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

Rob Goedman robjgoedman at me.com
Wed May 6 18:36:12 CEST 2009 

Loren,

The double click issues will go away if you select the 2 entries  
under  the line 'Max number of entries ...' in the Startup pref.

As a history workaround, for now just make sure the Startup pref for  
the history file is not .Rhistory, as you tested before.

Seems like d&d does what you want, I might just change the note. I  
know some folks start R.app by d&d-ing an xxx.R file on it.

Rob


On May 6, 2009, at 9:02 AM, Loren Engrav wrote:

> Hi and thank you
>
> Why d&d directory onto R.app?
>
> Now that I understand the common use of many Rdata's, one in each  
> working
> folder, and Pref notes say "d&d of file or directory on R icon will
> override", I was trying to get with common usage by starting up with  
> d&d
> onto R.app rather then double clicking R.app and then changing  
> location; did
> not try to d&d a file since the R files (Rhistory and Rdata) are  
> invisible;
> and then found that the "Always apply" directory is overridden; so  
> then
> confused about what does "Always apply" mean
>
> This is part of my "prefs are confusing" problem but not part of the
> "Rhistory commands being forgotten" problem; which is probably more
> important
>
> Today I said I would stop fiddling with Rhistory and do work, but I  
> find if
> I double click on the bottom entry in the history window, things go  
> wrong.
> Seems like returns are added and multiple commands are combined into  
> one
> entry in the file. Here is what the end of the history file looks  
> like in
> BBEdit
>
> .Machine$sizeof.pointer
> sessionInfo()
> ls()
> rm (ABeset_gcrmaNumhom)
> ls()
> AB_gcrmaNumhom <- gcrma(AA_ReadAffyNumhom, fast = FALSE)
> library(gcrma)
> .Machine$sizeof.pointer#
>
> .Machine$sizeof.pointer#
> #
>
> .Machine$sizeof.pointer#
>
> .Machine$sizeof.pointer#
> #
>
> .Machine$sizeof.pointer#
> #
> #
>
> .Machine$sizeof.pointer#
>
>
>
>> 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
>>>>>>>>>
>>>>>>>>> [[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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