visible global function definition for ‘read.delim’
meansd: no visible global function definition for ‘sd’
medianiqr: no visible global function definition for ‘median’
medianiqr: no visible global function definition for ‘quantile’
multiforest: no visible global function definition for ‘par’
multiforest: no visible global function definition for ‘plot.new’
multiforestPDF: no visible global function definition for ‘pdf’
multiforestPDF: no visible global function definition for ‘dev.off’
multiforestPNG: no visible global function definition for ‘png’
multiforestPNG: no visible global function definition for ‘dev.off’
percentConf: no visible global function definition for ‘binom.test’
summaryTable: no visible global function definition for ‘read.delim’
summaryTable: no visible global function definition for
  ‘capture.output’
summaryTable: no visible global function definition for ‘write.table’
textToDate : doconvertdate: no visible global function definition for
  ‘pvec’
textfileToDT: no visible global function definition for ‘read.delim’
textfileToDT: no visible global function definition for
  ‘capture.output’
transferVariables: no visible global function definition for
  ‘capture.output’
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
  binom.test capture.output category code daysdiff description dev.off
  enttype icd include indexdate keep lookup medcode median opcs par pdf
  plot.new png prodcode pt pvec qt quantile read.csv read.delim sd
  shortname unzip use value write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "png")
  importFrom("graphics", "par", "plot.new")
  importFrom("stats", "binom.test", "median", "pt", "qt", "quantile",
             "sd")
  importFrom("utils", "capture.output", "read.csv", "read.delim",
             "unzip", "write.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: cohortmethods.Rd:52-54: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘removeVariables’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [6s/6s] OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 4 NOTEs
See
  ‘/srv/rf/building/build_2018-01-31-19-04/RF_PKG_CHECK/PKGS/CALIBERdatamanage.Rcheck/00check.log’
for details.


Run time: 51.99 seconds.

Additional Logs:   00install.out
Thanks to:
Vienna University of Economics and Business University of Wisconsin - Madison Powered By FusionForge