Re: [Rd] R crashes when I open R files in R (PR#10402)
On 06/11/2007 9:05 AM, [EMAIL PROTECTED] wrote: > Full_Name: Jerome Lemaitre > Version: 2.6.0 > OS: Windows XP > Submission from: (NULL) (132.203.202.117) > > > Hello, > > I have recently downloaded the 2.6.0 version of R and I experience troubles > that > never happened to me with previous versions. > > I open an R session with an R shortcut in "My documents/Analyses". However, > when > I want to open R files such script using "File/open script" R crashes. I have > made some tests and it appears that the software is more prone to crash when > the > script in not located in the same folder as the R shortcut. For example, my > script may be in a subfolder: "My documents/Analyses/GLM". > > I hope you will find an easy way to fix this. We need to reproduce it first. I tried to follow your instructions, and didn't see a problem. Could you please give complete details of a reproducible way to cause the crash, starting from an R session with an empty workspace? Please be specific about the directory name, the file names, and the contents of the file you are trying to open. Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R crashes when I open R files in R (PR#10402)
Full_Name: Jerome Lemaitre Version: 2.6.0 OS: Windows XP Submission from: (NULL) (132.203.202.117) Hello, I have recently downloaded the 2.6.0 version of R and I experience troubles that never happened to me with previous versions. I open an R session with an R shortcut in "My documents/Analyses". However, when I want to open R files such script using "File/open script" R crashes. I have made some tests and it appears that the software is more prone to crash when the script in not located in the same folder as the R shortcut. For example, my script may be in a subfolder: "My documents/Analyses/GLM". I hope you will find an easy way to fix this. Thank you very much. Sincerely, __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Documentation bug in kruskal.test (PR#10404)
Full_Name: Björn Bornkamp Version: 2.6.0 OS: Windows XP Submission from: (NULL) (129.217.207.144) The literature reference in the documentation for the function kruskal.test is: Myles Hollander & Douglas A. Wolfe (1973), Nonparametric statistical inference. New York: John Wiley & Sons. Pages 115Â120. But I believe it should be Myles Hollander & Douglas A. Wolfe (1973), Nonparametric statistical methods. New York: John Wiley & Sons. Pages 115Â120. There is a different book from Jean Gibbons called "Nonparametric statistical inference", but I believe it does not describe the corrected Kruskal Wallis test statistic, when there are ties in the data... __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Misleading error message for quartz.save (PR#10406)
Full_Name: Christoph Bonitz
Version: 2.5.1
OS: Mac OS 10.4
Submission from: (NULL) (84.112.127.131)
When trying something like this:
quartz.save("/path/and/filename.pdf",type=pdf)
(notice: type=pdf instead of the correct type="pdf")
the error message is:
"Filename must be a string."
The filename actually *is* a string, the *file type* isn't, therefore the
message is misleading. Change to something like
"File type must be a string"
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Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
> "kM" == kamil Marcinkowski <[EMAIL PROTECTED]> > on Tue, 6 Nov 2007 17:02:56 -0700 writes: kM> Hello Prof Brian Ripley and list kM> There is no "d-p-q-r-tests.Rout" file, the following files do exists kM> and are being sent as attachments: kM> ./tests/d-p-q-r-tests.R , kM> ./tests/d-p-q-r-tests.Rout.save , kM> ./tests/d-p-q-r-tests.Rout.fail . Thank you , Kamil. It's only the fail one that is interesting to us (the other two are part of the R sources!). However, for attachments to make it through the anti-virus anti-spam filters, you need to give them MIME-type 'text/*' typically 'text/plain' whereas many e-mail programs nowadays just blindly put 'application/octet-stream' ... the same format that viruses are often using as well. One way to help your e-mail software to use the proper mime type, may be to rename the file to something like d-p-q-r-tests_Rout_fail.txt With regards, Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] 64-bit R-build on Mac OS X 10.4 - make check failures
On Nov 8, 2007, at 2:22 AM, Prof Brian Ripley wrote:
> I am not sure why Simon thought you should ask here
mainly because of the d-p-q-r-test - I was wondering whether it falls
in the category of too strict tests or is a more serious issue. I
can't look into it myself right now, so I was hoping someone might
have an idea ...
Thanks,
Simon
> (and not on R-sig-mac,
> say): it is almost certain these are problems with your system not R.
> For the first, use your debugger to find where the segfault
> occurred (it
> might be inadequate stack space). For the second, look at the
> values of
> dbeta(0, 0.9, 2.2, ncp = c(0, a)), and trace the C code to find out
> why
> you are not getting Inf (it is probably a broken libm function).
>
> I'd be worried about the first: the second is probably esoteric.
>
> On Wed, 7 Nov 2007, Steven McKinney wrote:
>
>> Hi all,
>>
>> I compiled 64-bit R on an Apple Mac G5 running OS X, but it failed
>> make check. Simon Urbanek suggested I post results to R-devel.
>>
>>> On Nov 6, 2007, at 10:23 PM, Steven McKinney wrote:
>>>
>>
Hi Simon,
Would you be able to give more guidance on how to compile 64-bit
libiconv for Tiger,
>>>
>>> You can get the sources from Apple and compile it:
>>> http://www.opensource.apple.com/darwinsource/tarballs/other/
>>> libiconv-13.2.tar.gz
>>>
>>> If you want to save yourself the hassle, my 64-bit build can be
>>> obtained and installed as follows:
>>> curl -s http://r.research.att.com/libiconv-quad.tar.gz | \
>>> sudo tar fvxz - -C /usr/lib
>>
>> Many thanks to Simon Urbanek for providing a 64-bit libiconv for
>> use on the Apple Mac OS X platform. This allowed compilation
>> on the Mac without having to use the '--without-iconv' switch
>> (for those of us who are not yet proficient at compiling 64-bit
>> libraries on the Mac).
>>
>> Compilation of 64-bit R succeeded, but make check did not.
>>
>> First failure was in ok-errors.R, and generated this output
>> in ok-errors.Rout.fail
>>
>>> ## bad infinite recursion / on.exit / ... interactions
>>> bar <- function() 1+1
>>> foo <- function() { on.exit(bar()); foo() }
>>> foo() # now simple "infinite recursion"
>>
>>*** caught segfault ***
>> address 0x7fffeff7ffe30, cause 'memory not mapped'
>>
>> Traceback:
>>1: foo()
>>2: foo()
>>3: foo()
>> ...
>> 2154: foo()
>> 2155: foo()
>> 2156: foo()
>> aborting ...
>>
>> Second error was in d-p-q-r-tests.Rout from this test:
>> ## dbeta(*, ncp):
>> a <- rlnorm(100)
>> stopifnot(All.eq(a, dbeta(0, 1, a, ncp=0)),
>> dbeta(0, 0.9, 2.2, ncp = c(0, a)) == Inf
>> )
>> ## the first gave 0, the 2nd NaN in R <= 2.3.0
>>
>> and generated this
>> output in d-p-q-r-tests.Rout.fail
>>
>>>
>>> ## dbeta(*, ncp):
>>> a <- rlnorm(100)
>>> stopifnot(All.eq(a, dbeta(0, 1, a, ncp=0)),
>> + dbeta(0, 0.9, 2.2, ncp = c(0, a)) == Inf
>> + )
>> Error: dbeta(0, 0.9, 2.2, ncp = c(0, a)) == Inf is not all TRUE
>> In addition: Warning message:
>> In dnbeta(x, shape1, shape2, ncp, log) : NaNs produced
>> Execution halted
>>
>> Everything else passed, so I'm not sure how serious these failures
>> are.
>>
>> I'd appreciate any suggestions about how to figure out what caused
>> these
>> failures (an inappropriate file somewhere in the path, a possible
>> bug, improper compilation commands etc.)
>>
>>
>> version information of compiled R (compilation information at end):
>>
>>
>>> sessionInfo()
>> R version 2.6.0 Patched (2007-10-29 r43302)
>> powerpc64-apple-darwin8.10.0
>>
>> locale:
>> C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] lme4_0.99875-8Matrix_0.999375-3 lattice_0.17-2
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.6.0 rcompgen_0.1-17
>>> R.Version()
>> $platform
>> [1] "powerpc64-apple-darwin8.10.0"
>>
>> $arch
>> [1] "powerpc64"
>>
>> $os
>> [1] "darwin8.10.0"
>>
>> $system
>> [1] "powerpc64, darwin8.10.0"
>>
>> $status
>> [1] "Patched"
>>
>> $major
>> [1] "2"
>>
>> $minor
>> [1] "6.0"
>>
>> $year
>> [1] "2007"
>>
>> $month
>> [1] "10"
>>
>> $day
>> [1] "29"
>>
>> $`svn rev`
>> [1] "43302"
>>
>> $language
>> [1] "R"
>>
>> $version.string
>> [1] "R version 2.6.0 Patched (2007-10-29 r43302)"
>>
>>> .Platform
>> $OS.type
>> [1] "unix"
>>
>> $file.sep
>> [1] "/"
>>
>> $dynlib.ext
>> [1] ".so"
>>
>> $GUI
>> [1] "X11"
>>
>> $endian
>> [1] "big"
>>
>> $pkgType
>> [1] "source"
>>
>> $path.sep
>> [1] ":"
>>
>> $r_arch
>> [1] ""
>>
>>>
>>
>> I built 64-bit R on Mac OS X 10.4.10 with these commands:
>>
>> export PATH='/usr/local/lib64/X11/bin:/usr/local/lib64/X11/etc:/
>> usr/local/lib64/X11/include:/usr/local/lib64/X11/lib:/usr/lib:/usr/
>> bin:/usr/local/sbin:/usr/local/bin:/bin:/usr/sbin:/sbin:/usr/local/
>> teTeX/bin/powerpc-apple-darwin-current:~/perl:~/bin'
>>
>> ./configure --host=powerpc64-apple-darwin8.10.0 --build=powerpc64-
Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
Hello list
Here are the results of the tests on R 2.6.0 patched:
> R version 2.6.0 Patched (2007-11-05 r43362)
> Copyright (C) 2007 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
...
> > str(.Machine, digits=7)
> List of 18
> $ double.eps : num 2.220446e-16
> $ double.neg.eps : num 1.110223e-16
> $ double.xmin : num 2.225074e-308
> $ double.xmax : num 1.797693e+308
> $ double.base : int 2
> $ double.digits: int 53
> $ double.rounding : int 2
> $ double.guard : int 0
> $ double.ulp.digits: int -52
> $ double.neg.ulp.digits: int -53
> $ double.exponent : int 11
> $ double.min.exp : int -1022
> $ double.max.exp : int 1024
> $ integer.max : int 2147483647
> $ sizeof.long : int 4
> $ sizeof.longlong : int 8
> $ sizeof.longdouble: int 16
> $ sizeof.pointer : int 4
>
> > dpois( 10, 10^(-290:-310), log=TRUE)
> [1] -6692.601 -6715.627 -6738.653 -6761.679 -6784.705 -6807.730
> -6830.756
> [8] -6853.782 -6876.808 -6899.834 -6922.860 -6945.886 -6968.911
> -6991.937
> [15] -7014.963 -7037.989 -7061.015 -7084.041 -Inf -
> Inf -Inf
>
> > All.eq(dpois( 10*1:2, 3e-308, log=TRUE), c(-7096.08037610806,
> -14204.2875435307))
> Error: could not find function "All.eq"
I copied the All.eq function from d-p-q-r-tests.R file and rerun he
test:
> > All.eq <- function(x,y) {
> all.equal.numeric(x,y, tolerance= 64*.Machine$double.eps,
> scale = max(0, mean(abs(x), na.rm=TRUE)))
> }
> + + + >
> > All.eq(dpois( 10*1:2, 3e-308, log=TRUE), c(-7096.08037610806,
> -14204.2875435307))
> [1] TRUE
>
Cheers,
Kamil
Kamil Marcinkowski Westgrid System Administrator
[EMAIL PROTECTED] University of Alberta site
Tel.780 492-0354 Research Computing Support
Fax.780 492-1729 Academic ICT
Edmonton, Alberta, CANADAUniversity of Alberta
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Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
Thanks a lot Kamil,
for the confirmation:
> "kM" == kamil Marcinkowski <[EMAIL PROTECTED]>
> on Thu, 8 Nov 2007 09:41:05 -0700 writes:
kM> Hello list
kM> Here are the results of the tests on R 2.6.0 patched:
>> R version 2.6.0 Patched (2007-11-05 r43362)
>> Copyright (C) 2007 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
kM> ...
>> > str(.Machine, digits=7)
>> List of 18
>> $ double.eps : num 2.220446e-16
>> $ double.neg.eps : num 1.110223e-16
>> $ double.xmin : num 2.225074e-308
>> $ double.xmax : num 1.797693e+308
>> $ double.base : int 2
>> $ double.digits: int 53
>> $ double.rounding : int 2
>> $ double.guard : int 0
>> $ double.ulp.digits: int -52
>> $ double.neg.ulp.digits: int -53
>> $ double.exponent : int 11
>> $ double.min.exp : int -1022
>> $ double.max.exp : int 1024
>> $ integer.max : int 2147483647
>> $ sizeof.long : int 4
>> $ sizeof.longlong : int 8
>> $ sizeof.longdouble: int 16
>> $ sizeof.pointer : int 4
>>
>> > dpois( 10, 10^(-290:-310), log=TRUE)
>> [1] -6692.601 -6715.627 -6738.653 -6761.679 -6784.705 -6807.730 -6830.756
>> [8] -6853.782 -6876.808 -6899.834 -6922.860 -6945.886 -6968.911 -6991.937
>> [15] -7014.963 -7037.989 -7061.015 -7084.041 -Inf -Inf -Inf
>>
>> > All.eq(dpois( 10*1:2, 3e-308, log=TRUE), c(-7096.08037610806,
>> -14204.2875435307))
>> Error: could not find function "All.eq"
kM> I copied the All.eq function from d-p-q-r-tests.R file and rerun he
kM> test:
>> > All.eq <- function(x,y) {
>> all.equal.numeric(x,y, tolerance= 64*.Machine$double.eps,
>> scale = max(0, mean(abs(x), na.rm=TRUE)))
>> }
>> + + + >
>> > All.eq(dpois( 10*1:2, 3e-308, log=TRUE), c(-7096.08037610806,
>> -14204.2875435307))
>> [1] TRUE
Very good.
So after, the SGI only has slight problems with so-called
denormalized numbers; this is not considered a big problem
and the next versions of R will have the check above, instead of
the one that gave an error.
Thank you again for your feedback!
Regards,
Martin Maechler, ETH Zurich
kM> Cheers,
kM> Kamil
kM> Kamil Marcinkowski Westgrid System Administrator
kM> [EMAIL PROTECTED] University of Alberta site
kM> Tel.780 492-0354 Research Computing Support
kM> Fax.780 492-1729 Academic ICT
kM> Edmonton, Alberta, CANADAUniversity of Alberta
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[Rd] Can a package override the default color palette?
Is it is possible for a package to override the default color palette used by "image". I've tried a few different ways, but was curious if there is an approved method. THK -- Timothy H. Keitt, University of Texas at Austin Contact info and schedule at http://www.keittlab.org/tkeitt/ Reprints at http://www.keittlab.org/tkeitt/papers/ ODF attachment? See http://www.openoffice.org/ __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] small performance enhancement suggestion (PR#10409)
Full_Name: Simon de Bernard Version: OS: Submission from: (NULL) (140.77.34.213) In src/main/dotcode.c, function RObjToCPtr, test for naok should be transferred outside of the loops... __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
