R Development Page

CALIBERdrugdose log file (check_x86_64_linux)

Wed Mar 17 13:07:09 2021: Checking package CALIBERdrugdose (SVN revision 67) ...
* using log directory ‘/srv/rf/building/build_2021-03-17-13-06/RF_PKG_CHECK/PKGS/CALIBERdrugdose.Rcheck’
* using R version 4.0.4 Patched (2021-03-05 r80074)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘CALIBERdrugdose/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CALIBERdrugdose’ version ‘0.1-3’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Anoop Shah ’

New submission

Found the following (possibly) invalid URLs:
  URL: http://onlinelibrary.wiley.com/doi/10.1002/pds.1151/ (moved to https://onlinelibrary.wiley.com/doi/10.1002/pds.1151/)
    From: man/CALIBERdoseconvert-package.Rd
          man/addterm.Rd
          man/as.drugdose_lookups.Rd
          man/as.drugdose_multiwords.Rd
          man/as.drugdose_patterns.Rd
          man/as.drugdose_singlewords.Rd
          man/doseconvert.Rd
          man/export.Rd
          man/interpret.Rd
          man/lookups.Rd
          man/multiwords.Rd
          man/patterns.Rd
          man/singlewords.Rd
          man/testdoseconvert.Rd
          man/testset.Rd
    Status: 404
    Message: Not Found

The Title field should be in title case. Current version is:
‘Extract Drug Dose From Unstructured Dosage Text’
In title case that is:
‘Extract Drug Dose from Unstructured Dosage Text’

The Date field is over a month old.
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 serialization versions ... OK
* checking whether package ‘CALIBERdrugdose’ can be installed ... [2s/2s] 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
addterm:
  function(x, ...)
addterm.drugdose_singlewords:
  function(x, words, replacement)

addterm:
  function(x, ...)
addterm.drugdose_multiwords:
  function(x, order, words, replacement, comment)

addterm:
  function(x, ...)
addterm.drugdose_patterns:
  function(x, order, words, qty, units, freq, tot, priority, max, time,
           change, choice, doubledose, duration, category, comment)

addterm:
  function(x, ...)
addterm.drugdose_lookups:
  function(x, textid, text, qty, units, freq, tot, max, time, change,
           choice, duration, daily_dose)

export:
  function(x, ...)
export.drugdose_singlewords:
  function(x, filename)

export:
  function(x, ...)
export.drugdose_multiwords:
  function(x, filename)

export:
  function(x, ...)
export.drugdose_patterns:
  function(x, filename)

export:
  function(x, ...)
export.drugdose_lookups:
  function(x, filename)

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 ... [4s/4s] NOTE
addterm.drugdose_lookups: no visible binding for global variable
  ‘words’
as.drugdose_lookups: no visible binding for global variable ‘qty’
as.drugdose_lookups: no visible binding for global variable ‘freq’
as.drugdose_lookups: no visible binding for global variable ‘tot’
as.drugdose_lookups: no visible binding for global variable ‘time’
as.drugdose_lookups: no visible binding for global variable ‘duration’
as.drugdose_lookups: no visible binding for global variable
  ‘daily_dose’
as.drugdose_lookups: no visible binding for global variable ‘text’
calculate_mg: no visible binding for global variable ‘daily_mg’
calculate_mg: no visible binding for global variable ‘daily_dose’
doseconvert: no visible binding for global variable ‘originalorder’
doseconvert: no visible binding for global variable ‘doseid’
doseconvert: no visible binding for global variable ‘dosestrings’
doseconvert : analysis: no visible global function definition for ‘.’
doseconvert : analysis: no visible binding for global variable ‘qty’
doseconvert : analysis: no visible binding for global variable ‘freq’
doseconvert : analysis: no visible binding for global variable ‘tot’
doseconvert : analysis: no visible binding for global variable ‘time’
doseconvert : analysis: no visible binding for global variable ‘change’
doseconvert : analysis: no visible binding for global variable ‘choice’
doseconvert : analysis: no visible binding for global variable
  ‘duration’
doseconvert : analysis: no visible binding for global variable
  ‘daily_dose’
doseconvert: no visible global function definition for ‘mclapply’
doseconvert : : no visible binding for global variable
  ‘doseid’
doseconvert: no visible binding for global variable ‘i.textid’
testdoseconvert: no visible binding for global variable ‘outcome’
testdoseconvert: no visible binding for global variable ‘qty’
testdoseconvert: no visible binding for global variable ‘freq’
testdoseconvert: no visible binding for global variable ‘tot’
testdoseconvert: no visible binding for global variable ‘time’
testdoseconvert: no visible binding for global variable ‘change’
testdoseconvert: no visible binding for global variable ‘choice’
testdoseconvert: no visible binding for global variable ‘duration’
testdoseconvert: no visible binding for global variable ‘daily_dose’
Undefined global functions or variables:
  . change choice daily_dose daily_mg doseid dosestrings duration freq
  i.textid mclapply originalorder outcome qty text time tot words
Consider adding
  importFrom("graphics", "text")
  importFrom("stats", "time")
to your NAMESPACE file.
* 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 ... [3s/3s] OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  ‘/srv/rf/building/build_2021-03-17-13-06/RF_PKG_CHECK/PKGS/CALIBERdrugdose.Rcheck/00check.log’
for details.


Run time: 62.21 seconds.