* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/ggDCA.Rcheck’
* using R Under development (unstable) (2023-04-09 r84208)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
    GNU Fortran (GCC) 11.3.1 20220421 (Red Hat 11.3.1-2)
* running under: Fedora 34 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘ggDCA/DESCRIPTION’ ... OK
* this is package ‘ggDCA’ version ‘1.1’
* 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 ‘ggDCA’ can be installed ... [10s/10s] OK
* checking package 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
Namespace in Imports field not imported from: ‘survival’
  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 ... [16s/16s] OK
* 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 LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘ggDCA-Ex.R’ failed
The error most likely occurred in:

> ### Name: ggplot.rFP.p100
> ### Title: Plot for decision curve
> ### Aliases: ggplot.rFP.p100 ggplot.dca.cph ggplot ggplot.dca.lrm
> 
> ### ** Examples
> 
> 
> library(ggDCA)
> library(rms)
Loading required package: Hmisc

Attaching package: ‘Hmisc’

The following objects are masked from ‘package:base’:

    format.pval, units

> 
> ######## logistic regression
> 
> model1 <- lrm(status~ANLN,LIRI)
> d <- dca(model1,model.names = 'ANLN')
> ggplot(d)
Warning: Removed 44 rows containing missing values (`geom_line()`).
> 
> ## No test: 
> 
> model2 <- lrm(status~ANLN+CENPA,LIRI)
> d <- dca(model2,model.names = 'ANLN+CENPA')
> ggplot(d)
Warning: Removed 48 rows containing missing values (`geom_line()`).
> 
> 
> model3 <- lrm(status~ANLN+CENPA+GPR182,LIRI)
> d <- dca(model3,model.names = 'ANLN+CENPA+GPR182')
> ggplot(d)
Warning: Removed 53 rows containing missing values (`geom_line()`).
> 
> model4 <- lrm(status~ANLN+CENPA+GPR182+BCO2,LIRI)
> d <- dca(model4,model.names = 'ANLN+CENPA+GPR182+BCO2')
> ggplot(d)
Warning: Removed 52 rows containing missing values (`geom_line()`).
> 
> 
> d <- dca(model1,model2,model3,model4,
+          model.names = c('ANLN',
+                          'ANLN+CENPA',
+                          'ANLN+CENPA+GPR182',
+                          'ANLN+CENPA+GPR182+BCO2'))
> ggplot(d,
+        linetype = FALSE,
+        color = c('blue','green','black','red','gray','gray'))
Warning: Removed 197 rows containing missing values (`geom_line()`).
> 
> 
> ##########  cox regression
> 
> # evaluate at median time
> 
> model1 <- coxph(Surv(time,status)~ANLN,LIRI)
Error in coxph(Surv(time, status) ~ ANLN, LIRI) : 
  could not find function "coxph"
Execution halted
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* checking for new files in some other directories ... OK
* DONE

Status: 1 ERROR, 1 NOTE
See
  ‘/data/blackswan/ripley/R/packages/tests-devel/ggDCA.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 1:27.95, 77.95 + 9.40