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]]
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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?
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