From sfalcon at fhcrc.org  Mon Sep  4 16:51:55 2006
From: sfalcon at fhcrc.org (Seth Falcon)
Date: Mon, 04 Sep 2006 07:51:55 -0700
Subject: [Rd] Unexpected source() behavior in R-devel
In-Reply-To: <44FC1DED.4010500@mail.nih.gov> (Sean Davis's message of "Mon,
	04 Sep 2006 08:37:01 -0400")
References: <200609031625.57963.sdavis2@mail.nih.gov>
	<x21wqsmzie.fsf@turmalin.kubism.ku.dk>
	<59d7961d0609031427v6239ac5bp16c7b2af679e996c@mail.gmail.com>
	<x2wt8klj76.fsf@turmalin.kubism.ku.dk> <m264g4cw9w.fsf@ziti.fhcrc.org>
	<44FC1DED.4010500@mail.nih.gov>
Message-ID: <m2bqpvbs6s.fsf@ziti.fhcrc.org>

Sean Davis <sdavis2 at mail.nih.gov> writes:
> Seth Falcon wrote:
>> Peter Dalgaard <p.dalgaard at biostat.ku.dk> writes:
>>
>>   
>>> "Henrik Bengtsson" <hb at stat.berkeley.edu> writes:
>>>
>>>     
>>>> This has been reported before on r-devel, e.g. May 9, 2006 "[Rd] Seg
>>>> fault when installing package from bad repository".
>>>>
>>>> It's happening on Mac OSX when trying to download non-existing
>>>> webpages (HTTP status 404). That's all I know (not using OSX myself).
>>>>       
>>> It is not entirely obvious that it is the same problem, but it might be.
>>>
>>> This happened to me on Linux (2.3.1 on FC5), but it has only happened
>>> that one time. I don't think I did anything particularly strange
>>> earlier in that session.
>>>
>>> Of course, with 20/20 hindsight, I should have taken the core dump
>>> option...
>>>     
>>
>> I'm pretty sure this is the same issue and one that has been fixed in
>> R-devel.
>>
>>     r38716 | ripley | 2006-07-30 00:19:35 -0700 (Sun, 30 Jul 2006) | 1 line
>>     Changed paths:
>>        M /trunk/src/modules/internet/internet.c
>>         crash workaround from Seth Falcon
>>
>>
>> Sean: can you try just download.file with a URL that gives 404?  Are
>> you running an R version prior to the above commit?
>>   
> Seth,
>
> As Peter pointed out, this looks like a simple server-side issue.
> Here is the sessionInfo() from my original post.  And below is the
> output of two versions of download.file.

Yes, there is an issue with the BioC website (investigating) and I
didn't mean to imply otherwise.  For now, as you discovered, use
http://www.bioconductor.org (note the 'www').

I only responded here because of the segfault you reported which most
certainly is not a simple server-side issue :-)

Did you see the segfault with a recent R or an older one?  If more
recent, then it might be worth trying to reproduce and tracking down
the bug.




[Rd] Unexpected source() behavior in R-devel
Seth Falcon