R help - Sep 2015 - Unable to run RcmdrPlugin.survival using 3.2.2 with Windows 10

Dear John,

You mention, "the Rcmdr manual (accessible via "Help > Introduction
to the R
Commander")".

Apologies for my dumbness, but the manual I did read - and found helpful - 
before posting is clearly a different one.   A 43 page pdf  with no section 
numbers nor any reference to the Workspace.   (Package ?Rcmdr?    August 19, 
2015     Version 2.2-0    Date 2015-08-14    Title R Commander ....//  snip 
//...   Author John Fox [aut, cre], Milan Bouchet-Valat [aut],  ..... // 
snip //").

Since the Help page you refer to doesn't seem to be here 
https://stat.ethz.ch/mailman/listinfo/r-help  or here 
http://finzi.psych.upenn.edu/,  I would be very grateful for an extra 
direction and apologise for getting a bit lost amongst all the 
possibilities.

Kind regards, Joyaa  (feeling like a fish in a new ocean).


-----Original Message----- 
From: Fox, John
Sent: Saturday, September 5, 2015 2:07 AM
To: Joyaa Antares
Cc: r-help at r-project.org
Subject: RE: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with Windows 
10

Dear Joyaa,
> -----Original Message-----
> From: Joyaa Antares [mailto:joyaa at goldcoastosteopathy.com.au]
> Sent: Friday, September 4, 2015 7:07 AM
> To: Fox, John
> Cc: r-help at r-project.org
> Subject: Re: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with
> Windows 10
>
> Dear John,
>
> Very many thanks.  Your hypothesis was completely correct - I did save
> the
> workspace, and this is what created the problem.   As a newbie, being
> part
> way through an "exercise", saving my workspace intuitively seemed
the
> right
> thing to do.   Clearly not!
It wouldn't have seemed the correct thing to do had you read the Rcmdr 
manual (accessible via "Help > Introduction to the R Commander").
See
Section 6.5.

I understand why saving the workspace was made the default on exiting the R 
Console -- after all, it can help users to avoid inadvertently losing 
work -- but it my experience it is a frequent source of confusion among new 
users of R, whether or not they're using the R Commander.
> So now, before I closed R and Rcmdr, I
> copied
> and pasted from Rcmdr's script file into a MS Word document, added a
few
> comments (with preceding #), and then closed without otherwise saving
> R's
> script, output, workspace or markdown.  I hope this is reasonable
> practice.
> If not, I would be grateful for guidance on this.
You've already received good advice from others about *not* using Word as a 
programming editor. I think that it's safe to say that the most popular 
programming editor for R (and for good reason) is RStudio. The Rcmdr script 
tab has basic editing capabilities, including saving and opening R scripts, 
and it offers to save the script when you exit.

You can, however, paste input and output, including graphs, from the Rcmdr 
into Word to create a report. It would be better, however, to use the Rcmdr 
Markdown tab to create reports in the form of HTML, PDF, or Word files. The 
Rcmdr includes an editor for R Markdown documents.  See Sections 6.1 and 6.2 
of the manual.

Best,
John
>
> Once again, very many thanks.  Joyaa
>
> -----Original Message-----
> From: Fox, John
> Sent: Friday, September 4, 2015 1:24 PM
> To: Joyaa Antares
> Cc: r-help at r-project.org
> Subject: RE: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with
> Windows
> 10
>
> Dear Joyaa,
>
> > -----Original Message-----
> > From: Joyaa Antares [mailto:joyaa at goldcoastosteopathy.com.au]
> > Sent: September 3, 2015 9:37 PM
> > To: Fox, John <jfox at mcmaster.ca>
> > Cc: r-help at r-project.org
> > Subject: Re: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with
> > Windows 10
> >
> > Dear John, Dear List,
> >
> > Thank you for responding.  Like you, I have tried uninstalling R and
> > reinstalling
> > again.  Question 1: having uninstalled R, how do you delete the
> package
> > library?
>
> You say below that you installed R packages when R was run as
> administrator
> and that you took all defaults. In that case,  the installed packages
> will
> be in C:\Program Files\R\R-3.2.2\library . Just delete the library
> directory, which will still be there after R 3.2.2 is uninstalled. I do
> recommend, by the way, that, for using the Rcmdr, you install R with the
> SDI
> rather than the default MDI, but that doesn't explain your
difficulties.
>
> >
> > I have used defaults throughout the process, except for running the
> whole
> > things
> > as Administrator rather than a User.  For the mirror, my first two
> install
> > attempts
> > were via a mirror in Germany.  My 3rd and 4th attempts via Cambridge,
> UK.
> >
> > Perhaps importantly: the first time I ran the RcmdrPlugin.survival
> plug-in
> > it
> > worked fine.
>
> If you said that before, I missed it.
>
> > I got half way through the exercise I was attempting, then closed
> > the programs for the night.  The next day, when I tried to reload the
> > plugin from
> > R Commander, the plugin asked me to restart R Commander, but on opting
> for
> > "Yes", this is when R Commander does not open properly.
>
> Here's my hypothesis: When you "closed" R, you saved the R
workspace. My
> guess is that this is the source of your problem. If so, the saved
> workspace
> is in the file .RData in your home directory; delete it and try again.
>
> If this works, in future, exit from the Rcmdr and R via the Rcmdr menus
> (or
> if closing R directly, don't save the workspace).
>
> I hope this helps,
> John
>
> -----------------------------
> John Fox, Professor
> McMaster University
> Hamilton, Ontario
> Canada L8S 4M4
> Web: socserv.mcmaster.ca/jfox
>
>
> >
> > My thanks to you and the list for your time.  Joyaa (Gold Coast,
> > Queensland,
> > Australia)
> >
> > -----Original Message-----
> > From: Fox, John
> > Sent: Friday, September 4, 2015 1:29 AM
> > To: Joyaa Antares
> > Cc: r-help at r-project.org
> > Subject: RE: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with
> > Windows
> > 10
> >
> > Dear Joyaa,
> >
> > I too run R 3.2.2 on a Windows 10 system. I uninstalled R, deleted my
> > package
> > library, and then reinstalled R and the Rcmdr and RcmdrPlugin.survival
> > packages.
> > I took all defaults, except that I selected the SDI rather than the
> > default MDI for
> > Rgui, but I seriously doubt that this is the source of your problem. I
> > used the 0-
> > Cloud mirror, both for R
> > 3.2.2 and for packages.
> >
> > I'm afraid that I can't duplicate your problem -- everything
works
> > perfectly fine
> > for me.
> >
> > You provided a reasonable amount of detail, but is there anything else
> you
> > can
> > add?
> >
> > Best,
> > John
> >
> > -----------------------------
> > John Fox, Professor
> > McMaster University
> > Hamilton, Ontario
> > Canada L8S 4M4
> > web: socserv.mcmaster.ca/jfox
> >
> >
> > ________________________________________
> > From: R-help [r-help-bounces at r-project.org] on behalf of Joyaa
Antares
> > [joyaa at goldcoastosteopathy.com.au]
> > Sent: September 3, 2015 8:31 AM
> > To: r-help at r-project.org
> > Subject: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with
> Windows
> > 10
> >
> > Hello r-help,
> >
> > I am quite new to R.  I downloaded R 3.2.2 for Windows to use with
> Windows
> > 10.
> >
> > On attempting to load the RcmdrPlugin.survival plug-in I got this
> error
> > message:
> >
> > Error in structure(.External(.C_dotTclObjv, objv), class =
"tclObj") :
> >   [tcl] invalid command name "configure".
> >
> > The lead-up to this was:
> >
> > * I uninstalled R 3.2.2 and deleted all R files I could find.
> > * Downloaded R 3.2.2 to do a fresh install
> > * Opened the .exe file as Administrator
> > * Ran 64-bit R as Administrator
> > * Updated all packages
> > * Installed Rcmdr and RcmdrPlugin.survival
> > * Ran Rcmdr using library(Rcmdr) from the console
> > * This required an install of a host of packages, which I installed
> > * Loaded RcmdrPlugin.survival from the Tools menu
> > * I was asked to restart R commander, and when I tried it didn't
open
> > properly
> > (showing only File/Edit/Data in the menu bar), and this wouldn't
close
> > properly
> > either.  The error message as above showed in the console.
> >
> > I haven't posted to the list before and would be very grateful for
> help.
> > Thank you.   Joyaa
> >         [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> > =

Dear Joyaa,
> -----Original Message-----
> From: Joyaa Antares [mailto:joyaa at goldcoastosteopathy.com.au]
> Sent: September 5, 2015 2:07 AM
> To: Fox, John <jfox at mcmaster.ca>
> Cc: r-help at r-project.org
> Subject: Re: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with
Windows 10
> 
> Dear John,
> 
> You mention, "the Rcmdr manual (accessible via "Help >
Introduction to the R
> Commander")".
> 
> Apologies for my dumbness, but the manual I did read - and found helpful -
> before posting is clearly a different one.   A 43 page pdf  with no section
> numbers nor any reference to the Workspace.   (Package ?Rcmdr?    August
19,
> 2015     Version 2.2-0    Date 2015-08-14    Title R Commander ....//  snip
> //...   Author John Fox [aut, cre], Milan Bouchet-Valat [aut],  ..... //
> snip //").
I'm at a loss to explain why your copy of the manual has no section numbers,
particularly since the version and date you cite are correct; as I've just
confirmed, the PDF manual distributed with version 2.2-0 of the Rcmdr does
indeed have section numbers, starting with "1 Introduction" near the
top of the first page. In case it's somehow ambiguous, this is section 1.
I'll send you a copy of the PDF separately, so as not to waste bandwidth on
the r-help list.
> 
> Since the Help page you refer to doesn't seem to be here
I'm sorry, but I don't recall referring to a help page and I don't
see a reference to a help page in this thread. Can you remind me what I
apparently said?

Best,
 John
> https://stat.ethz.ch/mailman/listinfo/r-help  or here
> http://finzi.psych.upenn.edu/,  I would be very grateful for an extra
direction
> and apologise for getting a bit lost amongst all the possibilities.
> 
> Kind regards, Joyaa  (feeling like a fish in a new ocean).
> 
> 
> -----Original Message-----
> From: Fox, John
> Sent: Saturday, September 5, 2015 2:07 AM
> To: Joyaa Antares
> Cc: r-help at r-project.org
> Subject: RE: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with
Windows
> 10
> 
> Dear Joyaa,
> 
> > -----Original Message-----
> > From: Joyaa Antares [mailto:joyaa at goldcoastosteopathy.com.au]
> > Sent: Friday, September 4, 2015 7:07 AM
> > To: Fox, John
> > Cc: r-help at r-project.org
> > Subject: Re: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with
> > Windows 10
> >
> > Dear John,
> >
> > Very many thanks.  Your hypothesis was completely correct - I did save
> > the
> > workspace, and this is what created the problem.   As a newbie, being
> > part
> > way through an "exercise", saving my workspace intuitively
seemed the
> > right
> > thing to do.   Clearly not!
> 
> It wouldn't have seemed the correct thing to do had you read the Rcmdr
manual
> (accessible via "Help > Introduction to the R Commander"). See
Section 6.5.
> 
> I understand why saving the workspace was made the default on exiting the R
> Console -- after all, it can help users to avoid inadvertently losing work
-- but it
> my experience it is a frequent source of confusion among new users of R,
> whether or not they're using the R Commander.
> 
> > So now, before I closed R and Rcmdr, I copied and pasted from
Rcmdr's
> > script file into a MS Word document, added a few comments (with
> > preceding #), and then closed without otherwise saving R's script,
> > output, workspace or markdown.  I hope this is reasonable practice.
> > If not, I would be grateful for guidance on this.
> 
> You've already received good advice from others about *not* using Word
as a
> programming editor. I think that it's safe to say that the most popular
> programming editor for R (and for good reason) is RStudio. The Rcmdr script
tab
> has basic editing capabilities, including saving and opening R scripts, and
it offers
> to save the script when you exit.
> 
> You can, however, paste input and output, including graphs, from the Rcmdr
> into Word to create a report. It would be better, however, to use the Rcmdr
> Markdown tab to create reports in the form of HTML, PDF, or Word files. The
> Rcmdr includes an editor for R Markdown documents.  See Sections 6.1 and
6.2
> of the manual.
> 
> Best,
> John
> 
> >
> > Once again, very many thanks.  Joyaa
> >
> > -----Original Message-----
> > From: Fox, John
> > Sent: Friday, September 4, 2015 1:24 PM
> > To: Joyaa Antares
> > Cc: r-help at r-project.org
> > Subject: RE: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with
> > Windows
> > 10
> >
> > Dear Joyaa,
> >
> > > -----Original Message-----
> > > From: Joyaa Antares [mailto:joyaa at goldcoastosteopathy.com.au]
> > > Sent: September 3, 2015 9:37 PM
> > > To: Fox, John <jfox at mcmaster.ca>
> > > Cc: r-help at r-project.org
> > > Subject: Re: [R] Unable to run RcmdrPlugin.survival using 3.2.2
with
> > > Windows 10
> > >
> > > Dear John, Dear List,
> > >
> > > Thank you for responding.  Like you, I have tried uninstalling R
and
> > > reinstalling again.  Question 1: having uninstalled R, how do you
> > > delete the
> > package
> > > library?
> >
> > You say below that you installed R packages when R was run as
> > administrator and that you took all defaults. In that case,  the
> > installed packages will be in C:\Program Files\R\R-3.2.2\library .
> > Just delete the library directory, which will still be there after R
> > 3.2.2 is uninstalled. I do recommend, by the way, that, for using the
> > Rcmdr, you install R with the SDI rather than the default MDI, but
> > that doesn't explain your difficulties.
> >
> > >
> > > I have used defaults throughout the process, except for running
the
> > whole
> > > things
> > > as Administrator rather than a User.  For the mirror, my first
two
> > install
> > > attempts
> > > were via a mirror in Germany.  My 3rd and 4th attempts via
> > > Cambridge,
> > UK.
> > >
> > > Perhaps importantly: the first time I ran the
RcmdrPlugin.survival
> > plug-in
> > > it
> > > worked fine.
> >
> > If you said that before, I missed it.
> >
> > > I got half way through the exercise I was attempting, then closed
> > > the programs for the night.  The next day, when I tried to reload
> > > the plugin from R Commander, the plugin asked me to restart R
> > > Commander, but on opting
> > for
> > > "Yes", this is when R Commander does not open properly.
> >
> > Here's my hypothesis: When you "closed" R, you saved the
R workspace.
> > My guess is that this is the source of your problem. If so, the saved
> > workspace is in the file .RData in your home directory; delete it and
> > try again.
> >
> > If this works, in future, exit from the Rcmdr and R via the Rcmdr
> > menus (or if closing R directly, don't save the workspace).
> >
> > I hope this helps,
> > John
> >
> > -----------------------------
> > John Fox, Professor
> > McMaster University
> > Hamilton, Ontario
> > Canada L8S 4M4
> > Web: socserv.mcmaster.ca/jfox
> >
> >
> > >
> > > My thanks to you and the list for your time.  Joyaa (Gold Coast,
> > > Queensland,
> > > Australia)
> > >
> > > -----Original Message-----
> > > From: Fox, John
> > > Sent: Friday, September 4, 2015 1:29 AM
> > > To: Joyaa Antares
> > > Cc: r-help at r-project.org
> > > Subject: RE: [R] Unable to run RcmdrPlugin.survival using 3.2.2
with
> > > Windows
> > > 10
> > >
> > > Dear Joyaa,
> > >
> > > I too run R 3.2.2 on a Windows 10 system. I uninstalled R,
deleted
> > > my package library, and then reinstalled R and the Rcmdr and
> > > RcmdrPlugin.survival packages.
> > > I took all defaults, except that I selected the SDI rather than
the
> > > default MDI for Rgui, but I seriously doubt that this is the
source
> > > of your problem. I used the 0- Cloud mirror, both for R
> > > 3.2.2 and for packages.
> > >
> > > I'm afraid that I can't duplicate your problem --
everything works
> > > perfectly fine for me.
> > >
> > > You provided a reasonable amount of detail, but is there anything
> > > else
> > you
> > > can
> > > add?
> > >
> > > Best,
> > > John
> > >
> > > -----------------------------
> > > John Fox, Professor
> > > McMaster University
> > > Hamilton, Ontario
> > > Canada L8S 4M4
> > > web: socserv.mcmaster.ca/jfox
> > >
> > >
> > > ________________________________________
> > > From: R-help [r-help-bounces at r-project.org] on behalf of Joyaa
> > > Antares [joyaa at goldcoastosteopathy.com.au]
> > > Sent: September 3, 2015 8:31 AM
> > > To: r-help at r-project.org
> > > Subject: [R] Unable to run RcmdrPlugin.survival using 3.2.2 with
> > Windows
> > > 10
> > >
> > > Hello r-help,
> > >
> > > I am quite new to R.  I downloaded R 3.2.2 for Windows to use
with
> > Windows
> > > 10.
> > >
> > > On attempting to load the RcmdrPlugin.survival plug-in I got this
> > error
> > > message:
> > >
> > > Error in structure(.External(.C_dotTclObjv, objv), class =
"tclObj") :
> > >   [tcl] invalid command name "configure".
> > >
> > > The lead-up to this was:
> > >
> > > * I uninstalled R 3.2.2 and deleted all R files I could find.
> > > * Downloaded R 3.2.2 to do a fresh install
> > > * Opened the .exe file as Administrator
> > > * Ran 64-bit R as Administrator
> > > * Updated all packages
> > > * Installed Rcmdr and RcmdrPlugin.survival
> > > * Ran Rcmdr using library(Rcmdr) from the console
> > > * This required an install of a host of packages, which I
installed
> > > * Loaded RcmdrPlugin.survival from the Tools menu
> > > * I was asked to restart R commander, and when I tried it
didn't
> > > open properly (showing only File/Edit/Data in the menu bar), and
> > > this wouldn't close properly either.  The error message as
above
> > > showed in the console.
> > >
> > > I haven't posted to the list before and would be very
grateful for
> > help.
> > > Thank you.   Joyaa
> > >         [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-help at r-project.org mailing list -- To UNSUBSCRIBE and more,
see
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
> > > http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible
code.
> > > =