Elad,
I disagree. This section:
It is undocumented where last.warning is stored nor that it is
visible, and this is subject to change. Prior to R 2.4.0 it was
stored in the workspace, but no longer.
already says that it won't work (or rather that there is no reason to think
it would work). It says that 'last.warning' is not stored in the workspace
(global environment), and hasn't been since 2.4.0. Thus it won't be
affected by an rm call that removes all visible objects from the global
environment.
Furthermore, the above section states that the location and visibility of
'last.warning' is undocumented, which means that it is not intended (or
safe) for direct manipulation by end users. As such, I agree with Scott.
This doesn't need to be made easier, as it isn't something that
beginner/intermediate users should need to be doing.
Finally, for your specific use case, see also ?withCallingHandlers which
can not only detect warnings, but also set callback functions which can
decide whether to abort or process and restart when a warning is thrown.
The documentation for that function is a little rough, though you can see
it in action in Hadley Wickham's evaluate package (specifically
evaluate/R/eval.r).
Hope that helps,
~G
On Sun, Dec 29, 2013 at 6:57 PM, Elad Zippory <elad.zipp...@gmail.com>wrote:
> Hi Scott,
>
> options(warn = 2) is a great idea. Thank you. My suggestion was not to
> change the behavior of last.warning, just to write what the behavior is
> very explicitly in the help page. But I guess this is just difference of
> opinions.
>
> Thanks for the suggestions,
> Elad
>
>
> On Sun, Dec 29, 2013 at 3:51 AM, Scott Kostyshak <skost...@princeton.edu
> >wrote:
>
> > On Sat, Dec 28, 2013 at 11:19 PM, Elad Zippory <elad.zipp...@gmail.com>
> > wrote:
> > > Hi Scott,
> > >
> > > Thank you for your detailed response. (btw, the reason why I didn't
> link
> > the
> > > Stack Overflow question is because I deleted it after I sent the
> e-mail).
> >
> > Hi Elad,
> >
> > Please keep the conversation on the list unless there is a reason for
> > it to be private, in which case please say so. This way everyone can
> > participate (and more importantly can correct my errors).
> >
> > > The rationale behind my proposal was because I was surprised to learn
> > that
> > > rm(list=ls()) does not clear the warning list. The reason why I was
> > > surprised is because it is not clear from the help page (if you are at
> a
> > > level that requires you to read the help page of such a base function,
> > the
> > > warning that I quoted does not fully warn the 'user', who is not a
> > > 'developer', what is going on. Environments in R are not trivial
> > knowledge
> > > that can be raised too concisely).
> >
> > In some cases environments can be thought of like lists. As for how
> > name look-up goes, yes it takes some studying to learn about that.
> >
> > > The reason why it mattered is because I am writing a program to be run
> on
> > > our HPC, and I want it to abort when there is a warning so I can attend
> > to
> > > it right away. No point to discover after expensive usage that some
> > warning
> > > should be investigated, casting doubt on several days of computation.
> It
> > is
> > > also useful when writing recursive code, to abort immediately when the
> > > warning list is populated as it is very hard to understand what went
> > wrong,
> > > and especially, where...
> >
> > This is a great programming strategy. You might be interested in one
> > of my favorite recommendations: treat warnings like errors.
> >
> > options(warn = 2) # asks R to treat warnings as errors. See ?options
> >
> > As far as knowing more precisely where something went wrong (where not
> > in the sense of what line of code, but in which function), consider
> > using the traceback function. Or, in addition to the above options
> > command, you might like:
> >
> > options(error = recover) # asks R to enter the debugger when there is an
> > error
> >
> > and because warnings are now errors, it also enters the debugger for
> > warnings. This way you can poke around where the warning occurred.
> >
> > > So, those were my motivations. Again, if I would know that I need a
> > fresh R
> > > session, I would get it. I don't like 'touching' what I don't
> > understand. I
> > > just wish I knew I needed to do so without wasting a day trying to
> debug
> > a
> > > warning, where all my actions to debug it were 'virtual'.
> >
> > I still don't see a need to manually access last.warning for the
> > situation you described.
> >
> > > Again, thank you for your detailed response, I hope that the case I am
> > > making is clearer now.
> >
> > Thank you for giving more details on what you're trying to accomplish.
> >
> > Scott
> >
> >
> > --
> > Scott Kostyshak
> > Economics PhD Candidate
> > Princeton University
> >
> > > Best regards,
> > > Elad Zippory
> > > Ph.D student
> > > Politics, NYU
> >
> > > On Sat, Dec 28, 2013 at 9:19 PM, Scott Kostyshak <
> skost...@princeton.edu
> > >
> > > wrote:
> > >>
> > >> On Sat, Dec 28, 2013 at 6:06 PM, Elad Zippory <elad.zipp...@gmail.com
> >
> > >> wrote:
> > >> > Hi,
> > >> >
> > >> > I raised this issue at stackoverflow and it was suggested to raise
> it
> > >> > here:
> > >> >
> > >> > >From the current help page, it is unclear that "warnings()" does
> not
> > >> > clear
> > >> > after rm(list=ls()). Currently the page states that:
> > >> >
> > >> > "Warning: It is undocumented where last.warning is stored nor that
> it
> > is
> > >> > visible, and this is subject to change. Prior to R 2.4.0 it was
> stored
> > >> > in
> > >> > the workspace, but no longer."
> > >> >
> > >> > Yet, I suggest that, if to keep the current behavior or until the
> > >> > behavior
> > >> > is changed, at least write explicitly in the help file something
> like
> > >> > "clearing the global environment will not clear the warning list. To
> > do
> > >> > so
> > >> > use assign("last.warning", NULL, envir = baseenv())"
> > >> >
> > >> > Thank you,
> > >> > Elad Zippory
> > >>
> > >> Hi Elad,
> > >>
> > >> I'm not a decision maker around here but I'm curious about your
> > >> suggestion. I always find it helpful to try to understand how people
> > >> use R and how they expect R to work.
> > >>
> > >> From what I understand, you agree that there's no contradiction of
> > >> behavior in terms of how R is documented to work and you agree that
> > >> rm(list=ls()) should indeed not clear the warnings list. First, let me
> > >> give my observation that I think the policy of writing R documentation
> > >> is to give sufficient information for what a function does. When there
> > >> is something surprising or there are performance issues to keep in
> > >> mind, occasionally the R documentation appropriately mentions what a
> > >> function does not do.
> > >>
> > >> I think you are interested in making more of a "let's make it easier
> > >> on the user" argument so let me try to address that. I think it's easy
> > >> to learn how to find the last.warning object. This would only require
> > >> a user to read the first line of ?warnings and then to know about the
> > >> getAnywhere function. That's it.
> > >>
> > >> In fact, I think that's too easy. I would personally be in favor of
> > >> making it _more_ difficult for a beginning user to modify
> > >> last.warning. I've never had to do such a thing and I would be
> > >> suspicious of beginning/intermediate users who claim there's a need
> > >> to. If you want a fresh R session, use a fresh R session. Clearing the
> > >> global environment will not give a fresh R session. Clearing the
> > >> global environment and clearing warnings will not do so either. In my
> > >> opinion, it is tricks like these that can lead to unfortunate
> > >> situations where results are not reproducible.
> > >>
> > >> Also, you mention a Stack Overflow question. If you are going to refer
> > >> to something, please provide a link (perhaps in a footnote like this
> > >> [1] if you do not want to put a long distracting URL in your message).
> > >> Maybe there is no useful discussion there, but maybe there is and the
> > >> discussion has already raised the points I raise in this email. The
> > >> reader of your message is thus left wondering.
> > >>
> > >> Let me note that I'm just an ordinary R user. I hope I don't scare you
> > >> off from giving more suggestions and wouldn't be surprised if others
> > >> disagree. I hope you send more messages like the one you just sent
> > >> because I'm interested in understanding what R users find confusing.
> > >>
> > >> Best regards,
> > >>
> > >> Scott
> > >>
> > >> [1] an old but related Stack Overflow question:
> > >>
> http://stackoverflow.com/questions/5725106/r-how-to-clear-all-warnings
> > >>
> > >> --
> > >> Scott Kostyshak
> > >> Economics PhD Candidate
> > >> Princeton University
> > >
> > >
> >
>
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>
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--
Gabriel Becker
Graduate Student
Statistics Department
University of California, Davis
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