- 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