Check results for 'RMark'

using R version 2.15.3 (2013-03-01)
using platform: i386-apple-darwin9.8.0 (32-bit)
using session charset: UTF-8
checking for file ‘RMark/DESCRIPTION’ ... OK
this is package ‘RMark’ version ‘2.1.4’
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 ‘RMark’ can be installed ... WARNING
Found the following significant warnings:
Warning: Software mark not found in path.
See ‘/Volumes/XT3/Rdev-web/QA/Simon/packages/leopard-universal/results/2.15/RMark.Rcheck/00install.out’ for details.
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 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 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 ... 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 examples ... ERROR
Running examples in ‘RMark-Ex.R’ failed
The error most likely occurred in:

> ### Name: Blackduck
> ### Title: Black duck known fate data
> ### Aliases: Blackduck
> ### Keywords: datasets
>
> ### ** Examples
>
> data(Blackduck)
> # Change BirdAge to numeric; starting with version 1.6.3 factor variables are
> # no longer allowed. They can work as in this example but they can be misleading
> # and fail if the levels are non-numeric. The real parameters will remain
> # unchanged but the betas will be different.
> Blackduck$BirdAge=as.numeric(Blackduck$BirdAge)-1
> run.Blackduck=function()
+ {
+ #
+ # Process data
+ #
+ bduck.processed=process.data(Blackduck,model="Known")
+ #
+ # Create default design data
+ #
+ bduck.ddl=make.design.data(bduck.processed)
+ #
+ # Add occasion specific data min < 0; I have no idea what it is
+ #
+ bduck.ddl$S$min=c(4,6,7,7,7,6,5,5)
+ #
+ # Define range of models for S
+ #
+ S.dot=list(formula=~1)
+ S.time=list(formula=~time)
+ S.min=list(formula=~min)
+ S.BirdAge=list(formula=~BirdAge)
+ #
+ # Note that in the following model in the MARK example, the covariates
+ # have been standardized. That means that the beta parameters will be different
+ # for BirdAge, Weight and their interaction but the likelihood and real parameter
+ # estimates are the same.
+ #
+ S.BirdAgexWeight.min=list(formula=~min+BirdAge*Weight)
+ S.BirdAge.Weight=list(formula=~BirdAge+Weight)
+ #
+ # Create model list and run assortment of models
+ #
+ model.list=create.model.list("Known")
+ bduck.results=mark.wrapper(model.list,data=bduck.processed,ddl=bduck.ddl,
+ invisible=FALSE,threads=2)
+
+ #
+ # Return model table and list of models
+ #
+ return(bduck.results)
+ }
> bduck.results=run.Blackduck()

S.BirdAge
sh: mark: command not found
Warning in file(con, "r") :
cannot open file 'mark001.out': No such file or directory
Error in file(con, "r") : cannot open the connection

********Following model failed to run : S(~BirdAge) **********

S.BirdAge.Weight
sh: mark: command not found
Warning in file(con, "r") :
cannot open file 'mark001.out': No such file or directory
Error in file(con, "r") : cannot open the connection

********Following model failed to run : S(~BirdAge + Weight) **********

S.BirdAgexWeight.min
sh: mark: command not found
Warning in file(con, "r") :
cannot open file 'mark001.out': No such file or directory
Error in file(con, "r") : cannot open the connection

********Following model failed to run : S(~min + BirdAge * Weight) **********

S.dot
sh: mark: command not found
Warning in file(con, "r") :
cannot open file 'mark001.out': No such file or directory
Error in file(con, "r") : cannot open the connection

********Following model failed to run : S(~1) **********

S.min
sh: mark: command not found
Warning in file(con, "r") :
cannot open file 'mark001.out': No such file or directory
Error in file(con, "r") : cannot open the connection

********Following model failed to run : S(~min) **********

S.time
sh: mark: command not found
Warning in file(con, "r") :
cannot open file 'mark001.out': No such file or directory
Error in file(con, "r") : cannot open the connection

********Following model failed to run : S(~time) **********

Model 1: S.BirdAge has not been run.
Model 2: S.BirdAge.Weight has not been run.
Model 3: S.BirdAgexWeight.min has not been run.
Model 4: S.dot has not been run.
Model 5: S.min has not been run.
Model 6: S.time has not been run.
Warning in min(result.table$AICc) :
no non-missing arguments to min; returning Inf
Error in result.table[order(result.table$DeltaAICc), ] :
incorrect number of dimensions
Calls: run.Blackduck -> mark.wrapper -> collect.models -> model.table
Execution halted
elapsed time (check, wall clock): 1:00