* using log directory ‘/home/bolker/lme4check2/check/mice.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 ‘mice/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mice’ version ‘2.22’
* 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 ‘mice’ 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:
‘lme4’ ‘nlme’ ‘pan’ ‘survival’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
appendbreak: no visible global function definition for ‘bs’
bwplot.mids: no visible global function definition for
‘lattice.getOption’
bwplot.mids: no visible global function definition for
‘latticeParseFormula’
densityplot.mids: no visible global function definition for
‘lattice.getOption’
densityplot.mids: no visible global function definition for
‘latticeParseFormula’
extractBS: no visible global function definition for ‘ranef’
extractBS: no visible global function definition for ‘fixef’
mice.impute.2l.pan: no visible global function definition for ‘pan’
nelsonaalen: no visible global function definition for ‘basehaz’
nelsonaalen: no visible global function definition for ‘coxph’
plot.mids : strip.combined: no visible global function definition for
‘panel.rect’
plot.mids : strip.combined: no visible global function definition for
‘panel.text’
pool: no visible global function definition for ‘fixef’
stripplot.mids: no visible global function definition for
‘lattice.getOption’
stripplot.mids: no visible global function definition for
‘latticeParseFormula’
xyplot.mids: no visible global function definition for
‘lattice.getOption’
xyplot.mids: no visible global function definition for
‘latticeParseFormula’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: ‘CALIBERrfimpute’
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs