• using R version 4.0.0 alpha (2020-04-01 r78130)
  • using platform: x86_64-apple-darwin17.0 (64-bit)
  • using session charset: UTF-8
  • checking for file ‘ClinReport/DESCRIPTION’ ... OK
  • checking extension type ... Package
  • this is package ‘ClinReport’ version ‘0.9.1.14’
  • package encoding: UTF-8
  • 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 whether package ‘ClinReport’ can be installed ... [10s/13s] OK
  • checking installed package size ... OK
  • checking package directory ... OK
  • checking ‘build’ 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 dependencies in R code ... NOTE
    Namespaces in Imports field not imported from:
      ‘car’ ‘emmeans’
      All declared Imports should be used.
  • checking S3 generic/method consistency ... OK
  • checking replacement functions ... OK
  • checking foreign function calls ... OK
  • checking R code for possible problems ... [9s/13s] OK
  • checking Rd files ... OK
  • checking Rd metadata ... 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 files in ‘vignettes’ ... OK
  • checking examples ... ERROR
    Running examples in ‘ClinReport-Ex.R’ failed
    The error most likely occurred in:

    > ### Name: report.quali.hlev
    > ### Title: 'Hierarchical Qualitative' statistics reporting (experimental)
    > ### Aliases: report.quali.hlev
    >
    > ### ** Examples
    >
    >
    > data(adverse_event)
    >
    > test=report.quali.hlev(data=adverse_event,subjid="SUBJID",var_upper="PTNAME",
    + var_lower="SOCNAME",lower.levels="System Organ Class",upper.levels="Prefered Terms",x1="randtrt")
    Error in match.names(clabs, names(xi)) :
      names do not match previous names
    Calls: report.quali.hlev -> report.quali.hlev -> rbind -> rbind -> match.names
    Execution halted
  • checking for unstated dependencies in vignettes ... OK
  • checking package vignettes in ‘inst/doc’ ... OK
  • checking running R code from vignettes ... [2s/2s] NONE
      ‘clinreport_graphics.Rmd’ using ‘UTF-8’... [0s/1s] OK
      ‘clinreport_modify_outputs.Rmd’ using ‘UTF-8’... [0s/0s] OK
      ‘clinreport_vignette_get_started.Rmd’ using ‘UTF-8’... [0s/0s] OK
      ‘clinreport_vignette_standard.Rmd’ using ‘UTF-8’... [0s/0s] OK
  • checking re-building of vignette outputs ... [25s/36s] WARNING
    Error(s) in re-building vignettes:
    --- re-building ‘clinreport_graphics.Rmd’ using knitr

    Attaching package: 'dplyr'

    The following object is masked from 'package:ClinReport':

        desc

    The following objects are masked from 'package:stats':

        filter, lag

    The following objects are masked from 'package:base':

        intersect, setdiff, setequal, union


    Attaching package: 'nlme'

    The following object is masked from 'package:dplyr':

        collapse

    Loading required package: carData

    Attaching package: 'car'

    The following object is masked from 'package:dplyr':

        recode

    --- finished re-building ‘clinreport_graphics.Rmd’

    --- re-building ‘clinreport_modify_outputs.Rmd’ using knitr
    --- finished re-building ‘clinreport_modify_outputs.Rmd’

    --- re-building ‘clinreport_vignette_get_started.Rmd’ using knitr

    Attaching package: 'dplyr'

    The following object is masked from 'package:ClinReport':

        desc

    The following objects are masked from 'package:stats':

        filter, lag

    The following objects are masked from 'package:base':

        intersect, setdiff, setequal, union


    Attaching package: 'nlme'

    The following object is masked from 'package:dplyr':

        collapse

    Loading required package: carData

    Attaching package: 'car'

    The following object is masked from 'package:dplyr':

        recode

    Fontconfig error: Cannot load default config file
    Quitting from lines 202-220 (clinreport_vignette_get_started.Rmd)
    Error: processing vignette 'clinreport_vignette_get_started.Rmd' failed with diagnostics:
    names do not match previous names
    --- failed re-building ‘clinreport_vignette_get_started.Rmd’

    --- re-building ‘clinreport_vignette_standard.Rmd’ using knitr

    Attaching package: 'dplyr'

    The following objects are masked from 'package:stats':

        filter, lag

    The following objects are masked from 'package:base':

        intersect, setdiff, setequal, union


    Attaching package: 'nlme'

    The following object is masked from 'package:dplyr':

        collapse

    Loading required package: carData

    Attaching package: 'car'

    The following object is masked from 'package:dplyr':

        recode

    --- finished re-building ‘clinreport_vignette_standard.Rmd’

    SUMMARY: processing the following file failed:
      ‘clinreport_vignette_get_started.Rmd’

    Error: Vignette re-building failed.
    Execution halted
  • checking PDF version of manual ... OK
  • DONE
    Status: 1 ERROR, 1 WARNING, 1 NOTE