Hi Double clicking bottom command: I want to keep dupes but double click problem seems to go away if I just check "cleanup"; if "cleanup" is necessary for proper behavior of bottom command, why have it optional?
Rhistory: I have R.app writing to .engravRhistory and Cleanup checked but Remove dupes not checked. Quit still cuts a duplicate history entry at the bottom; but so what? A duplicate at the bottom is unnecessary, but cutting it is unexpected D&D: seems confusing if d&d a file does one thing and d&d directory does another; would seem that neither should override the setting since it says "Always" Anyway With Cleanup checked ~/.engravRhistory locked in with the return Understanding the common use of and location of .Rdata Ignoring the little proliferating .Rhistory files I may in fact be "good to go" Thank you so much And installing 64bit stuff is surely easier now -- Loren Engrav, MD Professor, Surgery Associate Director, Burn Center, 1977-2001 Univ Washington Seattle > From: Rob Goedman <robjgoed...@me.com> > Date: Wed, 06 May 2009 09:36:12 -0700 > To: Loren Engrav <eng...@u.washington.edu> > Cc: "r-sig-mac@stat.math.ethz.ch" <r-sig-mac@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 <robjgoed...@me.com> >>> Date: Wed, 06 May 2009 08:02:29 -0700 >>> To: Loren Engrav <eng...@u.washington.edu> >>> Cc: "r-sig-mac@stat.math.ethz.ch" <r-sig-mac@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 <robjgoed...@me.com> >>>>> Date: Tue, 05 May 2009 21:34:16 -0700 >>>>> To: Loren Engrav <eng...@u.washington.edu> >>>>> Cc: "r-sig-mac@stat.math.ethz.ch" <r-sig-mac@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 <robjgoed...@me.com> >>>>>>> Date: Tue, 05 May 2009 12:20:51 -0700 >>>>>>> To: Loren Engrav <eng...@u.washington.edu> >>>>>>> Cc: "r-sig-mac@stat.math.ethz.ch" <r-sig-mac@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 <robjgoed...@me.com> >>>>>>>>> Date: Tue, 05 May 2009 11:36:25 -0700 >>>>>>>>> To: Loren Engrav <eng...@u.washington.edu> >>>>>>>>> Cc: "r-sig-mac@stat.math.ethz.ch" <r-sig-mac@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@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> >>>>> >>>> >>>> >>> >> >> > _______________________________________________ R-SIG-Mac mailing list R-SIG-Mac@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r-sig-mac