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.dun...@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<h...@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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