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eatDev log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2016-11-14-19-04/RF_PKG_CHECK/PKGS/eatDev.Rcheck'
* using R version 3.3.2 Patched (2016-11-12 r71650)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'eatDev/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'eatDev' version '0.0.2'
* checking CRAN incoming feasibility ... NOTE
Maintainer: 'Not me '

New submission

No package encoding and non-ASCII characters in the following R files:
  R/MH_ccv.sampling.R
    5: # col4.n: n auf das conditional upgesampled wird, wenn skalar dann fr alle th gleich, oder Vektor um fr jedes th zu setzen
    120: 		# ber Item-Datenstze schleifen
    123: 				# aktuelles Item, fr verbose Ausgaben
    140: 				### falls man das ausweiten wrde wollen auf polytom
    189: 								# randomly durcheinanderbringen, damit Verteilung mglichst gleich
    197: 								# sortieren von klein nach gro
    212: 										# wenn vals.unique NULL ist, dann egal (aus allen Personen, unabhngig vom value, ziehen)
    254: 								# neue Person in Variable sel in sel.env hinzufgen
    292: 		# ggf. upsampling col4.n.vec wenn gewnscht
    415: 		### observations raussamplen um NperItem zu gewhrleisten ###
    437: 				# Environment fr zu reduzierenden Datensatz d6
    467: 								# die Personen die viele observations haben (max), haben groe prob (1) rauszufliegen
    470: 								# bei unter 2 observations ist die Person nicht zum Deselektieren ziehbar, da diese sonst aus dem Datensatz fliegen wrde
    614: 		# kreiertes Environment zurcksetzen
    618: 		# Rckgabe
  R/MH_lmer.fixef.to.dfr.R
    19: 						# das hier ist natrlich etwas ungenau
    20: 						# msste strker elaboriert werden
  R/MH_nested.pooling.R
    3: # Rubin, D. B. (2003). Nested multiple imputation of NMES via partially incompatible MCMC. Statistica Neerlandica, 57(1), 3<80><93>18.
    14: 		# wenn Datensatz 3 Spalten hat, dann M.varname als die brig gebliebene defaulten, wenn M.varname NULL ist
  R/MH_pool.pv.R
    2: # pv ... Namen oder Indizes der PV-Variablen im Datensatz; oder regulrer Ausdruck
    15: 		# temporrer folder fr Sicherheitskopien
    167: 		# vorhandene Stufen auf pv.vars fr mode="cat"
    190: 		# Sortierung auf Split-vars aufheben um spter zu setzen
    230: 						# krzen bzgl. Parameter "interaction"
    238: 						# sortieren nach Lnge
    244: 						# adaptieren fr gewnschte Effekte
    249: 						# tatschlich relevante split.vars
    272: 						# split vars real (tatschlich relevante split.vars)
    345: 				# pv pooling auf Datenstzen
    567: 												# temporrer jk2.table Bug-Fix, muss gelabelt sein
    612: 												# ICC Kennwerte auswhlen (Funktion pool.corr)
    749: 				# falls NULL Datenstze, vorsorglich noch raus
    754: 				### lschen ###
    761: 				# Datenstze zusammenbinden
  R/bias.rmse.R
    14: 		# wenn method == "group" heisst das ber Groups die Kennwerte berechnet werden, und ber Replicates gemittelt
    15: 		# wenn method == "repl" heisst das ber Replicates die Kennwerte berechnet werden, und ber Groups gemittelt
    16: 		# das ist nur fr den biasfree.sd und RMSE relevant
    17: 		# bei "group" ist biasfree.sd/RMSE die Variabilitt ber die group-Elemente
    18: 		# bei "repl" ist biasfree.sd/RMSE die Variabilitt ber die replicates
    110: 								# in Abhngigkeit von method den split machen
    113: 										# d.h. Kennwerte werden ber group innerhalb jedes replicate berechnet
    122: 										# d.h. Kennwerte werden ber replicates innerhalb jedes Parameters berechnet
    145: 										# Checks abhngig von method
    223: 										### wenn method=repl, dann noch MAP, EAP, SE(=SD) fr die estimates berechnen

The Title field is just the package name: provide a real title.

The Description field should start with a capital letter.

The Date field is over a month old.
* 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 hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'eatDev' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... WARNING
Subdirectory 'data' contains no data sets.
* 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 use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' imports not declared from:
  'car' 'lme4' 'plyr' 'reshape2'
'library' or 'require' calls not declared from:
  'Hmisc' 'eatRep' 'ggplot2' 'lme4' 'mice' 'plotrix' 'reshape2'
'library' or 'require' calls in package code:
  'Hmisc' 'eatRep' 'ggplot2' 'lme4' 'mice' 'plotrix' 'reshape2'
  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
ccv.sampling: warning in ls(all = TRUE, envir = sel.env): partial
  argument match of 'all' to 'all.names'
ccv.sampling: warning in ls(all = TRUE, envir = d6.env): partial
  argument match of 'all' to 'all.names'
bias.rmse : f1: no visible binding for global variable 'e2'
bias.rmse : f1 : f2: no visible global function definition for
  'flush.console'
bias.rmse : f1 : f2 : f3: no visible global function definition for
  'flush.console'
bias.rmse : f1 : f2 : f3 : calc.cor: no visible global function
  definition for 'sd'
bias.rmse : f1 : f2 : f3 : calc.cor: no visible global function
  definition for 'cor'
bias.rmse : f1 : f2 : f3 : Mse: no visible global function definition
  for 'sd'
bias.rmse : f1 : f2 : f3: no visible global function definition for
  'sd'
bias.rmse: no visible binding for global variable 'true.l'
ccv.sampling: no visible global function definition for 'flush.console'
ccv.sampling : loop.items: no visible global function definition for
  'runif'
ccv.sampling : loop.items: no visible global function definition for
  'flush.console'
ccv.sampling : sampl1: no visible global function definition for
  'runif'
ccv.sampling: no visible global function definition for 'sd'
ccv.sampling : nperitem.downsample: no visible global function
  definition for 'runif'
check.var: no visible global function definition for 'var'
fneff: no visible global function definition for 'var'
fspec0: no visible global function definition for 'spec.ar'
get.lmer.effects: no visible global function definition for
  'installed.packages'
get.lmer.effects: no visible global function definition for 'VarCorr'
get.lmer.effects: no visible global function definition for 'vcov'
get.lmer.effects: no visible global function definition for 'pnorm'
get.lmer.effects: no visible global function definition for 'as'
get.lmer.effects: no visible global function definition for 'sigma'
get.lmer.effects: no visible global function definition for 'getME'
get.lmer.effects: no visible global function definition for 'logLik'
get.lmer.effects: no visible global function definition for 'AIC'
get.lmer.effects: no visible global function definition for 'BIC'
get.ranef: no visible global function definition for 'na.omit'
lmer.fixef.to.dfr: no visible global function definition for 'fixef'
lmer.fixef.to.dfr: no visible global function definition for
  'capture.output'
lmer.fixef.to.dfr: no visible global function definition for 'cast'
nested.pooling : : no visible global function definition for
  'var'
nested.pooling: no visible global function definition for 'pt'
plotJAGS : looppars : make.plots: no visible global function definition
  for 'ggplot'
plotJAGS : looppars : make.plots: no visible global function definition
  for 'aes'
plotJAGS : looppars : make.plots: no visible binding for global
  variable 'Iteration'
plotJAGS : looppars : make.plots: no visible binding for global
  variable 'Estimate'
plotJAGS : looppars : make.plots: no visible global function definition
  for 'geom_point'
plotJAGS : looppars : make.plots: no visible global function definition
  for 'geom_smooth'
plotJAGS: no visible global function definition for 'pdf'
plotJAGS: no visible global function definition for 'dev.off'
pool.corr: no visible global function definition for 'pool.scalar'
pool.corr: no visible global function definition for 'pnorm'
pool.corr: no visible global function definition for 'qnorm'
pool.pv: no visible global function definition for 'reshape'
pool.pv : f: no visible global function definition for 'combn'
pool.pv : pool.pv: no visible global function definition for
  'flush.console'
pool.pv : pool.pv: no visible binding for global variable 'std.error'
pool.pv : pool.pv: no visible binding for global variable 'wtd.mean'
pool.pv : pool.pv: no visible binding for global variable 'wtd.var'
pool.pv : pool.pv: no visible global function definition for 'jk2.mean'
pool.pv : pool.pv: no visible global function definition for
  'jk2.quantile'
pool.pv : pool.pv: no visible binding for global variable
  'uasdjfojwernhkjjsdfjkl'
pool.pv : pool.pv: no visible binding for global variable
  'asdfjasdejkkekk'
pool.pv : pool.pv: no visible global function definition for 'jk2.glm'
pool.pv : pool.pv: no visible global function definition for
  'jk2.table'
pool.pv : pool.pv : calc.icc: no visible binding for global variable
  'tried5'
pool.pv: no visible global function definition for 'flush.console'
resJAGS :  : : no visible global function
  definition for 'density'
resJAGS :  : : no visible global function
  definition for 'sd'
resJAGS :  : : no visible global function
  definition for 'qnorm'
resJAGS :  :  : : no visible global
  function definition for 'quantile'
Undefined global functions or variables:
  AIC BIC Estimate Iteration VarCorr aes as asdfjasdejkkekk
  capture.output cast combn cor density dev.off e2 fixef flush.console
  geom_point geom_smooth getME ggplot installed.packages jk2.glm
  jk2.mean jk2.quantile jk2.table logLik na.omit pdf pnorm pool.scalar
  pt qnorm quantile reshape runif sd sigma spec.ar std.error tried5
  true.l uasdjfojwernhkjjsdfjkl var vcov wtd.mean wtd.var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("methods", "as")
  importFrom("stats", "AIC", "BIC", "cor", "density", "logLik",
             "na.omit", "pnorm", "pt", "qnorm", "quantile", "reshape",
             "runif", "sd", "sigma", "spec.ar", "var", "vcov")
  importFrom("utils", "capture.output", "combn", "flush.console",
             "installed.packages")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
prepare_Rd: bias.rmse.Rd:40-41: Dropping empty section \seealso
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'bias.rmse.Rd':
  \usage lines wider than 90 characters:
     bias.rmse ( true , est , id.col , val.col , repl.col = NULL , group.col = NULL , method = c ( "group" , "repl" ) , verbose = FALSE )
  \examples lines wider than 100 characters:
     bias.rmse ( true , est , id.col = "variable" , val.col = "value" , group.col = "group" , verbose = TRUE )       
                                              "replicates" = c ( 1 , 2 , 1 , 2 ) ,                                    
     bias.rmse ( true , est , id.col = "variable" , val.col = "value" , group.col = "group" , repl.col = "replicates" , method = "group" , v ... [TRUNCATED]
     bias.rmse ( true , est , id.col = "variable" , val.col = "value" , group.col = "group" , repl.col = "replicates" , method = "repl" , ve ... [TRUNCATED]
     bias.rmse ( true , est , id.col = "variable" , val.col = "value" , group.col = "group" , repl.col = "replicates" , verbose = TRUE)      ... [TRUNCATED]
     bias.rmse ( true , est , id.col = "variable" , val.col = "value" , group.col = "group" , repl.col = "replicates" , verbose = TRUE )     ... [TRUNCATED]
     bias.rmse ( true , est , id.col = "variable" , val.col = "value" , group.col = "group" , repl.col = "replicates" , verbose = TRUE )     ... [TRUNCATED]
                                              "data.cond" = rep ( c ( rep ( 1 , 4 ) , rep ( 2 , 4 ) ) , 2 ) ,
     bias.rmse ( true , est , id.col = "variable" , val.col = "value" , group.col = "group" , repl.col = "replicates" , verbose = TRUE )
                                              "group" = c ( rep ( "items" , 2 ) , rep ( "persons" , 2 ) , NA ) , 
     bias.rmse ( true , est , id.col = "variable" , val.col = "value" , group.col = "group" , verbose = TRUE )       

These lines will be truncated in the PDF manual.
* 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 ... WARNING
Files not of a type allowed in a 'data' directory:
  'ctExample2.Rdata' 'd_6items_2processes_5timepoints.Rdata'
Please use e.g. 'inst/extdata' for non-R data files
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 WARNINGs, 5 NOTEs
See
  'R:/run/building/build_2016-11-14-19-04/RF_PKG_CHECK/PKGS/eatDev.Rcheck/00check.log'
for details.


Run time: 30.65 seconds.