Loren Engrav, MD
Professor, Surgery
Associate Director, Burn Center, 1977-2001
Univ Washington
Seattle
> From: Rob Goedman <robjgoedman at me.com>
> Date: Wed, 06 May 2009 09:36:12 -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,
>
> 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>
>>>>>
>>>>
>>>>
>>>
>>
>>
>