From murdoch.duncan at gmail.com  Tue May 17 12:54:17 2011
From: murdoch.duncan at gmail.com (Duncan Murdoch)
Date: Tue, 17 May 2011 06:54:17 -0400
Subject: [Rd] Reproducible use case for R crash after updating R
In-Reply-To: <BANLkTi=4ewhn1fm5EKS5hZ=pFtfgFT0PGw@mail.gmail.com>
References: <BANLkTi=zA1s+DwgN+0qhf7_4CkZ-VBPY9A@mail.gmail.com>	<BANLkTim0BpLDYtU=FebEriF7Q_AMmToGbA@mail.gmail.com>	<4DCDA3ED.4050607@gmail.com>
	<BANLkTi=4ewhn1fm5EKS5hZ=pFtfgFT0PGw@mail.gmail.com>
Message-ID: <4DD253D9.5070108@gmail.com>

On 11-05-16 11:59 PM, Henrik Bengtsson wrote:
> Great, thanks for this.
>
> On Fri, May 13, 2011 at 2:34 PM, Duncan Murdoch
> <murdoch.duncan at gmail.com>  wrote:
>> A simple version of a fix is now in R-devel:  if the .RData file can't be
>> loaded during startup, an error message is printed, and R starts with an
>> empty workspace.
>
> I've just verified with the R v2.14.0 devel (2011-05-16 r55916) on
> Windows.  For followers, here it is how it works now:
>
> # GENERATE AN INVALID .RData file:
> install.packages("fortunes")
> library("fortunes")
> foo<- fortune
> remove.packages("fortunes")
> q("yes")
>
> Startup behavior when using either Rterm or Rgui:
> [...]
> Type 'q()' to quit R.
>
> Error in loadNamespace(name) : there is no package called 'fortunes'
> During startup - Warning message:
> unable to restore saved data in .RData
>> cat("Hello world!\n")
> Hello world!
>>
>
>>
>> The name of the .RData file is printed.  It's usually just ".RData", because
>> that's what R tries to load; the file will be in the current directory if
>> you want to delete it.
>
> I've looked at the code behind this and I kind of understand what you
> mean by "just" .RData.  However, is there a reason for not reporting
> the full pathname to .RData, e.g. file.path(getwd(), ".RData")?  It
> would help the user further if the warning said:

This is coming from C code, so getting the current directory requires 
allocating memory for a buffer.  We're in a situation where something 
that normally succeeds has just failed, so it might not be safe to do that.

> (1) unable to restore saved data in .RData in directory /path/to/pwd/
> (2) unable to restore saved data in /path/to/pwd/.RData

If the file that it tried to load was named "/path/to/.RData", then your 
messages wouldn't be right:

  (1) unable to restore saved data in /path/to/.RData in directory 
/path/to/pwd/
  (2) unable to restore saved data in /path/to/pwd//path/to/.RData

You really want something like normalizePath(), but that's not a simple 
C function (and it has its own problems, e.g. if the file doesn't exist,
normalizePath doesn't work, at least on Windows).

Duncan Murdoch


> BTW, the following will not be correct if the working directory is
> changed by one of the .Rprofile startup scripts:
>
> (2) unable to restore saved data in .RData in the current working
> directory, cf. getwd()
>
> Thanks again
>
> /Henrik
>
>>   If it contains objects that you want to recover, you
>> can try to deal with the error message (e.g. by installing fortunes in your
>> example), exiting without saving, and then the next restart may succeed.
>>
>> Duncan Murdoch
>>
>>
>> On 11-05-12 2:26 PM, Henrik Bengtsson wrote:
>>>
>>> On Thu, May 12, 2011 at 10:55 AM, Henrik Bengtsson<hb at biostat.ucsf.edu>
>>>   wrote:
>>>>
>>>> This might have been discussed before, but below is a
>>>> "not-so-unlikely" use case where the user follows normal procedures,
>>>> updates R to a major release version, and then R crashes:
>>>>
>>>> 1. Use runs R stable (e.g. v2.13.0).
>>>> 2. User installs a package with a namespace, e.g.
>>>> install.packages("fortunes").
>>>> 3. User uses the package and one of the package's objects are assigned
>>>> to the global env, e.g. foo<- fortune.
>>>> 4. The user quits R and stores the session data, e.g. q("yes").  The
>>>> session is stored in users home directory.
>>>> 5. User update to new major release of R (e.g. 2.14.0).
>>>> 6. User starts R.  R crashes with "Fatal error: unable to restore
>>>> saved object in .RData" because 'fortunes' is not installed for this
>>>> new version of R.  There is also an error message before that
>>>> reporting "Error in loadNamespace(name) : there is no package called
>>>> 'fortunes'".
>>>>
>>>> This can also be reproduced using a single R version as follows:
>>>>
>>>> 1. Start R and do:
>>>> install.packages("fortunes")
>>>> library("fortunes")
>>>> foo<- fortune
>>>> remove.packages("fortunes")
>>>> q("yes")
>>>> 2. Restart R.  R crashes.
>>>>
>>>> For a GUI-only user this is complicated, because although the users
>>>> sees the informative error message that "Error in loadNamespace(name)
>>>> : there is no package called 'fortunes'", s/he cannot get to the point
>>>> where it is possible to install that missing package.  The key for the
>>>> user is to understand to remove the .RData.  In order to do this, s/he
>>>> has to locate that file first.
>>>>
>>>> To simplify this, a few alternatives exists:
>>>>
>>>> 1. R reports the full path to the problematic .RData file.
>>>> 2. R renames the problematic .RData file to
>>>> erroneous_20110512-123404UTC.RData and reports the new full pathname.
>>>>
>>>> In both cases there could be the option for R to either exit, or
>>>> ignore the problematic .RData file and give the user access to the
>>>> prompt.  One could also imaging a fancy recovery feature where R
>>>> detects "erroneous" .RData files and asks the user if s/he wish to try
>>>> to load them (maybe the packages has been installed since).
>>>
>>> On Windows, the easiest way to give a GUI-only user access to the R
>>> prompt is to also install an "R (vanilla mode)" shortcut/icon on the
>>> Startup menu and Desktop (with target "...\Rgui.exe" --vanilla) in
>>> addition to the default one.
>>>
>>> /Henrik
>>>
>>>>
>>>> I'm sure there are complications to implement the above, because
>>>> .RData is loaded during startup, but that's my $.02 to this problem
>>>>
>>>> /Henrik
>>>>
>>>
>>> ______________________________________________
>>> R-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> ______________________________________________
>> R-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>



[Rd] Reproducible use case for R crash after updating R
Duncan Murdoch