R.app history forgets

From: Rob Goedman <robjgoedman at me.com>
Date: Wed, 06 May 2009 08:02:29 -0700
To: Loren Engrav <engrav at u.washington.edu>
Cc: "r-sig-mac at stat.math.ethz.ch" <r-sig-mac at stat.math.ethz.ch>
Subject: Re: [R-SIG-Mac] R.app history forgets

Loren,

I will look into the 'Always apply', your understanding is correct and
it should not change the working directory on drag&drop of a file or a
directory if 'Always apply' is selected (according to my own note :-).
It seems to work fine for a file but not for a directory.

Simon, do you recall if there was a specific reason why we treated
files and directories similar? What's the point of d&d-ing a directory
on the R.app icon other than to set the working dir?

Loren, why do you d&d a dir on R.app?

A quick test with 'R-in-a-terminal' indeed does show R creates a
history file after answering the q() question with yes. Not sure if
that is R or maybe some initial default behavior. Of course, in a
terminal the file actually contains history commands. I fully agree
with Simon, deviating from R haunts you for many years (but at that
time of making those changes I did not want to drop the old R.app
multi-line history feature).

Rob


On May 6, 2009, at 7:10 AM, Loren Engrav wrote:

No no, thank you for helping

To clarify, I am not out to "fix" or "change" anything, or report
bugs, I
just want to understand how to efficiently use R.app, my problems are

1-on my systems (one 32 and one 64), Rhistory "forgets" commands
which is
how this all started, and
2-I find the Startup Preferences confusing

Ok, Rdata: several explained that in the workspace, a new object "x"
will
overwrite an old object "x" without warning, by keeping Rdata's
separate one
can use "x" many times for different things, I have always manually
saved
important Rdata's and ignored the default Rdata, but I can change,
or do
both now that I understand

Now Directory in Preferences: I have checked Always apply and the
directory
is ~; the notes say dd of directory will override if not enforced;
but if I
dd a folder onto R, the working directory is not ~ but rather the
one dd'd
onto R, so does not seem "Always apply" is working

Now Rhistory: again the problem is Rhistory forgets commands on my
system,
which is why I got into this, but then I find Rhistory(s) all over

in Prefs I have checked Read on startup and the history file is
~/.Rhistory
(return saves that value, thank you again, this might be in the
notes) and I
checked Cleanup history.

It appears that if I work in some directory and then quit w save, the
history is written to both ~/.Rhistory and the directory. So I had 33
.Rhistory(s) on the drive even tho I told R.app to use one.

So I tried your second idea, changed the R.app history name
to .xxxRhistory
and voila, ".xxxRhistory" appears where R.app Preferences say and
".Rhistory" appears in the working directory, so would appear you are
correct; R.app is writing out .xxxRhistory and somebody else is
writing
.Rhistory

Now if I work in the default directory AND have R.app set to write
.xxxRhistory AND quit/save, I again find in the directory
both .xxxRhistory
and .Rhistory, so you are again correct; R.app writes .xxxRhistory and
somebody else writes .Rhistory

And the .Rhistory file is written about 4 sec after the .xxxRhistory
file
and the .Rhistory file is 0kb

So then your third idea might be correct; ie if R.app
writes .Rhistory it is
overwritten by the second writing of .Rhistory and if the
second .Rhistory
is missing commands, then it would appear that R.app is forgetting
commands

In sum
1-is it possible that .Rhistory from R overwrites .Rhistory from
R.app and
the history that R uses is incomplete so commands are "forgotten"
2-and of course what is the work around for #2
3-and lesser, what does "Always apply" do for the directory

From: Rob Goedman <robjgoedman at me.com>
Date: Tue, 05 May 2009 21:34:16 -0700
To: Loren Engrav <engrav at u.washington.edu>
Cc: "r-sig-mac at stat.math.ethz.ch" <r-sig-mac at stat.math.ethz.ch>
Subject: Re: [R-SIG-Mac] R.app history forgets

Loren,

Please find my comments inserted below. Thank you for being
persistent!

On May 5, 2009, at 4:13 PM, Loren Engrav wrote:

Ok, so Rdata goes to the directory one is working in; and so will
have
Rdata's in many folders which seems strange

As a counter example, I work on 5 or 6 different projects
simultaneously,
each in its own directory sub tree. Several of the projects need to
store the
workspace after I'm done. This is implemented as the default
mechanism.

Through the .Last mechanism you can get your desired behavior. But
unfortunately, it will take some extra work to define the .Last
function.
That should take care of many .RData's.

As for Rhistory if one declines to save workspace, Rhistory is
written to
the directory specified; if one saves workspace Rhistory is written
to both
the directory specified and the workspace directory, ie to both;
this also
seems strange.

Could it be R, not R.app that creates the .Rhistory file if the
workspace is
saved????? I am not aware of this behavior (the fact that R creates a
history file when asked to save the workspace), or simply might have
missed it if it was introduced in the 4 or 5 years since I worked
on the
history mechanism for R.app.

And the troubled history is attached

This seems problematic; not knowing where these files are going and
winding
up with many; and then the forgetful Rhistory as well

And indeed, in that case, if the name of the history file set in the
R.app
preferences is the same as R's default name (.Rhistory) ***and*** the
workspace is saved, the history file seems to forget recent commands
because R.app writes its history file which is subsequently
overwitten
by R.

Maybe someone familiar with the R source can confirm this behavior, I
have
rarely looked at the R source, just at the R.app code.

Rob

Thank you

From: Rob Goedman <robjgoedman at me.com>
Date: Tue, 05 May 2009 12:20:51 -0700
To: Loren Engrav <engrav at u.washington.edu>
Cc: "r-sig-mac at stat.math.ethz.ch" <r-sig-mac at stat.math.ethz.ch>
Subject: Re: [R-SIG-Mac] R.app history forgets

Loren,

Thanks for the screen shot.

A bit more experimentation and a quick look at the code refreshed
my
memory.

If you exit R, .RData is always written to the directory you are
in.

In your setting, on q() to quit, R.app should ask for
conformation to
save the workspace.

If you don't change your directory it should create a .RData in
your
home directory (that's where your R.app started).

Preferences do not provide help here, but you could create a .Last
function with a save.image() command in it to force storing
the .RData
file to a fixed directory. In that case you can opt to set the Quit
preferences to 'No' (don't ask me to store the workspace).

For history its a (tiny) bit more flexible. By selecting an
absolute
path, like you have in your setting, it will always store the
current
available history commands in that file (including the ones that
were
read in during startup, so the new commands are at the end of the
file).

If this does not work for you, can you send me your ~/.Rhistory
file
after executing a last new command in R.app, maybe something like
'testHist <- 1' and quitting R.app?

As you found in the archives, a few folks did have trouble (usually
because R.app could not write to the selected directory).

After this email it might be better to take this discussion off-
line.

Regards,
Rob


On May 5, 2009, at 11:50 AM, Loren Engrav wrote:

Thank you
attached

From: Rob Goedman <robjgoedman at me.com>
Date: Tue, 05 May 2009 11:36:25 -0700
To: Loren Engrav <engrav at u.washington.edu>
Cc: "r-sig-mac at stat.math.ethz.ch" <r-sig-mac at stat.math.ethz.ch>
Subject: Re: [R-SIG-Mac] R.app history forgets

Loren,

Can you send me a screen copy of the Startup preferences ( with
the
cursor inside the Startup Preferences window, press Command-
Shift-4,
followed by pressing the spacebar, followed by a click of the
mouse
button, this should write it to your Deskop as 'Picture 1').

Rob

On May 5, 2009, at 11:24 AM, Loren Engrav wrote:

Mac OS 10.5.5 and R.app 2.9.0

I start up, run a few things, and quit (w or wo save) and no
directory
changes

Then I restart and the recent commands are no longer in Rhistory

The only box I have checked in History preferences is Read on
Startup and I
have max entries set to 5000

I see queries about this before but I could find no solution

Thank you

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On May 5, 2009, at 9:37 AM, Loren Engrav wrote:

Thank you
The return before clicking anywhere else solved that problem,
clever

So I trash all invisible .Rhistory and .Rdata files
Then made a new folder (called R_History_Data) and aim Preferences
at this
folder (using the return)
Then run R.app and yes, I have one .Rhistory and one .Rdata in
that
folder

But then I change the working directory and do some stuff
Then quit and save working directory
And now I have two of each invisible files, one in R_History_Data
and one in
the working directory folder

So it still appears as I move from directory to directory I will
leave
invisible .Rhistory and .Rdata files all over

Is it possible to have Rhistory and Rdata always written to the
R_History_Data folder?

<TroubledHistory.history>