R Development Page

CALIBERdatamanage log file (check_x86_64_linux)

Tue Nov 23 13:28:09 2021: Checking package CALIBERdatamanage (SVN revision 70) ...
* using log directory ‘/srv/rf/building/build_2021-11-23-13-27/RF_PKG_CHECK/PKGS/CALIBERdatamanage.Rcheck’
* using R version 4.1.2 Patched (2021-11-16 r81199)
* 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 ‘0.1-15’
* 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
    From: man/multiforest.Rd
    Status: Error
    Message: libcurl error code 60:
      	SSL: certificate subject name (*.stowers.org) does not match target host name 'research.stowers-institute.org'
      	(Status without verification: 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 ... [3s/3s] WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘grid::pattern’ by ‘ff::pattern’ when loading ‘CALIBERdatamanage’
See ‘/srv/rf/building/build_2021-11-23-13-27/RF_PKG_CHECK/PKGS/CALIBERdatamanage.Rcheck/00install.out’ for details.
* 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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [6s/6s] 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’
as.data.table.ffdf: no visible binding for global variable ‘temp’
as.data.table.ffdf: no visible binding for global variable ‘origname’
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 origname prodcode pvec shortname temp use value
* checking Rd files ... [0s/0s] 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, 3 NOTEs
See
  ‘/srv/rf/building/build_2021-11-23-13-27/RF_PKG_CHECK/PKGS/CALIBERdatamanage.Rcheck/00check.log’
for details.


Run time: 46.21 seconds.