RKward-temp1

QDir::mkpath: Empty or null file name(s)
Assert failed at /build/buildd/rkward-0.5.5.z+0.5.6/rkward/rkward.cpp - function startR line 269
Command failed (other)
failed command was: 'rk.set.output.html.file ("/rk_out.html")
'
- error message was: ''
rkward(2651)/kdecore (services) KMimeTypeFactory::parseMagic: Now parsing  "/usr/share/mime/magic"
rkward(2651)/kdecore (services) KMimeTypeFactory::parseMagic: Now parsing  "/home/sc/.local/share/mime/magic"
rkward(2651)/kparts KParts::PartManager::addPart: Part ' "" ' has a widget  "khtml_part_widget"  with a focus policy of NoFocus. It should have at least a ClickFocus policy, for part activation to work well.

Command failed (other)
failed command was: 'rk.save.workplace(description="base::::file:///media/sda2/Data/Postdoctoral%20Research/Statistical%20Data%20Analysis
workspace::sidebar,0::
commandlog::sidebar,3::
filebrowser::sidebar,0::
pendingjobs::sidebar,4::
console::sidebar,3::
helpsearch::sidebar,3::")'
- error message was: ''
Command failed (other)
failed command was: 'rk.restore.workplace()'
- error message was: ''
Command failed (other)
failed command was: 'local({
## Prepare
## Compute
load (file="/media/sda2/Data/Postdoctoral Research/Statistical Data Analysis/GA.rdata", envir=globalenv())
## Print result
rk.header("Load data", parameters=list("File", "/media/sda2/Data/Postdoctoral Research/Statistical Data Analysis/GA.rdata",
	"Import to environment", "globalenv()"))
})'
- error message was: ''
Command failed (other)
failed command was: '.rk.rerun.plugin.link(plugin="rkward::load_r_object", settings="envir.active=0\nenvir.objectname=my.env\nenvir.parent=.GlobalEnv\nfile.selection=/media/sda2/Data/Postdoctoral Research/Statistical Data Analysis/GA.rdata", label="Run again")
.rk.make.hr()'
- error message was: ''
Command failed (other)
failed command was: 'local({
## Prepare
require (foreign)
## Compute
data <- read.spss ("/media/sda2/Data/Postdoctoral Research/Statistical Data Analysis/GA.rdata", to.data.frame=TRUE, max.value.labels=1000000)

# set variable labels for use in RKWard
labels <- attr (data, "variable.labels");
if (!is.null (labels)) {
	for (i in 1:length (labels)) {
		col <- make.names (names (labels[i]))
		if (!is.null (col)) {
			rk.set.label (data[[col]], labels[i])
		}
	}
}

.GlobalEnv$my.spss.data <- data		# assign to globalenv()
rk.edit (.GlobalEnv$my.spss.data)
## Print result
rk.header("Import SPSS data", parameters=list("File", "/media/sda2/Data/Postdoctoral Research/Statistical Data Analysis/GA.rdata",
	"Import as", "my.spss.data"))
})'
- error message was: ''
Command failed (other)
failed command was: '.rk.rerun.plugin.link(plugin="rkward::import_spss", settings="convert_var_labels.state=1\ndata_frame.state=1\ndo_locale_conversion.state=0\ndoedit.state=1\nfile.selection=/media/sda2/Data/Postdoctoral Research/Statistical Data Analysis/GA.rdata\nlabels_limit.real=1000000.00\nsaveto.objectname=my.spss.data\nsaveto.parent=.GlobalEnv\ntrim_labels.state=0\nuse_labels.state=1", label="Run again")
.rk.make.hr()'
- error message was: ''
Not found or not a property: isrow.state
No option left enabled. Disable the entire component 'dec', instead!
No option left enabled. Disable the entire component 'sep', instead!
Command failed (other)
failed command was: 'local({
## Prepare
## Compute
imported <- read.delim (file="/media/sda2/Data/Postdoctoral Research/Articles - drafts/Data & Figures/GA_RKward_text.txt",  na.strings = "NA", nrows = -1, skip = 0, check.names = TRUE, strip.white = FALSE, blank.lines.skip = TRUE)

# copy from the local environment to globalenv()
.GlobalEnv$my.csv.data <- imported

rk.edit (.GlobalEnv$my.csv.data)
## Print result
rk.header("Import text / csv data", parameters=list("File", "/media/sda2/Data/Postdoctoral Research/Articles - drafts/Data & Figures/GA_RKward_text.txt",
	"Import as", "my.csv.data"))
})'
- error message was: ''
Command failed (other)
failed command was: '.rk.rerun.plugin.link(plugin="rkward::import_csv", settings="allow_escapes.state=\nblanklinesskip.state=TRUE\ncheckname.state=TRUE\ncolclass.string=\ncolname.string=\ndec.string='.'\ndoedit.state=1\nfile.selection=/media/sda2/Data/Postdoctoral Research/Articles - drafts/Data & Figures/GA_RKward_text.txt\nflush.state=\nna.text=NA\nname.objectname=my.csv.data\nname.parent=.GlobalEnv\nnrows.text=-1\nquick.string=delim\nquote.string='\\\\\\\"'\nrowname.string=auto\nsep.string='\\\\t'\nskip.text=0\nstrings_as_factors.string=\nstripwhite.state=FALSE", label="Run again")
.rk.make.hr()'
- error message was: ''
XML-parsing '/usr/share/kde4/apps/rkward/plots/box_plot.xml' document: Expected exactly one element 'help' but found 0
Command failed (other)
failed command was: 'local({
## Prepare
## Compute
## Print result
data_list <- list (my.csv.data[["Treatment"]], my.csv.data[["MeJA.conc.in.tissues"]])		#convert single sample variables to list
rk.header ("Boxplot", list ("Variable(s)", rk.get.description (my.csv.data[["Treatment"]], my.csv.data[["MeJA.conc.in.tissues"]], paste.sep=", ")))
rk.graph.on()
try (boxplot (data_list, notch = FALSE, outline = TRUE, horizontal = FALSE)) #actuall boxplot function
rk.graph.off ()
})'
- error message was: ''
Command failed (other)
failed command was: '.rk.rerun.plugin.link(plugin="rkward::box_plot", settings="mean.state=\nnames_exp.text=names (x)\nnames_mode.string=default\nnotch.state=FALSE\norientation.string=FALSE\noutline.state=TRUE\nplotoptions.add_grid.state=0\nplotoptions.asp.real=0.00\nplotoptions.main.text=\nplotoptions.pointcolor.color.string=\nplotoptions.pointtype.string=\nplotoptions.sub.text=\nplotoptions.xaxt.state=\nplotoptions.xlab.text=\nplotoptions.xlog.state=\nplotoptions.xmaxvalue.text=\nplotoptions.xminvalue.text=\nplotoptions.yaxt.state=\nplotoptions.ylab.text=\nplotoptions.ylog.state=\nplotoptions.ymaxvalue.text=\nplotoptions.yminvalue.text=\nsd.state=\nx.available=my.csv.data[[\\\"Treatment\\\"]]\\nmy.csv.data[[\\\"MeJA.conc.in.tissues\\\"]]", label="Run again")
.rk.make.hr()'
- error message was: ''
XML-parsing '/usr/share/kde4/apps/rkward/uni1.2/description.xml' document: Expected exactly one element 'help' but found 0
Command failed (other)
failed command was: 'local({
## Prepare
## Compute
vars <- list (substitute (my.csv.data[["MeJA.conc.in.tissues"]]), substitute (my.csv.data[["Treatment"]]))
results <- data.frame ('Variable Name'=rep (NA, length (vars)), check.names=FALSE)

for (i in 1:length (vars))  {
	var <- eval (vars[[i]], envir=globalenv());
	results[i, 'Variable Name'] <- rk.get.description(vars[[i]], is.substitute=TRUE)


	#robust statistics
}

## Print result
rk.header ("Univariate statistics", parameters=list (
"Remove Missing values", TRUE))

rk.results (results)
})'
- error message was: ''
Command failed (other)
failed command was: '.rk.rerun.plugin.link(plugin="rkward::basic_statistics", settings="autre.real=0.00\nhuber.state=\nirq.state=0\nlength.state=0\nmad.state=\nmaximum.state=0\nmean.state=0\nmedian.state=0\nminimum.state=0\nnarm.state=1\nnbmaximum.real=0.00\nnbminimum.real=0.00\nquartile.state=0\nsaveas.active=0\nsaveas.objectname=rk.univariate\nsaveas.parent=.GlobalEnv\nsd.state=0\ntrim.state=\nvari.state=0\nz.available=my.csv.data[[\\\"MeJA.conc.in.tissues\\\"]]\\nmy.csv.data[[\\\"Treatment\\\"]]", label="Run again")
.rk.make.hr()'
- error message was: ''
Not found or not a property: isrow.state
No option left enabled. Disable the entire component 'dec', instead!
No option left enabled. Disable the entire component 'sep', instead!
Command failed (other)
failed command was: 'local({
## Prepare
## Compute
imported <- read.delim (file="/media/sda2/Data/Postdoctoral Research/Articles - drafts/Data & Figures/GA2.txt",  na.strings = "NA", nrows = -1, skip = 0, check.names = TRUE, strip.white = FALSE, blank.lines.skip = TRUE)

# copy from the local environment to globalenv()
.GlobalEnv$test <- imported

rk.edit (.GlobalEnv$test)
## Print result
rk.header("Import text / csv data", parameters=list("File", "/media/sda2/Data/Postdoctoral Research/Articles - drafts/Data & Figures/GA2.txt",
	"Import as", "test"))
})'
- error message was: ''
Command failed (other)
failed command was: '.rk.rerun.plugin.link(plugin="rkward::import_csv", settings="allow_escapes.state=\nblanklinesskip.state=TRUE\ncheckname.state=TRUE\ncolclass.string=\ncolname.string=\ndec.string='.'\ndoedit.state=1\nfile.selection=/media/sda2/Data/Postdoctoral Research/Articles - drafts/Data & Figures/GA2.txt\nflush.state=\nna.text=NA\nname.objectname=test\nname.parent=.GlobalEnv\nnrows.text=-1\nquick.string=delim\nquote.string='\\\\\\\"'\nrowname.string=auto\nsep.string='\\\\t'\nskip.text=0\nstrings_as_factors.string=\nstripwhite.state=FALSE", label="Run again")
.rk.make.hr()'
- error message was: ''
XML-parsing '/usr/share/kde4/apps/rkward/plots/box_plot.xml' document: Expected exactly one element 'help' but found 0
Command failed (other)
failed command was: 'local({
## Prepare
## Compute
## Print result
data_list <- list (test[["MeJA"]])		#convert single sample variables to list
rk.header ("Boxplot", list ("Variable(s)", rk.get.description (test[["MeJA"]], paste.sep=", ")))
rk.graph.on()
try (boxplot (data_list, notch = FALSE, outline = TRUE, horizontal = FALSE)) #actuall boxplot function
rk.graph.off ()
})'
- error message was: ''
Command failed (other)
failed command was: '.rk.rerun.plugin.link(plugin="rkward::box_plot", settings="mean.state=\nnames_exp.text=names (x)\nnames_mode.string=default\nnotch.state=FALSE\norientation.string=FALSE\noutline.state=TRUE\nplotoptions.add_grid.state=0\nplotoptions.asp.real=0.00\nplotoptions.main.text=\nplotoptions.pointcolor.color.string=\nplotoptions.pointtype.string=\nplotoptions.sub.text=\nplotoptions.xaxt.state=\nplotoptions.xlab.text=\nplotoptions.xlog.state=\nplotoptions.xmaxvalue.text=\nplotoptions.xminvalue.text=\nplotoptions.yaxt.state=\nplotoptions.ylab.text=\nplotoptions.ylog.state=\nplotoptions.ymaxvalue.text=\nplotoptions.yminvalue.text=\nsd.state=\nx.available=test[[\\\"MeJA\\\"]]", label="Run again")
.rk.make.hr()'
- error message was: ''
XML-parsing '/usr/share/kde4/apps/rkward/plots/scatterplot.xml' document: Expected exactly one element 'help' but found 0
Command failed (other)
failed command was: 'local({
## Prepare
## Compute
Xvars <- list(test[["Treatment"]])
Yvars <- list(test[["MeJA"]])

if (length(Xvars) != length(Yvars)) {
	stop("Unequal number of X and Y variables given")
}
# find range of X/Y values needed
Xrange <- range (c (Xvars), na.rm=TRUE)
Yrange <- range (c (Yvars), na.rm=TRUE)

type <- rep (c ('p'), length.out=length (Xvars));
col <- rep ('black', length.out=length (Xvars));
cex <- rep (1, length.out=length (Xvars));
pch <- rep (1, length.out=length (Xvars));
## Print result
rk.header ("Scatterplot", parameters = list (
	"X variables"=paste (rk.get.description (test[["Treatment"]]), collapse=", "),
	"Y variables"=paste (rk.get.description (test[["MeJA"]]), collapse=", ")))

rk.graph.on()

try ({
	# make frame and axes
	plot(Xrange, Yrange, type="n")

	# plot variables one X/Y pair at a time
	for (i in 1:length(Xvars)) {
		points (
			Xvars[[i]],
			Yvars[[i]],
			type = type[[i]],
			col = col[[i]],
			cex = cex[[i]],
			pch = pch[[i]]
		)
	}
})

rk.graph.off()
})'
- error message was: ''
Command failed (other)
failed command was: '.rk.rerun.plugin.link(plugin="rkward::scatterplot", settings="cex.text=1\ncol.text='black'\ncolor.string=all\nisCex.string=all\nisPch.string=all\npch.text=1\nplotoptions.add_grid.state=0\nplotoptions.asp.real=0.00\nplotoptions.main.text=\nplotoptions.pointcolor.color.string=\nplotoptions.pointtype.string=\nplotoptions.sub.text=\nplotoptions.xaxt.state=\nplotoptions.xlab.text=\nplotoptions.xlog.state=\nplotoptions.xmaxvalue.text=\nplotoptions.xminvalue.text=\nplotoptions.yaxt.state=\nplotoptions.ylab.text=\nplotoptions.ylog.state=\nplotoptions.ymaxvalue.text=\nplotoptions.yminvalue.text=\npointtype.string=p\ntype_mode.string=all\nx.available=test[[\\\"Treatment\\\"]]\ny.available=test[[\\\"MeJA\\\"]]", label="Run again")
.rk.make.hr()'
- error message was: ''
Assert failed at /build/buildd/rkward-0.5.5.z+0.5.6/rkward/misc/rkxmlguisyncer.cpp - function uiRcFileChanged line 85
Assert failed at /build/buildd/rkward-0.5.5.z+0.5.6/rkward/misc/rkxmlguisyncer.cpp - function uiRcFileChanged line 85
rkward(2651)/kio (KDirModel) KDirModelPrivate::_k_slotDeleteItems: No node found for item that was just removed: KUrl("file:///media/sda2/Data/Postdoctoral Research/Articles - drafts/Data & Figures/GA.csv")
rkward(2651)/kio (KDirModel) KDirModelPrivate::_k_slotDeleteItems: No node found for item that was just removed: KUrl("file:///media/sda2/Data/Postdoctoral Research/Articles - drafts/Data & Figures/GA.csv")
Command failed (other)
failed command was: '.rk.make.hr()'
- error message was: ''
Assert failed at /build/buildd/rkward-0.5.5.z+0.5.6/rkward/misc/rkxmlguisyncer.cpp - function uiRcFileChanged line 85
Assert failed at /build/buildd/rkward-0.5.5.z+0.5.6/rkward/misc/rkxmlguisyncer.cpp - function uiRcFileChanged line 85
rkward(2651)/kio (KDirModel) KDirModelPrivate::_k_slotDeleteItems: No node found for item that was just removed: KUrl("file:///media/sda2/Data/Postdoctoral Research/Articles - drafts/Data & Figures/GA.csv")
Command failed (other)
failed command was: '.rk.make.hr()'
- error message was: ''
Assert failed at /build/buildd/rkward-0.5.5.z+0.5.6/rkward/misc/rkxmlguisyncer.cpp - function uiRcFileChanged line 85
Assert failed at /build/buildd/rkward-0.5.5.z+0.5.6/rkward/misc/rkxmlguisyncer.cpp - function uiRcFileChanged line 85
Command failed (other)
failed command was: 'rk.save.workplace(description="base::::file:///media/sda2/Data/Postdoctoral%20Research/Statistical%20Data%20Analysis
data::::my.csv.data
data::::test
workspace::sidebar,0::
commandlog::sidebar,3::
filebrowser::sidebar,0::
pendingjobs::sidebar,4::
console::sidebar,3::
helpsearch::sidebar,3::")'
- error message was: ''