- using R version 2.14.2 RC (2012-02-23 r58468)
- using platform: i686-pc-linux-gnu (32-bit)
- using session charset: UTF-8
- checking for file ‘bcrm/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘bcrm’ version ‘0.2’
- 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 whether package ‘bcrm’ can be installed ... OK
- checking installed package size ... OK
- checking package directory ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking DESCRIPTION meta-information ... OK
- checking top-level 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 for unstated 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 ... NOTE
HTGamma: no visible binding for global variable ‘N1’
HTGamma: no visible global function definition for ‘pow’
HTGamma: no visible binding for global variable ‘d’
HTLogNormal: no visible binding for global variable ‘N1’
HTLogNormal: no visible global function definition for ‘pow’
HTLogNormal: no visible binding for global variable ‘d’
HTLogNormal: no visible binding for global variable ‘p2’
HTUnif: no visible binding for global variable ‘N1’
HTUnif: no visible global function definition for ‘pow’
HTUnif: no visible binding for global variable ‘d’
LogisticGamma: no visible binding for global variable ‘N1’
LogisticGamma: no visible binding for global variable ‘d’
LogisticLogNormal: no visible binding for global variable ‘N1’
LogisticLogNormal: no visible binding for global variable ‘d’
LogisticLogNormal: no visible binding for global variable ‘p2’
LogisticUnif: no visible binding for global variable ‘N1’
LogisticUnif: no visible binding for global variable ‘d’
PowerGamma: no visible binding for global variable ‘N1’
PowerGamma: no visible global function definition for ‘pow’
PowerGamma: no visible binding for global variable ‘d’
PowerLogNormal: no visible binding for global variable ‘N1’
PowerLogNormal: no visible global function definition for ‘pow’
PowerLogNormal: no visible binding for global variable ‘d’
PowerLogNormal: no visible binding for global variable ‘p2’
PowerUnif: no visible binding for global variable ‘N1’
PowerUnif: no visible global function definition for ‘pow’
PowerUnif: no visible binding for global variable ‘d’
TwoPLogisticLogNormal: no visible binding for global variable ‘N1’
TwoPLogisticLogNormal: no visible global function definition for
‘logit<-’
TwoPLogisticLogNormal: no visible binding for global variable
‘log.alpha’
TwoPLogisticLogNormal: no visible binding for global variable ‘d’
TwoPLogisticLogNormal: no visible global function definition for
‘inverse’
TwoPLogisticLogNormal: no visible binding for global variable ‘p2’
plot.bcrm: no visible binding for global variable ‘q2.5’
plot.bcrm: no visible binding for global variable ‘q97.5’
plot.bcrm: no visible binding for global variable ‘q50’
plot.bcrm: no visible binding for global variable ‘q25’
plot.bcrm: no visible binding for global variable ‘q75’
plot.bcrm: no visible binding for global variable ‘target.tox’
plot.bcrm: no visible binding for global variable ‘est’
plot.bcrm: no visible binding for global variable ‘tox.cutpoints’
plot.bcrm: no visible binding for global variable ‘xmin’
plot.bcrm: no visible binding for global variable ‘ymin’
plot.bcrm: no visible binding for global variable ‘xmax’
plot.bcrm: no visible binding for global variable ‘ymax’
plot.bcrm: no visible binding for global variable ‘Loss’
plot.bcrm: no visible binding for global variable ‘Outcome’
- 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 examples ... ERROR
Running examples in ‘bcrm-Ex.R’ failed
The error most likely occurred in:
> ### Name: Posterior
> ### Title: Calculate posterior distribution of CRM model parameter(s)
> ### Aliases: Posterior.exact Posterior.BRugs Posterior.R2WinBUGS
>
> ### ** Examples
>
> ## Dose-escalation cancer trial example as described in Neuenschwander et al 2008.
> ## Pre-defined doses
> dose<-c(1,2.5,5,10,15,20,25,30,40,50,75,100,150,200,250)
> ## Pre-specified probabilities of toxicity
> ## [dose levels 11-15 not specified in the paper, and are for illustration only]
> p.tox0<-c(0.010,0.015,0.020,0.025,0.030,0.040,0.050,0.100,0.170,0.300,0.400,0.500,0.650
+ ,0.800,0.900)
> ## Data from the first 5 cohorts of 18 patients
> tox<-c(0,0,0,0,0,0,2,0,0,0,0,0,0,0,0)
> notox<-c(3,4,5,4,0,0,0,0,0,0,0,0,0,0,0)
> ## Target toxicity level
> target.tox<-0.30
> ## Lognormal prior
> prior.alpha<-list(3,0,1.34^2)
> ## Power functional form
> ff<-"power"
> ## Standardised doses
> sdose<-find.x(ff,p.tox0,alpha=1)
>
> ## Posterior distribution of the model parameter
> posterior.samples<-Posterior.BRugs(tox,notox,sdose,ff,prior.alpha
+ ,burnin.itr=2000,production.itr=2000)
Loading required package: BRugs
Loading required package: coda
Loading required package: lattice
Loading required package: R2WinBUGS
Warning in file(file, ifelse(append, "a", "w")) :
cannot open file '/cmds.txt': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
Calls: Posterior.BRugs ... .OpenBUGS.platform -> .OpenBUGS.helper -> write -> cat -> file
Execution halted