R Development Page

cRacker log file (check_x86_64_linux)

Thu Aug 29 12:21:35 2013: Checking package cRacker (SVN revision 51) ...
Additional arguments to R CMD check: --no-examples --no-tests --no-vignettes
* using log directory ‘/mnt/building/build_2013-08-29-12-09/RF_PKG_CHECK/PKGS/cRacker.Rcheck’
* using R version 3.0.1 Patched (2013-08-27 r63742)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-examples --no-tests --no-vignettes’
* checking for file ‘cRacker/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cRacker’ version ‘1.496’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Henrik Zauber ’
New submission
* 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 ‘cRacker’ can be installed ... [2s/2s] WARNING
Found the following significant warnings:
  Warning: /mnt/building/build_2013-08-29-12-09/RF_PKG_CHECK/PKGS/cRacker.Rcheck/00_pkg_src/cRacker/man/cRacker-package.Rd:31: unexpected '}'
See ‘/mnt/building/build_2013-08-29-12-09/RF_PKG_CHECK/PKGS/cRacker.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 13.6Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
* 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 ... WARNING
Found the following file with non-ASCII characters:
  hz.matrix.creator.R
Portable packages must use only ASCII characters in their R code,
except perhaps in comments.
Use \uxxxx escapes for other characters.
* 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 ... WARNING
‘library’ or ‘require’ calls not declared from:
  ‘gplots’ ‘grid’ ‘pcaMethods’ ‘seqinr’ ‘tcltk’ ‘tcltk2’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... WARNING
image:
  function(x, ...)
image.button:
  function(level, title.help, text.help, bgcol, image, fgcol, size, bf)

See section ‘Generic functions and methods’ of the ‘Writing R
Extensions’ manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
hz.design: warning in make.names(cut.path(as.vector(temp.all[, 1])),
  allow = F): partial argument match of 'allow' to 'allow_'
hz.design: warning in make.names(cut.path(as.vector(temp.all[, 2])),
  allow = F): partial argument match of 'allow' to 'allow_'
hz.matrix.creator: warning in make.names(tolower(exp.set.2[, 1]), allow
  = FALSE): partial argument match of 'allow' to 'allow_'
hz.matrix.creator: warning in make.names(tolower(exp.set.2[, 2]), allow
  = FALSE): partial argument match of 'allow' to 'allow_'
hz.matrix.creator: warning in make.names(tolower(exp.set.2[, 5]), allow
  = FALSE): partial argument match of 'allow' to 'allow_'
hz.matrix.creator: warning in make.names(tolower(x$rawfilename), allow
  = FALSE): partial argument match of 'allow' to 'allow_'
hz.matrix.creator: warning in make.names(tolower(x$sam_id), allow =
  FALSE): partial argument match of 'allow' to 'allow_'
hz.matrix.creator: warning in round(as.numeric(temp.i$mcr), digit = 0):
  partial argument match of 'digit' to 'digits'
hz.matrix.creator: warning in round(test[, 1], digit = 0): partial
  argument match of 'digit' to 'digits'
hz.matrix.creator: warning in make.names(exp.group.shape[, 1], allow =
  F): partial argument match of 'allow' to 'allow_'
hz.matrix.creator: warning in round(abs(n15.mean - n15.correct.expect),
  digit = 4): partial argument match of 'digit' to 'digits'
hz.script: warning in make.names(.data$rawfilename, allow = F): partial
  argument match of 'allow' to 'allow_'
hz.script: warning in rgb(240, 228, 66, max = 255): partial argument
  match of 'max' to 'maxColorValue'
hz.script: warning in rgb(230, 159, 0, max = 255): partial argument
  match of 'max' to 'maxColorValue'
hz.script: warning in rgb(213, 94, 0, max = 255): partial argument
  match of 'max' to 'maxColorValue'
hz.script: warning in rgb(0, 158, 115, max = 255): partial argument
  match of 'max' to 'maxColorValue'
hz.script: warning in rgb(204, 121, 167, max = 255): partial argument
  match of 'max' to 'maxColorValue'
hz.script: warning in rgb(86, 180, 233, max = 255): partial argument
  match of 'max' to 'maxColorValue'
hz.script: warning in rgb(0, 133, 178, max = 255): partial argument
  match of 'max' to 'maxColorValue'
hz.script: warning in make.names(tolower(.data[, i]), allow = FALSE):
  partial argument match of 'allow' to 'allow_'
hz.script: warning in make.names(.design[, 2], allow = F): partial
  argument match of 'allow' to 'allow_'
hz.script: warning in make.names(.design[, 1], allow = F): partial
  argument match of 'allow' to 'allow_'
hz.script.exp.design: warning in make.names(.design[, 2], allow = F):
  partial argument match of 'allow' to 'allow_'
hz.script.exp.design: warning in make.names(.design[, 1], allow = F):
  partial argument match of 'allow' to 'allow_'
hz.script.exp.design: warning in make.names(.design[, 5], allow = F):
  partial argument match of 'allow' to 'allow_'
hz.script.exp.design: warning in rgb(0, 133, 178, max = 255): partial
  argument match of 'max' to 'maxColorValue'
hz.write.table: warning in round(test, digit = 5): partial argument
  match of 'digit' to 'digits'
cRacker.starter: no visible global function definition for ‘biocLite’
cRacker.starter: no visible global function definition for
  ‘tkmessageBox’
cRacker.starter: no visible global function definition for
  ‘tk2font.set’
cRacker.starter: no visible global function definition for ‘tclvalue’
help.button: no visible global function definition for ‘tk2button’
help.tk: no visible global function definition for ‘tkfont.create’
help.tk: no visible global function definition for ‘tktoplevel’
help.tk: no visible global function definition for ‘tkwm.title’
help.tk: no visible global function definition for ‘tkgrid’
help.tk: no visible global function definition for ‘tk2label’
help.tk: no visible global function definition for ‘tk2button’
help.tk : : no visible global function definition for
  ‘tkdestroy’
hz.agg.fun: no visible binding for global variable
  ‘cracker.counter.temp’
hz.agg.fun: no visible binding for global variable
  ‘cracker.ratio.prog.temp’
hz.agg.fun: no visible binding for global variable ‘i’
hz.aov: no visible binding for global variable ‘aov.export’
hz.aov : hz.print.des: no visible global function definition for
  ‘textbox’
hz.aov : hz.print.des: no visible global function definition for
  ‘grid.newpage’
hz.aov: no visible global function definition for ‘grid.text’
hz.aov: no visible binding for global variable ‘console’
hz.go.input: no visible global function definition for
  ‘tk_choose.files’
hz.go.input: no visible binding for global variable ‘cracker.ui.tk’
hz.go.input: no visible global function definition for ‘tclvalue’
hz.go.input: no visible global function definition for ‘tk_messageBox’
hz.identifier.import: no visible global function definition for
  ‘tktoplevel’
hz.identifier.import: no visible global function definition for
  ‘tclVar’
hz.identifier.import: no visible global function definition for
  ‘tkentry’
hz.identifier.import: no visible global function definition for
  ‘tkgrid’
hz.identifier.import: no visible global function definition for
  ‘tklabel’
hz.identifier.import: no visible global function definition for
  ‘tclvalue<-’
hz.identifier.import: no visible global function definition for
  ‘ttkcombobox’
hz.identifier.import: no visible global function definition for
  ‘tk2button’
hz.identifier.import : : no visible global function
  definition for ‘tclvalue<-’
hz.identifier.import : : no visible global function
  definition for ‘tkdestroy’
hz.identifier.import: no visible global function definition for
  ‘tkbind’
hz.identifier.import: no visible global function definition for
  ‘tkwait.window’
hz.identifier.import: no visible global function definition for
  ‘tclvalue’
hz.import: no visible binding for global variable ‘cracker.ui.tk’
hz.import: no visible global function definition for ‘tclvalue’
hz.import: no visible global function definition for ‘tkmessageBox’
hz.info.search: no visible binding for global variable
  ‘cracker.ratio.prog.temp’
hz.info.search: no visible binding for global variable
  ‘cracker.counter.temp’
hz.info.search : : no visible binding for global variable
  ‘cracker.ratio.prog.temp’
hz.info.search : : no visible binding for global variable
  ‘cracker.counter.temp’
hz.library.fasta: no visible binding for global variable
  ‘cracker.ui.tk’
hz.library.fasta: no visible global function definition for
  ‘read.fasta’
hz.matrix.creator: no visible binding for global variable ‘path2’
hz.matrix.creator: no visible global function definition for
  ‘grid.clip’
hz.matrix.creator: no visible global function definition for
  ‘grid.polygon’
hz.matrix.creator: no visible global function definition for ‘gpar’
hz.matrix.creator: no visible global function definition for
  ‘grid.segments’
hz.matrix.creator: no visible global function definition for
  ‘tkmessageBox’
hz.matrix.creator: no visible global function definition for ‘plotCI’
hz.matrix.creator : : no visible binding for global variable
  ‘database’
hz.matrix.creator: no visible binding for global variable ‘time2’
hz.matrix.creator: no visible binding for global variable ‘time1’
hz.matrix.creator: no visible binding for global variable ‘import.list’
hz.norm : : no visible binding for global variable ‘temp.k’
hz.path.empai: no visible global function definition for ‘tktoplevel’
hz.path.empai: no visible global function definition for ‘tkwm.title’
hz.path.empai: no visible global function definition for ‘tclvalue’
hz.path.empai: no visible global function definition for
  ‘tkimage.create’
hz.path.empai: no visible global function definition for ‘tkframe’
hz.path.empai: no visible global function definition for ‘tclVar’
hz.path.empai : buttonRcmdr: no visible global function definition for
  ‘ttkbutton’
hz.path.empai : onBrowse: no visible global function definition for
  ‘tclvalue<-’
hz.path.empai : onBrowse: no visible global function definition for
  ‘tk_choose.files’
hz.path.empai: no visible global function definition for
  ‘tkcheckbutton’
hz.path.empai: no visible global function definition for ‘tkconfigure’
hz.path.empai: no visible global function definition for ‘tkgrid’
hz.path.empai: no visible global function definition for ‘tklabel’
hz.path.empai: no visible global function definition for ‘ttkentry’
hz.path.empai : test: no visible global function definition for
  ‘tclvalue<-’
hz.path.empai : test: no visible global function definition for
  ‘tclvalue’
hz.path.empai: no visible global function definition for ‘ttkscrollbar’
hz.path.empai : : no visible global function definition for
  ‘tkxview’
hz.path.empai : : no visible global function definition for
  ‘tkset’
hz.path.empai: no visible global function definition for ‘tk2button’
hz.path.empai : : no visible global function definition for
  ‘tclvalue<-’
hz.path.empai : : no visible global function definition for
  ‘tkdestroy’
hz.path.empai: no visible global function definition for ‘tkbind’
hz.path.empai: no visible global function definition for
  ‘tkwait.window’
hz.path.empai: no visible global function definition for ‘tkmessageBox’
hz.path.set: no visible global function definition for ‘tk2font.set’
hz.path.set: no visible global function definition for ‘tkfont.create’
hz.path.set: no visible global function definition for ‘tktoplevel’
hz.path.set: no visible global function definition for ‘tkwm.resizable’
hz.path.set: no visible global function definition for ‘tkwm.title’
hz.path.set: no visible global function definition for ‘tkimage.create’
hz.path.set: no visible global function definition for ‘tkframe’
hz.path.set: no visible global function definition for ‘tclVar’
hz.path.set: no visible global function definition for ‘tclvalue<-’
hz.path.set: no visible global function definition for ‘ttkcombobox’
hz.path.set : buttonRcmdr: no visible global function definition for
  ‘ttkbutton’
hz.path.set : onBrowse1: no visible global function definition for
  ‘tclvalue<-’
hz.path.set : onBrowse1: no visible global function definition for
  ‘tclvalue’
hz.path.set : onBrowse1: no visible global function definition for
  ‘tkchooseDirectory’
hz.path.set : onBrowse2: no visible global function definition for
  ‘tclvalue<-’
hz.path.set : onBrowse2: no visible global function definition for
  ‘tclvalue’
hz.path.set : onBrowse2: no visible global function definition for
  ‘tkgetOpenFile’
hz.path.set: no visible global function definition for ‘ttkentry’
hz.path.set : test: no visible global function definition for
  ‘tclvalue<-’
hz.path.set : test: no visible global function definition for
  ‘tclvalue’
hz.path.set: no visible global function definition for ‘ttkscrollbar’
hz.path.set : : no visible global function definition for
  ‘tkxview’
hz.path.set: no visible global function definition for ‘tkconfigure’
hz.path.set : : no visible global function definition for
  ‘tkset’
hz.path.set: no visible global function definition for ‘tkgrid’
hz.path.set: no visible global function definition for ‘tklabel’
hz.path.set: no visible global function definition for ‘ttklabelframe’
hz.path.set: no visible global function definition for ‘tk2button’
hz.path.set : : no visible global function definition for
  ‘tclvalue<-’
hz.path.set : : no visible global function definition for
  ‘tkdestroy’
hz.path.set: no visible global function definition for ‘tkbind’
hz.path.set: no visible global function definition for ‘tkwait.window’
hz.path.set: no visible global function definition for ‘tclvalue’
hz.path.set: no visible global function definition for ‘tkmessageBox’
hz.read.empai.parameters : binary.rewrite: no visible global function
  definition for ‘tclvalue’
hz.read.empai.parameters: no visible global function definition for
  ‘tclVar’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2font.set’
hz.read.empai.parameters: no visible global function definition for
  ‘tkfont.create’
hz.read.empai.parameters : hz.path.set: no visible global function
  definition for ‘tclvalue’
hz.read.empai.parameters : hz.path.set: no visible global function
  definition for ‘tkchooseDirectory’
hz.read.empai.parameters: no visible global function definition for
  ‘tktoplevel’
hz.read.empai.parameters: no visible global function definition for
  ‘tkwm.title’
hz.read.empai.parameters: no visible global function definition for
  ‘tkwm.resizable’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2menu’
hz.read.empai.parameters: no visible global function definition for
  ‘tkconfigure’
hz.read.empai.parameters: no visible global function definition for
  ‘tkframe’
hz.read.empai.parameters: no visible global function definition for
  ‘tkimage.create’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2label’
hz.read.empai.parameters: no visible global function definition for
  ‘tkfocus’
hz.read.empai.parameters: no visible global function definition for
  ‘tkgrid’
hz.read.empai.parameters: no visible global function definition for
  ‘tklabel’
hz.read.empai.parameters: no visible global function definition for
  ‘tkadd’
hz.read.empai.parameters : : no visible global function
  definition for ‘tkmessageBox’
hz.read.empai.parameters : : no visible global function
  definition for ‘tclvalue’
hz.read.empai.parameters: no visible global function definition for
  ‘tkentry’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2separator’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2button’
hz.read.empai.parameters : : no visible global function
  definition for ‘tkdestroy’
hz.read.empai.parameters : : no visible global function
  definition for ‘tclvalue<-’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2notebook’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2notetab’
hz.read.empai.parameters: no visible global function definition for
  ‘tcl’
hz.read.empai.parameters: no visible global function definition for
  ‘tclvalue’
hz.read.empai.parameters: no visible global function definition for
  ‘tkscale’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2checkbutton’
hz.read.empai.parameters: no visible global function definition for
  ‘tclvalue<-’
hz.read.empai.parameters: no visible global function definition for
  ‘ttkcombobox’
hz.read.empai.parameters : onArgEdit: no visible global function
  definition for ‘tclvalue<-’
hz.read.empai.parameters : onArgEdit: no visible global function
  definition for ‘tclvalue’
hz.read.empai.parameters : onArgEdit: no visible global function
  definition for ‘tkconfigure’
hz.read.empai.parameters : onArgEdit: no visible global function
  definition for ‘tclVar’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2frame’
hz.read.empai.parameters : buttonRcmdr: no visible global function
  definition for ‘ttkbutton’
hz.read.empai.parameters : onBrowse: no visible global function
  definition for ‘tclvalue<-’
hz.read.empai.parameters : onBrowse: no visible global function
  definition for ‘tclvalue’
hz.read.empai.parameters : onBrowse: no visible global function
  definition for ‘tkgetOpenFile’
hz.read.empai.parameters: no visible global function definition for
  ‘ttkentry’
hz.read.empai.parameters: no visible global function definition for
  ‘ttkscrollbar’
hz.read.empai.parameters : : no visible global function
  definition for ‘tkxview’
hz.read.empai.parameters : : no visible global function
  definition for ‘tkset’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2radiobutton’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2labelframe’
hz.read.empai.parameters: no visible global function definition for
  ‘tk2entry’
hz.read.empai.parameters : onBrowse: no visible global function
  definition for ‘tkchooseDirectory’
hz.read.empai.parameters : test: no visible global function definition
  for ‘tclvalue<-’
hz.read.empai.parameters : test: no visible global function definition
  for ‘tclvalue’
hz.read.empai.parameters: no visible global function definition for
  ‘tkbind’
hz.read.empai.parameters: no visible global function definition for
  ‘tkdestroy’
hz.read.empai.parameters: no visible global function definition for
  ‘tkwait.window’
hz.read.parameters: no visible global function definition for ‘tclVar’
hz.read.parameters: no visible global function definition for
  ‘tk2font.set’
hz.read.parameters: no visible global function definition for
  ‘tkfont.create’
hz.read.parameters : hz.path.set: no visible global function definition
  for ‘tclvalue’
hz.read.parameters : hz.path.set: no visible global function definition
  for ‘tkchooseDirectory’
hz.read.parameters: no visible global function definition for
  ‘tktoplevel’
hz.read.parameters: no visible global function definition for
  ‘tkwm.title’
hz.read.parameters: no visible global function definition for
  ‘tkwm.resizable’
hz.read.parameters: no visible global function definition for ‘tk2menu’
hz.read.parameters: no visible global function definition for
  ‘tkconfigure’
hz.read.parameters: no visible global function definition for ‘tkframe’
hz.read.parameters: no visible global function definition for
  ‘tkimage.create’
hz.read.parameters: no visible global function definition for
  ‘tk2label’
hz.read.parameters: no visible global function definition for ‘tkfocus’
hz.read.parameters: no visible global function definition for ‘tkgrid’
hz.read.parameters: no visible global function definition for ‘tklabel’
hz.read.parameters: no visible global function definition for ‘tkadd’
hz.read.parameters : : no visible global function definition
  for ‘tkmessageBox’
hz.read.parameters : : no visible global function definition
  for ‘tclvalue’
hz.read.parameters: no visible global function definition for ‘tkentry’
hz.read.parameters: no visible global function definition for
  ‘tk2separator’
hz.read.parameters: no visible global function definition for
  ‘tk2button’
hz.read.parameters : : no visible global function definition
  for ‘tkdestroy’
hz.read.parameters : : no visible global function definition
  for ‘tclvalue<-’
hz.read.parameters: no visible global function definition for
  ‘tk2notebook’
hz.read.parameters: no visible global function definition for
  ‘tk2notetab’
hz.read.parameters: no visible global function definition for ‘tcl’
hz.read.parameters: no visible global function definition for
  ‘tk2checkbutton’
hz.read.parameters: no visible global function definition for
  ‘tclvalue<-’
hz.read.parameters: no visible global function definition for
  ‘ttkcombobox’
hz.read.parameters: no visible global function definition for
  ‘tclvalue’
hz.read.parameters: no visible global function definition for ‘tkscale’
hz.read.parameters : onArgEdit: no visible global function definition
  for ‘tclvalue<-’
hz.read.parameters : onArgEdit: no visible global function definition
  for ‘tclvalue’
hz.read.parameters : onArgEdit: no visible global function definition
  for ‘tkconfigure’
hz.read.parameters : onArgEdit: no visible global function definition
  for ‘tclVar’
hz.read.parameters: no visible global function definition for
  ‘tk2radiobutton’
hz.read.parameters: no visible global function definition for
  ‘tk2frame’
hz.read.parameters: no visible global function definition for
  ‘tk2labelframe’
hz.read.parameters: no visible global function definition for
  ‘tk2entry’
hz.read.parameters : buttonRcmdr: no visible global function definition
  for ‘ttkbutton’
hz.read.parameters : onBrowse: no visible global function definition
  for ‘tclvalue<-’
hz.read.parameters : onBrowse: no visible global function definition
  for ‘tclvalue’
hz.read.parameters : onBrowse: no visible global function definition
  for ‘tkgetOpenFile’
hz.read.parameters: no visible global function definition for
  ‘ttkentry’
hz.read.parameters: no visible global function definition for
  ‘ttkscrollbar’
hz.read.parameters : : no visible global function definition
  for ‘tkxview’
hz.read.parameters : : no visible global function definition
  for ‘tkset’
hz.read.parameters : onBrowse: no visible global function definition
  for ‘tkchooseDirectory’
hz.read.parameters : test: no visible global function definition for
  ‘tclvalue<-’
hz.read.parameters : test: no visible global function definition for
  ‘tclvalue’
hz.read.parameters: no visible global function definition for
  ‘tkdestroy’
hz.read.parameters: no visible global function definition for ‘tkbind’
hz.read.parameters: no visible global function definition for
  ‘tkwait.window’
hz.read.parameters : binary.rewrite: no visible global function
  definition for ‘tclvalue’
hz.redefine.settings: no visible global function definition for
  ‘tktoplevel’
hz.redefine.settings: no visible global function definition for
  ‘tkwm.title’
hz.redefine.settings: no visible global function definition for
  ‘tclVar’
hz.redefine.settings: no visible global function definition for
  ‘tclvalue<-’
hz.redefine.settings: no visible global function definition for
  ‘ttkcombobox’
hz.redefine.settings: no visible global function definition for
  ‘tkgrid’
hz.redefine.settings: no visible global function definition for
  ‘tklabel’
hz.redefine.settings: no visible global function definition for
  ‘tkframe’
hz.redefine.settings: no visible global function definition for
  ‘tk2button’
hz.redefine.settings : : no visible global function
  definition for ‘tclvalue<-’
hz.redefine.settings : : no visible global function
  definition for ‘tkdestroy’
hz.redefine.settings: no visible global function definition for
  ‘tkbind’
hz.redefine.settings: no visible global function definition for
  ‘tkwait.window’
hz.redefine.settings: no visible global function definition for
  ‘tclvalue’
hz.remove.data: no visible global function definition for ‘tktoplevel’
hz.remove.data: no visible global function definition for ‘tclVar’
hz.remove.data: no visible global function definition for ‘tclvalue<-’
hz.remove.data: no visible global function definition for ‘ttkcombobox’
hz.remove.data: no visible global function definition for ‘tkgrid’
hz.remove.data: no visible global function definition for ‘tklabel’
hz.remove.data: no visible global function definition for ‘tk2button’
hz.remove.data : : no visible global function definition for
  ‘tclvalue<-’
hz.remove.data : : no visible global function definition for
  ‘tkdestroy’
hz.remove.data: no visible global function definition for ‘tkbind’
hz.remove.data: no visible global function definition for
  ‘tkwait.window’
hz.remove.data: no visible global function definition for ‘tclvalue’
hz.remove.data: no visible binding for global variable ‘e’
hz.row.plot: no visible global function definition for ‘tkmessageBox’
hz.row.plot: no visible global function definition for ‘plotCI’
hz.row.plot: no visible global function definition for ‘barplot2’
hz.save.control: no visible global function definition for
  ‘tk_messageBox’
hz.script: no visible global function definition for ‘tk2font.set’
hz.script: no visible binding for global variable ‘cracker.ui.tk’
hz.script: no visible global function definition for ‘tkmessageBox’
hz.script : hz.write.unique.prots.seq: no visible global function
  definition for ‘barplot2’
hz.script.anova: no visible binding for global variable ‘x’
hz.script.bp: no visible binding for global variable ‘sd.error’
hz.script.graph: no visible global function definition for
  ‘graph.data.frame’
hz.script.graph: no visible global function definition for ‘V’
hz.script.graph: no visible global function definition for ‘V<-’
hz.script.graph: no visible binding for global variable ‘layout.spring’
hz.script.graph: no visible global function definition for ‘E’
hz.script.graph: no visible global function definition for ‘E<-’
hz.script.graph: no visible global function definition for ‘degree’
hz.script.heatmap2: no visible global function definition for
  ‘tkmessageBox’
hz.script.heatmap2: no visible global function definition for
  ‘heatmap.2’
hz.script.heatmap2.time: no visible binding for global variable
  ‘.design’
hz.script.heatmap2.time: no visible global function definition for
  ‘heatmap.2’
hz.script.heatmap2.time: no visible binding for global variable
  ‘dendro.gclus’
hz.script.heatmap2.time: no visible binding for global variable
  ‘jet.colors’
hz.script.heatmap2.time: no visible binding for global variable
  ‘hm.input’
hz.script.heatmap2.time: no visible binding for global variable
  ‘heatmap.max’
hz.script.pca: no visible global function definition for ‘pca’
hz.script.pca: no visible global function definition for ‘barplot2’
hz.script.pca : plot.biplot: no visible global function definition for
  ‘barplot2’
hz.script.phospho: no visible binding for global variable
  ‘hz.script.y.lab.return’
hz.script.phospho: no visible binding for global variable
  ‘cracker.ui.tk’
hz.script.plot.main: no visible global function definition for
  ‘tkmessageBox’
hz.start: no visible global function definition for ‘biocLite’
hz.start: no visible global function definition for ‘tkmessageBox’
hz.start: no visible global function definition for ‘tk2font.set’
hz.start: possible error in hz.script(path2 = .path2, path2.set =
  .path2.set, path2.input.file = .path2.input.file, import.list =
  .import.list, path1 = .path1): unused arguments (path2 = .path2,
  path2.input.file = .path2.input.file)
hz.start: no visible global function definition for ‘tclvalue’
hz.volcano.mapping.barplot: no visible global function definition for
  ‘barplot2’
hz.write.design: no visible binding for global variable ‘ui’
hz.write.design: no visible global function definition for
  ‘tkmessageBox’
hz.write.table: no visible binding for global variable ‘.acc’
hz.write.table: no visible global function definition for
  ‘grid.newpage’
hz.write.table: no visible binding for global variable ‘i’
hz.write.table: no visible binding for global variable ‘.data2’
hz.write.table: no visible global function definition for ‘grid.text’
hz.write.table: no visible global function definition for ‘gpar’
image.button: no visible global function definition for ‘tkbutton’
pb.modified: no visible global function definition for ‘tcl’
pb.modified: no visible global function definition for ‘tclRequire’
pb.modified: no visible global function definition for ‘tktoplevel’
pb.modified: no visible global function definition for ‘tkwm.geometry’
pb.modified: no visible global function definition for ‘tkwm.resizable’
pb.modified: no visible global function definition for ‘tkwm.title’
pb.modified: no visible global function definition for ‘tkfont.create’
pb.modified: no visible global function definition for ‘tklabel’
pb.modified: no visible global function definition for ‘tkpack’
pb.modified : up: no visible global function definition for
  ‘tkconfigure’
pb.modified: no visible global function definition for ‘tclVar’
pb.modified: no visible global function definition for ‘ttkprogressbar’
pb.modified: no visible global function definition for ‘tkwidget’
pb.modified : up: no visible global function definition for
  ‘tclvalue<-’
pb.modified : kill: no visible global function definition for
  ‘tkdestroy’
pb.modified : title: no visible global function definition for
  ‘tkwm.title’
pb.modified : lab: no visible global function definition for
  ‘tkconfigure’
pb.modified: no visible global function definition for ‘tkbind’

Found the following assignments to the global environment:
File ‘cRacker/R/hz.agg.fun.R’:
  assign("cRacker.temp.aov.data.2", aov.data.2, envir = .GlobalEnv)
  assign("temp.o", temp.o, envir = .GlobalEnv)
  assign("cracker.counter.temp", cracker.counter.temp + 1, envir = .GlobalEnv)
File ‘cRacker/R/hz.import.R’:
  assign("data.import", data.import, envir = .GlobalEnv)
  assign("data.import.all", data.import.all, envir = .GlobalEnv)
File ‘cRacker/R/hz.info.search.R’:
  assign("cracker.counter.temp", 1, envir = .GlobalEnv)
  assign("cracker.ratio.prog.temp", ratio.prog, envir = .GlobalEnv)
  assign("cracker.counter.temp", cracker.counter.temp + 1, envir = .GlobalEnv)
  assign("x", x, envir = .GlobalEnv)
File ‘cRacker/R/hz.matrix.creator.R’:
  assign("sam.mean", sam.mean, envir = .GlobalEnv)
  assign("sam.mean.phospho", sam.mean.phospho, envir = .GlobalEnv)
  assign("cracker.counter.temp", 1, envir = .GlobalEnv)
  assign("cracker.ratio.prog.temp", ratio.prog, envir = .GlobalEnv)
File ‘cRacker/R/hz.row.plot.R’:
  assign("temp.x.m", temp.x.m, envir = .GlobalEnv)
  assign("plot.data.all", plot.data.all, envir = .GlobalEnv)
File ‘cRacker/R/hz.script.phospho.R’:
  assign("hz.exp.des.parse.data2", hz.exp.des.parse.data2, envir = .GlobalEnv)

Found the following calls to data() loading into the global environment:
File ‘cRacker/R/hz.script.R’:
  data(cracker.ui.tk)
See section ‘Good practice’ in ‘?data’.
* checking Rd files ... WARNING
prepare_Rd: cRacker-package.Rd:31: unexpected '}'
prepare_Rd: cRacker-package.Rd:27-28: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file ‘/mnt/building/build_2013-08-29-12-09/RF_PKG_CHECK/PKGS/cRacker.Rcheck/00_pkg_src/cRacker/man/hz.script.Rd’:
  \usage lines wider than 90 characters:
             list(path = /data/list.txt, engine = maxquant, settings = default),  import.list = default)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘ReadAffy’ ‘help.button’ ‘help.tk’ ‘hz.agg.fun’ ‘hz.aov’
  ‘hz.brake.strings’ ‘hz.change.nodePar’ ‘hz.cracker.default.settings’
  ‘hz.design’ ‘hz.exp.des.parse’ ‘hz.function.file’ ‘hz.go.input’
  ‘hz.identifier.import’ ‘hz.import’ ‘hz.import.config.modifier’
  ‘hz.inf.replace’ ‘hz.info.search’ ‘hz.library.fasta’
  ‘hz.loading.cracker.functions’ ‘hz.matrix.creator’ ‘hz.merge.control’
  ‘hz.norm’ ‘hz.oneside.ttest’ ‘hz.parameter.report’ ‘hz.path.empai’
  ‘hz.path.set’ ‘hz.read.empai.parameters’ ‘hz.read.parameters’
  ‘hz.redefine.settings’ ‘hz.remove.data’ ‘hz.row.plot’
  ‘hz.save.control’ ‘hz.script.anova’ ‘hz.script.bp’
  ‘hz.script.exp.design’ ‘hz.script.go.terms’ ‘hz.script.graph’
  ‘hz.script.heatmap’ ‘hz.script.heatmap2’ ‘hz.script.heatmap2.time’
  ‘hz.script.hiercl’ ‘hz.script.kmeans’ ‘hz.script.kmeans.timeboxplots’
  ‘hz.script.kmeans.timeplots’ ‘hz.script.pca’ ‘hz.script.phospho’
  ‘hz.script.plot.main’ ‘hz.script.row.plot’ ‘hz.script.volcano’
  ‘hz.script.y.lab’ ‘hz.shape’ ‘hz.show.path’ ‘hz.start’
  ‘hz.temp.order.fun’ ‘hz.volcano.mapping.barplot’ ‘hz.write.design’
  ‘hz.write.table’ ‘image.button’ ‘pb.modified’
Undocumented data sets:
  ‘cracker.ui.tk’ ‘help-file’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'cRacker.starter':
cRacker.starter
  Code: function(.path1 = NA)
  Docs: function()
  Argument names in code not in docs:
    .path1

* checking Rd \usage sections ... WARNING
Bad \usage lines found in documentation object 'hz.script':
  hz.script(path1, path2.set = 
  	list(path = /data/list.txt, engine = maxquant, settings = default),  import.list = default)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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:
  ‘cRacker-logo-grey.pnm’ ‘cRackerEmPAI-Arabidopsis_20110903’
  ‘cRackerMapping-ATH_GO_GOSLIM’
  ‘cRackerMapping-Ath-AGI-TAIR9-Jan2010-cut2’
  ‘cRackerMapping-Ath-AGI-TAIR9-Jan2010-cut3’
  ‘cRackerMapping-Ath_AGI_TAIR9_Jan2010’
  ‘cRackerMapping-Suba3-2012-10-27_4-18’
  ‘cRackerSequence-Arabidopsis_20110903’ ‘hz.script.Rdata’
  ‘import-binary.Rdata’ ‘import-config’ ‘settings-standard.Rdata’
  ‘settings.Rdata’ ‘testCrackerSILAC’
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 ... SKIPPED
* checking PDF version of manual ... OK

WARNING: There were 9 warnings.
NOTE: There were 4 notes.
See
  ‘/mnt/building/build_2013-08-29-12-09/RF_PKG_CHECK/PKGS/cRacker.Rcheck/00check.log’
for details.

Run time: 87.37 seconds.