Re: [Rd] S4 changes - sp fails
On Fri, 1 Sep 2006, John Chambers wrote:
> General comments. A number of packages will likely be showing weird
> warnings on attach() about packages being out of date. Likely caused by
> a confusion when two packages define the same generic. The bug is being
> worked on, but there are some issues of package design that will need
> discussion later.
>
> Early revisions with the new code did have a C-level problem but that is
> now fixed AFAIK, so any hard evidence of protection problems would be
> valuable.
>From 39062 on a fresh login, R and offending package fresh on the machine
with problems reported earlier, no failure. With 39062 on my usual login
but after a thorough make distclean and control over errant R_LIBS, no
failure. This morning with make distclean and updates to methods - svn
39076, no failure. So I think the failures were probably provoked by stale
software components as Brian Ripley suggested, rather than by unresolved
methods package issues as such. Happily, rgdal (depends on sp) also
passed check at R 39076.
Roger
>
> There have been some changes, up to svn revision 39037 at the moment,
> but there will be some more. All reports are appreciated. Some are
> easier for me to check out than others (I'm working from a home setup
> that does not have all of CRAN available (!) so it takes time to test a
> package with many dependencies in "CMD check"s view of things.)
>
> John
>
>
> Roger Bivand wrote:
> > On Fri, 1 Sep 2006, Roger Bivand wrote:
> >
> >
> >> On Fri, 1 Sep 2006, Prof Brian Ripley wrote:
> >>
> >>
> >>> Since writing that, I have found that there is a similar problem with
> >>> testing mvoutliers (which does load sp), and it depends on exactly what
> >>> has been done in what order. (I'll forward to you the exact description.)
> >>>
> >
> > On a different RHEL 4 i386 with R version 2.4.0 (2006-09-01 r39049), and
> > fully updated sp CVS from
> >
> > cvs -z3 -d:pserver:[EMAIL PROTECTED]:/cvsroot/r-spatial checkout sp
> >
> > CND check sp passes with no error (with RColorBrewer the only installed
> > package in a test library).
> >
> > I'll try again on the first machine (which is also RHEL 4 i386, but where
> > R was at 2006-08-31 r39045, and where there may have been configuration
> > issues (wrong library path?).
> >
> > Roger
> >
> >
> >> Thanks.
> >>
> >> I reran the interactive test:
> >>
> >> library(sp, lib.loc="sp.Rcheck")
> >> example("DMS-class")
> >>
> >> which ran without problems.
> >>
> >>
> >>> .libPaths()
> >>>
> >> [1] "/home/rsb/topics/r_libs"
> >> [2] "/home/rsb/topics/Rtobe240/lib/R/library"
> >>
> >>> list.files(.libPaths()[1])
> >>>
> >> [1] "abind""maptools" "pixmap" "RColorBrewer" "R.css"
> >>
> >> [6] "rgdal""SparseM" "spdep""tripack"
> >>
> >>> sessionInfo()
> >>>
> >> R version 2.4.0 Under development (unstable) (2006-08-31 r39045)
> >> i686-pc-linux-gnu
> >>
> >> locale:
> >> LC_CTYPE=en_GB;LC_NUMERIC=C;LC_TIME=en_GB;LC_COLLATE=en_GB;LC_MONETARY=en_GB;LC_
> >> MESSAGES=en_GB;LC_PAPER=en_GB;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREME
> >> NT=en_GB;LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets"
> >> [7] "base"
> >>
> >> other attached packages:
> >> sp
> >> "0.8-19"
> >>
> >>
> >>> I now suspect there is a protection problem in the new S4 dispatch code.
> >>> Using gctorture/valgrind may help locate it.
> >>>
> >> Running check --use-gct sp now.
> >>
> >> Roger
> >>
> >>
> >>> Brian
> >>>
> >>> On Fri, 1 Sep 2006, Roger Bivand wrote:
> >>>
> >>>
> On Fri, 1 Sep 2006, Prof Brian Ripley wrote:
>
>
> > Roger,
> >
> > I had managed to run R CMD check on sp successfully on r39021 and
> > r39043
> > (current) in my nightly checks. (There are a couple of tests where the
> > show/print method is not being invoked, but that is not new.)
> >
> > All I can suggest is to install R from scratch (make distclean), and
> > then
> > reinstall all relevant packages. At a guess, your interactive use and
> > R
> > CMD check are picking up different libraries.
> >
> Brian,
>
> I added .libPaths() and sessionInfo() to the offending example, and tried
> with a fresh svn checkout built in a fresh directory and installed in a
> fresh directory (no sp or methods in /home/rsb/topics/r_libs, which was
> set with export R_LIBS=):
>
>
> > data(state)
> > .libPaths()
> >
> [1] "/home/rsb/topics/packages/sp-bundle/sp.Rcheck"
> [2] "/home/rsb/topics/r_libs"
> [3] "/home/rsb/topics/Rtobe240/lib/R/library"
>
> > sessionInfo()
> >
> R version 2.4.0 Under development (
[Rd] lm, weights and ...
> lm2 <- function(...) lm(...) > lm2(mpg ~ wt, data=mtcars) Call: lm(formula = ..1, data = ..2) Coefficients: (Intercept) wt 37.285 -5.344 > lm2(mpg ~ wt, weights=cyl, data=mtcars) Error in eval(expr, envir, enclos) : ..2 used in an incorrect context, no ... to look in Can anyone explain why this is happening? (Obviously this is a manufactured example, but it crops up in ggplot when you want to provide a function to perform smoothing) Thanks, Hadley __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Internal flag for S4 objects
A recent revision (svn version 39077) has introduced an internal flag (a bit in the C structure) that is turned on by the code that generates objects from an S4 class. There are corresponding tests for an S4 object, isS4() in R and IS_S4_OBJECT() in C. These are fast and reliable, and should replace any heuristic tests previously used. The tests are not currently used widely, but in the future could be combined with some of the other recent changes to improve reliability and efficiency of computations with S4 objects. Most such changes are more likely for 2.5.x than 2.4.0. S4 objects in saved sessions and other binary files will not have the bit set, so they should be regenerated. A likely symptom that you have not done so is that the objects will not print automatically with the standard S4 method, because the internal code now checks for an S4 object before dispatching show(). John __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] lm, weights and ...
"hadley wickham" <[EMAIL PROTECTED]> writes: > > lm2 <- function(...) lm(...) > > lm2(mpg ~ wt, data=mtcars) > > Call: > lm(formula = ..1, data = ..2) > > Coefficients: > (Intercept) wt > 37.285 -5.344 > > > lm2(mpg ~ wt, weights=cyl, data=mtcars) > Error in eval(expr, envir, enclos) : ..2 used in an incorrect context, > no ... to look in > > > Can anyone explain why this is happening? (Obviously this is a > manufactured example, but it crops up in ggplot when you want to > provide a function to perform smoothing) Presumably this is due to the nonstandard evaluation of the weights argument. This is a long story, the short version is that the argument ought to have been designed to be a model formula, but we haven't been willing to sacrifice S-PLUS compatibility. A more extensive white-paper on the issues, written by Thomas Lumley, is at http://developer.r-project.org/nonstandard-eval.pdf -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Internal flag for S4 objects
John Chambers wrote: > A recent revision (svn version 39077) has introduced an internal flag (a > bit in the C structure) that is turned on by the code that generates > objects from an S4 class. > > There are corresponding tests for an S4 object, isS4() in R and > IS_S4_OBJECT() in C. These are fast and reliable, and should replace > any heuristic tests previously used. > > The tests are not currently used widely, but in the future could be > combined with some of the other recent changes to improve reliability > and efficiency of computations with S4 objects. Most such changes are > more likely for 2.5.x than 2.4.0. > > S4 objects in saved sessions and other binary files will not have the > bit set, so they should be regenerated. A likely symptom that you have > not done so is that the objects will not print automatically with the > standard S4 method, because the internal code now checks for an S4 > object before dispatching show(). > > John Dear R-devel testers under Windows, this means that I won't upload the newly built Windows binary packages right now, but I will rebuild all of them again under current R-devel tomorrow. They won't appear on CRAN master before Wednesday. In the meantime, the link to R-2.3.x packages will remain active and some packages simply won't work. Best, Uwe Ligges __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] lm, weights and ...
If you change it to: lm3 <- function(...) eval.parent(substitute(lm(...))) then it works. > lm3(mpg ~ wt, weights=cyl, data=mtcars) Call: lm(formula = mpg ~ wt, data = mtcars, weights = cyl) Coefficients: (Intercept) wt 35.50-4.91 On 9/3/06, hadley wickham <[EMAIL PROTECTED]> wrote: > > lm2 <- function(...) lm(...) > > lm2(mpg ~ wt, data=mtcars) > > Call: > lm(formula = ..1, data = ..2) > > Coefficients: > (Intercept) wt > 37.285 -5.344 > > > lm2(mpg ~ wt, weights=cyl, data=mtcars) > Error in eval(expr, envir, enclos) : ..2 used in an incorrect context, > no ... to look in > > > Can anyone explain why this is happening? (Obviously this is a > manufactured example, but it crops up in ggplot when you want to > provide a function to perform smoothing) > > Thanks, > > Hadley > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Unexpected source() behavior in R-devel
Why am I seeing the following in R-devel (sept 2, 2006 build) on opensuse
10.1? I'm sure it is something simple I am missing, but I just don't see it
(output below).
Thanks,
Sean
> readLines(url("http://www.bioconductor.org/biocLite.R";))
[1] "source(\"http://bioconductor.org/getBioC.R\";)"
[2] ""
[3] "biocLite <- function(pkgs, groupName=\"lite\", ...)"
[4] "{"
[5] "if (missing(pkgs))"
[6] "getBioC(groupName=groupName, ...)"
[7] "else"
[8] "getBioC(pkgs=pkgs, groupName=groupName, ...)"
[9] "}"
> source(url("http://www.bioconductor.org/biocLite.R";))
Error in file(file, "r", encoding = encoding) :
unable to open connection
In addition: Warning message:
cannot open: HTTP status was '404 Not Found'
> sessionInfo()
R version 2.4.0 Under development (unstable) (2006-09-02 r39068)
x86_64-unknown-linux-gnu
locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
attached base packages:
[1] "methods" "stats" "graphics" "grDevices" "utils" "datasets"
[7] "base"
>
__
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Re: [Rd] Unexpected source() behavior in R-devel
Sean Davis <[EMAIL PROTECTED]> writes:
> Why am I seeing the following in R-devel (sept 2, 2006 build) on opensuse
> 10.1? I'm sure it is something simple I am missing, but I just don't see it
> (output below).
>
> Thanks,
> Sean
>
>
> > readLines(url("http://www.bioconductor.org/biocLite.R";))
> [1] "source(\"http://bioconductor.org/getBioC.R\";)"
> [2] ""
> [3] "biocLite <- function(pkgs, groupName=\"lite\", ...)"
> [4] "{"
> [5] "if (missing(pkgs))"
> [6] "getBioC(groupName=groupName, ...)"
> [7] "else"
> [8] "getBioC(pkgs=pkgs, groupName=groupName, ...)"
> [9] "}"
> > source(url("http://www.bioconductor.org/biocLite.R";))
> Error in file(file, "r", encoding = encoding) :
> unable to open connection
> In addition: Warning message:
> cannot open: HTTP status was '404 Not Found'
> > sessionInfo()
> R version 2.4.0 Under development (unstable) (2006-09-02 r39068)
> x86_64-unknown-linux-gnu
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets"
> [7] "base"
> >
Hmm, something is up. I got
> source(url("http://www.bioconductor.org/biocLite.R";))
Error in file(file, "r", encoding = encoding) :
unable to open connection
In addition: Warning message:
cannot open: HTTP status was '404 Not Found'
> source(url("http://www.bioconductor.org/biocLite.R";))
*** caught segfault ***
address 0x21, cause 'memory not mapped'
Traceback:
1: file(file, "r", encoding = encoding)
2: source("http://bioconductor.org/getBioC.R";)
3: eval.with.vis(expr, envir, enclos)
4: eval.with.vis(ei, envir)
5: source(url("http://www.bioconductor.org/biocLite.R";))
Possible actions:
1: abort (with core dump)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
Oops...
The immediate cause would seem to be that
http://bioconductor.org/getBioC.R is non-existent (needs to be
www.bioconductor.org).
That's a server-side issue, not an R problem, but what was that bit
with the segfault? I can't seem to reproduce it in a fresh session.
--
O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Unexpected source() behavior in R-devel
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).
/Henrik
On 03 Sep 2006 23:06:01 +0200, Peter Dalgaard <[EMAIL PROTECTED]> wrote:
> Sean Davis <[EMAIL PROTECTED]> writes:
>
> > Why am I seeing the following in R-devel (sept 2, 2006 build) on opensuse
> > 10.1? I'm sure it is something simple I am missing, but I just don't see it
> > (output below).
> >
> > Thanks,
> > Sean
> >
> >
> > > readLines(url("http://www.bioconductor.org/biocLite.R";))
> > [1] "source(\"http://bioconductor.org/getBioC.R\";)"
> > [2] ""
> > [3] "biocLite <- function(pkgs, groupName=\"lite\", ...)"
> > [4] "{"
> > [5] "if (missing(pkgs))"
> > [6] "getBioC(groupName=groupName, ...)"
> > [7] "else"
> > [8] "getBioC(pkgs=pkgs, groupName=groupName, ...)"
> > [9] "}"
> > > source(url("http://www.bioconductor.org/biocLite.R";))
> > Error in file(file, "r", encoding = encoding) :
> > unable to open connection
> > In addition: Warning message:
> > cannot open: HTTP status was '404 Not Found'
> > > sessionInfo()
> > R version 2.4.0 Under development (unstable) (2006-09-02 r39068)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets"
> > [7] "base"
> > >
>
> Hmm, something is up. I got
>
> > source(url("http://www.bioconductor.org/biocLite.R";))
> Error in file(file, "r", encoding = encoding) :
> unable to open connection
> In addition: Warning message:
> cannot open: HTTP status was '404 Not Found'
> > source(url("http://www.bioconductor.org/biocLite.R";))
>
> *** caught segfault ***
> address 0x21, cause 'memory not mapped'
>
> Traceback:
> 1: file(file, "r", encoding = encoding)
> 2: source("http://bioconductor.org/getBioC.R";)
> 3: eval.with.vis(expr, envir, enclos)
> 4: eval.with.vis(ei, envir)
> 5: source(url("http://www.bioconductor.org/biocLite.R";))
>
> Possible actions:
> 1: abort (with core dump)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
>
> Oops...
>
> The immediate cause would seem to be that
> http://bioconductor.org/getBioC.R is non-existent (needs to be
> www.bioconductor.org).
>
> That's a server-side issue, not an R problem, but what was that bit
> with the segfault? I can't seem to reproduce it in a fresh session.
>
> --
>O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B
> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
> (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
> ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
>
__
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Re: [Rd] Unexpected source() behavior in R-devel
"Henrik Bengtsson" <[EMAIL PROTECTED]> 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... > > Possible actions: > > 1: abort (with core dump) > > 2: normal R exit > > 3: exit R without saving workspace > > 4: exit R saving workspace -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Unexpected source() behavior in R-devel
Peter Dalgaard wrote:
> Sean Davis <[EMAIL PROTECTED]> writes:
>
>
>> Why am I seeing the following in R-devel (sept 2, 2006 build) on opensuse
>> 10.1? I'm sure it is something simple I am missing, but I just don't see it
>> (output below).
>>
>> Thanks,
>> Sean
>>
>>
>>
>>> readLines(url("http://www.bioconductor.org/biocLite.R";))
>>>
>> [1] "source(\"http://bioconductor.org/getBioC.R\";)"
>> [2] ""
>> [3] "biocLite <- function(pkgs, groupName=\"lite\", ...)"
>> [4] "{"
>> [5] "if (missing(pkgs))"
>> [6] "getBioC(groupName=groupName, ...)"
>> [7] "else"
>> [8] "getBioC(pkgs=pkgs, groupName=groupName, ...)"
>> [9] "}"
>>
>>> source(url("http://www.bioconductor.org/biocLite.R";))
>>>
>> Error in file(file, "r", encoding = encoding) :
>> unable to open connection
>> In addition: Warning message:
>> cannot open: HTTP status was '404 Not Found'
>>
>>> sessionInfo()
>>>
>> R version 2.4.0 Under development (unstable) (2006-09-02 r39068)
>> x86_64-unknown-linux-gnu
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] "methods" "stats" "graphics" "grDevices" "utils" "datasets"
>> [7] "base"
>>
>
> Hmm, something is up. I got
>
>
>> source(url("http://www.bioconductor.org/biocLite.R";))
>>
> Error in file(file, "r", encoding = encoding) :
> unable to open connection
> In addition: Warning message:
> cannot open: HTTP status was '404 Not Found'
>
>> source(url("http://www.bioconductor.org/biocLite.R";))
>>
>
> *** caught segfault ***
> address 0x21, cause 'memory not mapped'
>
> Traceback:
> 1: file(file, "r", encoding = encoding)
> 2: source("http://bioconductor.org/getBioC.R";)
> 3: eval.with.vis(expr, envir, enclos)
> 4: eval.with.vis(ei, envir)
> 5: source(url("http://www.bioconductor.org/biocLite.R";))
>
> Possible actions:
> 1: abort (with core dump)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
> Selection:
>
>
> Oops...
>
> The immediate cause would seem to be that
> http://bioconductor.org/getBioC.R is non-existent (needs to be
> www.bioconductor.org).
>
> That's a server-side issue, not an R problem, but what was that bit
> with the segfault? I can't seem to reproduce it in a fresh session.
>
>
Thanks, Peter, for pointing out the obvious. I'll talk to the bioc folks.
On that other point, I have not gotten any segmentation faults so far.
If I do, I'll repost.
Sean
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Re: [Rd] Unexpected source() behavior in R-devel
Peter Dalgaard <[EMAIL PROTECTED]> writes: > "Henrik Bengtsson" <[EMAIL PROTECTED]> 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? Bw, + seth __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Unexpected source() behavior in R-devel
Seth Falcon wrote:
> Peter Dalgaard <[EMAIL PROTECTED]> writes:
>
>
>> "Henrik Bengtsson" <[EMAIL PROTECTED]> 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
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Re: [Rd] Unexpected source() behavior in R-devel
On 9/4/06, Sean Davis <[EMAIL PROTECTED]> wrote:
> Seth Falcon wrote:
> > Peter Dalgaard <[EMAIL PROTECTED]> writes:
> >
> >
> >> "Henrik Bengtsson" <[EMAIL PROTECTED]> 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
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