* using log directory ‘/home/bolker/lme4check2/check/MethComp.Rcheck’
* using R Under development (unstable) (2015-06-08 r68489)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘MethComp/DESCRIPTION’ ... OK
* this is package ‘MethComp’ version ‘2.0’
* 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 ‘MethComp’ can be installed ... OK
* 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 ... 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 ... NOTE
'library' or 'require' calls in package code:
‘coda’ ‘rjags’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
‘lattice’ ‘nlme’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
almost never needs to use ::: for its own objects:
‘VC.est.fixed’ ‘VC.est.random’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
AltReg: no visible global function definition for ‘lme’
BA.est: no visible global function definition for ‘lmeControl’
MCmcmc: no visible global function definition for ‘jags.model’
MCmcmc: no visible global function definition for ‘coda.samples’
VC.est: no visible global function definition for ‘lmeControl’
VC.est.fixed: no visible global function definition for ‘lmeControl’
VC.est.fixed: no visible global function definition for ‘lme’
VC.est.fixed: no visible global function definition for ‘pdIdent’
VC.est.fixed: no visible global function definition for ‘varIdent’
VC.est.fixed: no visible global function definition for ‘pdDiag’
VC.est.fixed: no visible global function definition for ‘pdSymm’
VC.est.random: no visible global function definition for ‘lmeControl’
VC.est.random: no visible global function definition for ‘lme’
VC.est.random: no visible global function definition for ‘pdBlocked’
VC.est.random: no visible global function definition for ‘pdIdent’
VC.est.random: no visible global function definition for ‘varIdent’
VC.est.random: no visible global function definition for ‘ranef’
VC.est.random: no visible global function definition for ‘pdDiag’
addcols.mcmc: no visible global function definition for ‘as.mcmc.list’
find.mean: no visible global function definition for ‘varnames’
find.vars: no visible global function definition for ‘varnames’
mcmc.MCmcmc: no visible global function definition for ‘as.mcmc’
pairs.MCmcmc: no visible global function definition for ‘nchain’
pairs.MCmcmc: no visible global function definition for ‘niter’
pairs.MCmcmc: no visible global function definition for ‘varnames’
post.mean: no visible global function definition for ‘as.mcmc’
post.mean: no visible global function definition for ‘densityplot’
post.sd: no visible global function definition for ‘as.mcmc’
post.sd: no visible global function definition for ‘densityplot’
subset.MCmcmc : char.2.num: no visible global function definition for
‘varnames’
subset.MCmcmc: no visible global function definition for ‘nchain’
trace.mean: no visible global function definition for ‘xyplot’
trace.sd: no visible global function definition for ‘xyplot’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs