* using log directory ‘/data/blackswan/ripley/R/packages/tests-devel/HybridDesign.Rcheck’
* using R Under development (unstable) (2024-06-26 r86836)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)
GNU Fortran (GCC) 13.2.1 20240316 (Red Hat 13.2.1-7)
* running under: Fedora Linux 38 (Workstation Edition)
* using session charset: UTF-8
* checking for file ‘HybridDesign/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HybridDesign’ version ‘1.0’
* 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 ‘HybridDesign’ can be installed ... 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 code 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [13s/13s] 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 examples ... OK
* checking examples with --run-donttest ... ERROR
Running examples in ‘HybridDesign-Ex.R’ failed
The error most likely occurred in:
> ### Name: get_oc_hybrid
> ### Title: Generate operating characteristics for single-agent dose-finding
> ### studies using the Hybrid design
> ### Aliases: get_oc_hybrid
>
> ### ** Examples
>
> ## No test:
> get_oc_hybrid(trueMTD=12, trueDLTvec=c(0.15,0.20,0.25,0.30,0.35), dose=c(3, 6, 12, 18, 24),
+ target=0.25, ncohort=10, cohortsize=3, eps1=0.05, eps2=0.05, a=1, b=1,
+ cutoff.eli=0.95, tox.control=TRUE, cut.tox=0.8, esc.control=FALSE, cut.esc=0.5,
+ ntrial=100, seednum=10000)
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Warning in hoslem.test(ptox, stats::fitted(model)) :
The data did not allow for the requested number of bins.
Error in hoslem.test(ptox, stats::fitted(model)) :
The number of bins led to negative df.
Calls: get_oc_hybrid -> hybrid -> hoslem.test
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
See
‘/data/blackswan/ripley/R/packages/tests-devel/HybridDesign.Rcheck/00check.log’
for details.
Command exited with non-zero status 1
Time 1:14.43, 63.98 + 9.87