Check results for 'RMark'

using R version 4.3.0 beta (2023-04-07 r84200)
using platform: aarch64-apple-darwin20 (64-bit)
R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
running under: macOS Big Sur 11.6.7
using session charset: UTF-8
checking for file ‘RMark/DESCRIPTION’ ... OK
this is package ‘RMark’ version ‘3.0.0’
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 ‘RMark’ can be installed ... [7s/8s] WARNING
Found the following significant warnings:
Warning: Software mark not found in path.
See https://www.r-project.org/nosvn/R.check/r-release-macos-arm64/RMark-00install.html for details.
checking installed package size ... 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 ... [1s/1s] OK
checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
checking whether the package can be unloaded cleanly ... [1s/1s] OK
checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
checking loading without being on the library search path ... [1s/1s] OK
checking startup messages can be suppressed ... [1s/1s] NOTE
Warning: Software mark not found in path.
If you have mark executable, you will need to set MarkPath object to its location (e.g. MarkPath="C:/Users/Jeff Laake/Desktop"

It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
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 ... [10s/12s] OK
checking Rd files ... [1s/1s] 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 ... [0s/0s] OK
checking data for ASCII and uncompressed saves ... OK
checking examples ... [1s/1s] 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=1,delete=TRUE)
+
+ #
+ # Return model table and list of models
+ #
+ return(bduck.results)
+ }
> bduck.results=run.Blackduck()

S.BirdAge

sh: mark: command not found
Warning in system(paste("mark i=", inputfile, " o=", outfile, " v=", vcvfile, :
  error in running command
Error in run.mark.model(model, invisible = invisible, adjust = adjust, :

Output file does not exist. Unable to find or run mark.exe

S.BirdAge.Weight

sh: mark: command not found
Warning in system(paste("mark i=", inputfile, " o=", outfile, " v=", vcvfile, :
  error in running command
Error in run.mark.model(model, invisible = invisible, adjust = adjust, :

Output file does not exist. Unable to find or run mark.exe

S.BirdAgexWeight.min

sh: mark: command not found
Warning in system(paste("mark i=", inputfile, " o=", outfile, " v=", vcvfile, :
  error in running command
Error in run.mark.model(model, invisible = invisible, adjust = adjust, :

Output file does not exist. Unable to find or run mark.exe

S.dot

sh: mark: command not found
Warning in system(paste("mark i=", inputfile, " o=", outfile, " v=", vcvfile, :
  error in running command
Error in run.mark.model(model, invisible = invisible, adjust = adjust, :

Output file does not exist. Unable to find or run mark.exe

S.min

sh: mark: command not found
Warning in system(paste("mark i=", inputfile, " o=", outfile, " v=", vcvfile, :
  error in running command
Error in run.mark.model(model, invisible = invisible, adjust = adjust, :

Output file does not exist. Unable to find or run mark.exe

S.time

sh: mark: command not found
Warning in system(paste("mark i=", inputfile, " o=", outfile, " v=", vcvfile, :
  error in running command
Error in run.mark.model(model, invisible = invisible, adjust = adjust, :

Output file does not exist. Unable to find or run mark.exe

No mark models found

Error in collect.models() :
Calls: run.Blackduck -> mark.wrapper -> collect.models
Execution halted
checking PDF version of manual ... [8s/9s] OK
DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
using check arguments '--no-clean-on-error '