RKward error_Apr21_9-11PM

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()"))
})
.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 in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: local ... eval -> eval -> eval -> eval -> rk.header -> sink -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: rk.print.literal -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
An unspecified error occurred while running the command.
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.rerun.plugin.link -> .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: rk.print.literal -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
An unspecified error occurred while running the command.
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"))
})
.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()
Loading required package: foreign
Error in read.spss("/media/sda2/Data/Postdoctoral Research/Statistical Data Analysis/GA.rdata",  :
  file '/media/sda2/Data/Postdoctoral Research/Statistical Data Analysis/GA.rdata' is not in any supported SPSS format
Calls: local ... eval.parent -> eval -> eval -> eval -> eval -> read.spss -> .Call
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: rk.print.literal -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
An unspecified error occurred while running the command.
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.rerun.plugin.link -> .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: rk.print.literal -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
An unspecified error occurred while running the command.
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"))
})
.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 in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: local ... eval -> eval -> eval -> eval -> rk.header -> sink -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: rk.print.literal -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
An unspecified error occurred while running the command.
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.rerun.plugin.link -> .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: rk.print.literal -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
An unspecified error occurred while running the command.
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 ()
})
.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 in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: local ... eval -> eval -> eval -> eval -> rk.header -> sink -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: rk.print.literal -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
An unspecified error occurred while running the command.
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.rerun.plugin.link -> .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: rk.print.literal -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
An unspecified error occurred while running the command.
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)
})
.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 in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: local ... eval -> eval -> eval -> eval -> rk.header -> sink -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: rk.print.literal -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
An unspecified error occurred while running the command.
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.rerun.plugin.link -> .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: .rk.cat.output -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
Error in file(file, ifelse(append, "a", "w")) :
  cannot open the connection
Calls: rk.print.literal -> cat -> file
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
  cannot open file '/rk_out.html': Permission denied
An unspecified error occurred while running the command.