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

[Henrik Bengtsson]

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:

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

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
>>>
>>
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>
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