On 9/4/06, Sean Davis <sdavis2 at mail.nih.gov> wrote:
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.
sessionInfo()
R version 2.4.0 Under development (unstable) (2006-09-02 r39068)
> download.file('http://bioconductor.org/getBioC.R',destfile='/tmp/junk.R')
trying URL 'http://bioconductor.org/getBioC.R' Error in download.file("http://bioconductor.org/getBioC.R", destfile = "/tmp/junk.R") : cannot open URL 'http://bioconductor.org/getBioC.R' In addition: Warning message: cannot open: HTTP status was '404 Not Found'
>
download.file('http://www.bioconductor.org/getBioC.R',destfile='/tmp/junk.R')
trying URL 'http://www.bioconductor.org/getBioC.R'
Content type 'text/plain; charset=ISO-8859-1' length 1345 bytes
opened URL
==================================================
downloaded 1345 bytes
Yes, there's been some problems with the Bioconductor server the last few days, e.g. http://bioconductor.org/biocLite.R is not working either. It was down on Monday night too and then it was not possible to install any packages from them. I think they are aware of this problem, but maybe not that it is down in this very minute. I've cross-posted this reply to the bioc-devel to make sure the right person gets it. However, a HTTP 404 response should not crash R regardless. For instance, the code for install.packages() tries to download PACKAGES.gz and if missing it tries to download PACKAGES. All of a sudden I started to receive reports for OSX users that tried to install my packages from http://www.braju.com/R/ saying my code core dumped their R session. I didn't have PACKAGE.gz and it worked for everyone but OSX users. It sounds like they've located and solved this problem in R-devel by the end of July. /Henrik