* using log directory 'd:/Rcompile/CRANpkg/local/3.3/survminer.Rcheck'
* using R version 3.3.2 (2016-10-31)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* checking for file 'survminer/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'survminer' version '0.2.2'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: 'RTCGA.clinical'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'survminer' can be installed ... 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'ggcoxdiagnostics.Rd':
  'ggtheme'

Missing link or links in documentation object 'ggcoxfunctional.Rd':
  'ggtheme'

Missing link or links in documentation object 'ggcoxzph.Rd':
  'ggtheme'

Missing link or links in documentation object 'ggsurvplot.Rd':
  'ggtheme'

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... ERROR
Running examples in 'survminer-Ex.R' failed
The error most likely occurred in:

> ### Name: ggsurvplot
> ### Title: Drawing Survival Curves Using ggplot2
> ### Aliases: ggsurvplot print.ggsurvplot
> 
> ### ** Examples
> 
> 
> #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> # Example 1: Survival curves with two groups
> #%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> # Fit survival curves
> #++++++++++++++++++++++++++++++++++++
> require("survival")
Loading required package: survival
> fit<- survfit(Surv(time, status) ~ sex, data = lung)
> 
> # Drawing survival curves
> ggsurvplot(fit)
> 
> # Change font size, style and color
> #++++++++++++++++++++++++++++++++++++
> ## Not run: 
> ##D # Change font size, style and color at the same time
> ##D ggsurvplot(fit, main = "Survival curve",
> ##D    font.main = c(16, "bold", "darkblue"),
> ##D    font.x = c(14, "bold.italic", "red"),
> ##D    font.y = c(14, "bold.italic", "darkred"),
> ##D    font.tickslab = c(12, "plain", "darkgreen"))
> ## End(Not run)
> 
> # Legend: title, labels and position
> #++++++++++++++++++++++++++++++++++++
> 
> # Change the legend title and labels
> ggsurvplot(fit, legend = "bottom",
+           legend.title = "Sex",
+           legend.labs = c("Male", "Female"))
> 
> # Specify legend position by its coordinates
> ggsurvplot(fit, legend = c(0.2, 0.2))
> 
> 
> # format
> #++++++++++++++++++++++++++++++++++++
> # change line size --> 1
> # Change line types by groups (i.e. "strata")
> # and change color palette
> ggsurvplot(fit,  size = 1,  # change line size
+           linetype = "strata", # change line type by groups
+           break.time.by = 250, # break time axis by 250
+           palette = c("#E7B800", "#2E9FDF"), # custom color palette
+           conf.int = TRUE, # Add confidence interval
+           pval = TRUE # Add p-value
+ )
> 
> # Use brewer color palette "Dark2"
> # Add risk table
> ggsurvplot(fit, linetype = "strata",
+           conf.int = TRUE, pval = TRUE,
+           palette = "Dark2", risk.table = TRUE)
Warning in is.na(x) :
  is.na() applied to non-(list or vector) of type 'NULL'
Error in -x : invalid argument to unary operator
Calls: ggsurvplot ... summary.survfit -> findrow -> find2 -> findInterval
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Quitting from lines 55-64 (Informative_Survival_Plots.Rmd) 
Error: processing vignette 'Informative_Survival_Plots.Rmd' failed with diagnostics:
there is no package called 'RTCGA.clinical'
Execution halted

* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 WARNINGs, 1 NOTE