• using R version 4.5.0 beta (2025-03-29 r88069)
  • using platform: aarch64-apple-darwin20
  • R was compiled by     Apple clang version 14.0.0 (clang-1400.0.29.202)     GNU Fortran (GCC) 14.2.0
  • running under: macOS Ventura 13.4
  • 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 the install log 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 code 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
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  • checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
  • checking loading without being on the library search path ... [1s/1s] OK
  • checking whether 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 ... [9s/11s] 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 ... [7s/10s] OK
  • DONE Status: 1 ERROR, 1 WARNING, 1 NOTE
  • using check arguments '--no-clean-on-error '