[R-SIG-Mac] R.app history forgets

Rob Goedman robjgoedman at me.com
Wed May 6 17:02:29 CEST 2009 

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
>>>>>>>
>>>>>>> [[alternative HTML version deleted]]
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> R-SIG-Mac mailing list
>>>>>>> R-SIG-Mac at stat.math.ethz.ch
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>>>>
>>>>>
>>>>> <Picture 3.png>
>>>>
>>>> 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>
>>
>
>

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