[Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta
make check of R-alpha_2006-04-08_r37675 fails on Debian GNU/Linux 3.1 running
on an Intel P4 computer.
> version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status alpha
major 2
minor 3.0
year 2006
month 04
day08
svn rev37675
language R
version.string Version 2.3.0 alpha (2006-04-08 r37675)
I'm using ATLAS with the SSE2 extensions, and get the same error with ATLAS
3.2.1 (packages atlas2-* 3.2.1ln-15 in Debian) and 3.6.0 (packages atlas3-*
3.6.0-19 in Debian). I've also tried without external BLAS (--without-blas),
but the error still occurs.
43 (0) $ ./configure
[...]
R is now configured for i686-pc-linux-gnu
Source directory: .
Installation directory:/usr/local
C compiler:gcc -g -O2 -std=gnu99
Fortran 77 compiler: g77 -g -O2
C++ compiler: g++ -g -O2
Fortran 90/95 compiler:g77 -g -O2
Interfaces supported: X11, tcltk
External libraries:readline, BLAS(ATLAS)
Additional capabilities: PNG, JPEG, iconv, MBCS, NLS
Options enabled: R profiling
Recommended packages: yes
44 (0) $ make
[...]
45 (0) $ make check
[...]
running code in 'd-p-q-r-tests.R' ... OK
comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ...777,778d776
< Warning message:
< full precision was not achieved in 'qbeta'
make[3]: *** [d-p-q-r-tests.Rout] Error 1
[...]
46 (0) $ diff tests/d-p-q-r-tests.Rout.{save,fail}
3c3
< Version 2.3.0 alpha (2006-04-03 r37628)
---
> Version 2.3.0 alpha (2006-04-08 r37675)
791a792,793
> Warning message:
> full precision was not achieved in 'qbeta'
1073c1075
< Time elapsed: 2.53 0.03 2.55 0 0
---
> Time elapsed: 4.939 0.024 4.967 0 0
The (hopefully) interesting part of tests/d-p-q-r-tests.Rout.fail:
> ## Check q*(p* ( log ), log) = identity
> All.eq(Rbeta, qbeta(log(Pbeta), shape1 = .8, shape2 = 2, log=TRUE))
[1] TRUE
Warning message:
full precision was not achieved in 'qbeta'
Please let me know if there is more I can provide to help trace this!
--
Bjørn-Helge Mevik
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] using R in a java application
Selon Lothar Rubusch <[EMAIL PROTECTED]>: > Dear All, > > I'd like to write a little application in java wich should pass some commands > and data to R and displays the results (tables and charts) in a java frame. > First I wanted to work with Omegahat's SJava but had lots of issues already > at the installation. > > Then I heard some rumors that SJava generally is not a very active project > and runs rather buggy (that's true?). So my question is, are there > alternatives to use R in a Java application, like other libraries? What would > you recommend me? I appreciate any usefull links on that topic: Java and R. > > Thank you in advance, > Lothar Rubusch Hi, Give Rserve a shot : http://stats.math.uni-augsburg.de/Rserve/ Romain __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta
[EMAIL PROTECTED] (Bjørn-Helge Mevik) writes:
> make check of R-alpha_2006-04-08_r37675 fails on Debian GNU/Linux 3.1 running
> on an Intel P4 computer.
>
> > version
>_
> platform i686-pc-linux-gnu
> arch i686
> os linux-gnu
> system i686, linux-gnu
> status alpha
> major 2
> minor 3.0
> year 2006
> month 04
> day08
> svn rev37675
> language R
> version.string Version 2.3.0 alpha (2006-04-08 r37675)
>
> I'm using ATLAS with the SSE2 extensions, and get the same error with ATLAS
> 3.2.1 (packages atlas2-* 3.2.1ln-15 in Debian) and 3.6.0 (packages atlas3-*
> 3.6.0-19 in Debian). I've also tried without external BLAS (--without-blas),
> but the error still occurs.
>
> 43 (0) $ ./configure
> [...]
> R is now configured for i686-pc-linux-gnu
>
> Source directory: .
> Installation directory:/usr/local
>
> C compiler:gcc -g -O2 -std=gnu99
> Fortran 77 compiler: g77 -g -O2
>
> C++ compiler: g++ -g -O2
> Fortran 90/95 compiler:g77 -g -O2
>
> Interfaces supported: X11, tcltk
> External libraries:readline, BLAS(ATLAS)
> Additional capabilities: PNG, JPEG, iconv, MBCS, NLS
> Options enabled: R profiling
>
> Recommended packages: yes
>
> 44 (0) $ make
> [...]
>
> 45 (0) $ make check
> [...]
> running code in 'd-p-q-r-tests.R' ... OK
> comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ...777,778d776
> < Warning message:
> < full precision was not achieved in 'qbeta'
> make[3]: *** [d-p-q-r-tests.Rout] Error 1
> [...]
>
> 46 (0) $ diff tests/d-p-q-r-tests.Rout.{save,fail}
> 3c3
> < Version 2.3.0 alpha (2006-04-03 r37628)
> ---
> > Version 2.3.0 alpha (2006-04-08 r37675)
> 791a792,793
> > Warning message:
> > full precision was not achieved in 'qbeta'
> 1073c1075
> < Time elapsed: 2.53 0.03 2.55 0 0
> ---
> > Time elapsed: 4.939 0.024 4.967 0 0
>
> The (hopefully) interesting part of tests/d-p-q-r-tests.Rout.fail:
>
> > ## Check q*(p* ( log ), log) = identity
> > All.eq(Rbeta, qbeta(log(Pbeta), shape1 = .8, shape2 = 2, log=TRUE))
> [1] TRUE
> Warning message:
> full precision was not achieved in 'qbeta'
>
> Please let me know if there is more I can provide to help trace this!
I suspect that this is related to recent changes in the zero-finder,
and that it is relatively benign. (If it is the effect that I'm
thinking of, then the warning is spurious, and it is mainly a matter
of whether we want to try to get rid of the warning or update the
.Rout.save file.)
--
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] using R in a java application
On 9 April 2006 at 16:49, [EMAIL PROTECTED] wrote: | Selon Lothar Rubusch <[EMAIL PROTECTED]>: | > I'd like to write a little application in java wich should pass some commands | > and data to R and displays the results (tables and charts) in a java frame. | > First I wanted to work with Omegahat's SJava but had lots of issues already | > at the installation. | > | > Then I heard some rumors that SJava generally is not a very active project | > and runs rather buggy (that's true?). So my question is, are there | > alternatives to use R in a Java application, like other libraries? What would | > you recommend me? I appreciate any usefull links on that topic: Java and R. | > | > Thank you in advance, | > Lothar Rubusch | | Hi, | | Give Rserve a shot : | http://stats.math.uni-augsburg.de/Rserve/ Or maybe even rJava, also by Simon, and now on CRAN too. Dirk -- Hell, there are no rules here - we're trying to accomplish something. -- Thomas A. Edison __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] using R in a java application
> -Ursprüngliche Nachricht- > Von: Dirk Eddelbuettel <[EMAIL PROTECTED]> > Gesendet: 09.04.06 18:52:57 > An: [EMAIL PROTECTED] > CC: r-devel@r-project.org > Betreff: Re: [Rd] using R in a java application > > On 9 April 2006 at 16:49, [EMAIL PROTECTED] wrote: > | Selon Lothar Rubusch <[EMAIL PROTECTED]>: > | > I'd like to write a little application in java wich should pass some > commands > | > and data to R and displays the results (tables and charts) in a java > frame. > | > First I wanted to work with Omegahat's SJava but had lots of issues > already > | > at the installation. > | > > | > Then I heard some rumors that SJava generally is not a very active project > | > and runs rather buggy (that's true?). So my question is, are there > | > alternatives to use R in a Java application, like other libraries? What > would > | > you recommend me? I appreciate any usefull links on that topic: Java and > R. > | > > | > Thank you in advance, > | > Lothar Rubusch > | > | Hi, > | > | Give Rserve a shot : > | http://stats.math.uni-augsburg.de/Rserve/ > > Or maybe even rJava, also by Simon, and now on CRAN too. > > Dirk > > -- > Hell, there are no rules here - we're trying to accomplish something. > -- Thomas A. Edison Thank you all for your answers! I started with the link to Rserve and continued to read about the JRI interface. The JRI sounds to me slightly simplier than RServe, perhaps I'll give both a try or would you recommend me rather to one of them? Concerning RJava - well, I read that it is an interface for R applications, connecting only from R to Java (?). Thus I haven't read more about it. Lothar ___ SMS schreiben mit WEB.DE FreeMail - einfach, schnell und __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta
On Sun, 9 Apr 2006, Peter Dalgaard wrote:
[EMAIL PROTECTED] (Bjørn-Helge Mevik) writes:
make check of R-alpha_2006-04-08_r37675 fails on Debian GNU/Linux 3.1 running
on an Intel P4 computer.
version
_
platform i686-pc-linux-gnu
arch i686
os linux-gnu
system i686, linux-gnu
status alpha
major 2
minor 3.0
year 2006
month 04
day08
svn rev37675
language R
version.string Version 2.3.0 alpha (2006-04-08 r37675)
I'm using ATLAS with the SSE2 extensions, and get the same error with ATLAS
3.2.1 (packages atlas2-* 3.2.1ln-15 in Debian) and 3.6.0 (packages atlas3-*
3.6.0-19 in Debian). I've also tried without external BLAS (--without-blas),
but the error still occurs.
43 (0) $ ./configure
[...]
R is now configured for i686-pc-linux-gnu
Source directory: .
Installation directory:/usr/local
C compiler:gcc -g -O2 -std=gnu99
Fortran 77 compiler: g77 -g -O2
C++ compiler: g++ -g -O2
Fortran 90/95 compiler:g77 -g -O2
Interfaces supported: X11, tcltk
External libraries:readline, BLAS(ATLAS)
Additional capabilities: PNG, JPEG, iconv, MBCS, NLS
Options enabled: R profiling
Recommended packages: yes
44 (0) $ make
[...]
45 (0) $ make check
[...]
running code in 'd-p-q-r-tests.R' ... OK
comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ...777,778d776
< Warning message:
< full precision was not achieved in 'qbeta'
make[3]: *** [d-p-q-r-tests.Rout] Error 1
[...]
46 (0) $ diff tests/d-p-q-r-tests.Rout.{save,fail}
3c3
< Version 2.3.0 alpha (2006-04-03 r37628)
---
Version 2.3.0 alpha (2006-04-08 r37675)
791a792,793
Warning message:
full precision was not achieved in 'qbeta'
1073c1075
< Time elapsed: 2.53 0.03 2.55 0 0
---
Time elapsed: 4.939 0.024 4.967 0 0
The (hopefully) interesting part of tests/d-p-q-r-tests.Rout.fail:
## Check q*(p* ( log ), log) = identity
All.eq(Rbeta, qbeta(log(Pbeta), shape1 = .8, shape2 = 2, log=TRUE))
[1] TRUE
Warning message:
full precision was not achieved in 'qbeta'
Please let me know if there is more I can provide to help trace this!
I suspect that this is related to recent changes in the zero-finder,
and that it is relatively benign. (If it is the effect that I'm
thinking of, then the warning is spurious, and it is mainly a matter
of whether we want to try to get rid of the warning or update the
.Rout.save file.)
I am not seeing it on my platforms (FC3 x86_64 and i686 Linux with gcc
3.4.5 and 4.1.0, i386 Windows and Solaris, with various compilers) and the
zero-finder changes postdate r37675 (and qbeta does not use it). I think
several other people are testing i686 Debian, including the daiuly CRAN
package checks
I suspect it is a real (and long-standing) problem of loss of accuracy
(2.2.1 did a check but did not report the results: it seems to be a
convergence failure looking at qbeta.c). What compiler version is this?
ATLAS is not involved. You'll need to trace qbeta.c.
--
Brian D. Ripley, [EMAIL PROTECTED]
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UKFax: +44 1865 272595__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] make check of R-alpha_2006-04-08_r37675 fails: qbeta
Prof Brian Ripley <[EMAIL PROTECTED]> writes:
> >> Source directory: .
> >> Installation directory:/usr/local
> >>
> >> C compiler:gcc -g -O2 -std=gnu99
> >> Fortran 77 compiler: g77 -g -O2
> >>
> >> C++ compiler: g++ -g -O2
> >> Fortran 90/95 compiler:g77 -g -O2
> >>
> >> Interfaces supported: X11, tcltk
> >> External libraries:readline, BLAS(ATLAS)
> >> Additional capabilities: PNG, JPEG, iconv, MBCS, NLS
> >> Options enabled: R profiling
> >>
> >> Recommended packages: yes
> >>
> >> 44 (0) $ make
> >> [...]
> >>
> >> 45 (0) $ make check
> >> [...]
> >> running code in 'd-p-q-r-tests.R' ... OK
> >> comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save'
> >> ...777,778d776
> >> < Warning message:
> >> < full precision was not achieved in 'qbeta'
> >> make[3]: *** [d-p-q-r-tests.Rout] Error 1
> >> [...]
> >>
> >> 46 (0) $ diff tests/d-p-q-r-tests.Rout.{save,fail}
> >> 3c3
> >> < Version 2.3.0 alpha (2006-04-03 r37628)
> >> ---
> >>> Version 2.3.0 alpha (2006-04-08 r37675)
> >> 791a792,793
> >>> Warning message:
> >>> full precision was not achieved in 'qbeta'
> >> 1073c1075
> >> < Time elapsed: 2.53 0.03 2.55 0 0
> >> ---
> >>> Time elapsed: 4.939 0.024 4.967 0 0
> >>
> >> The (hopefully) interesting part of tests/d-p-q-r-tests.Rout.fail:
> >>
> >>> ## Check q*(p* ( log ), log) = identity
> >>> All.eq(Rbeta, qbeta(log(Pbeta), shape1 = .8, shape2 = 2, log=TRUE))
> >> [1] TRUE
> >> Warning message:
> >> full precision was not achieved in 'qbeta'
> >>
> >> Please let me know if there is more I can provide to help trace this!
> >
> > I suspect that this is related to recent changes in the zero-finder,
> > and that it is relatively benign. (If it is the effect that I'm
> > thinking of, then the warning is spurious, and it is mainly a matter
> > of whether we want to try to get rid of the warning or update the
> > .Rout.save file.)
>
> I am not seeing it on my platforms (FC3 x86_64 and i686 Linux with gcc
> 3.4.5 and 4.1.0, i386 Windows and Solaris, with various compilers) and
> the zero-finder changes postdate r37675 (and qbeta does not use it). I
> think several other people are testing i686 Debian, including the
> daiuly CRAN package checks
>
> I suspect it is a real (and long-standing) problem of loss of accuracy
> (2.2.1 did a check but did not report the results: it seems to be a
> convergence failure looking at qbeta.c). What compiler version is
> this?
>
> ATLAS is not involved. You'll need to trace qbeta.c.
I don't see it with a current version either. What happens if you
reduce the optimization level? (I've tried both "-g" and -g "-O3").
Is that -std=gnu99 bit necessary?
--
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] make check of R-alpha_2006-04-08_r37675 fails: qbeta
Prof Brian Ripley wrote: > I am not seeing it on my platforms (FC3 x86_64 and i686 Linux with gcc > 3.4.5 and 4.1.0, i386 Windows and Solaris, with various compilers) and > the zero-finder changes postdate r37675 (and qbeta does not use it). I > think several other people are testing i686 Debian, including the > daiuly CRAN package checks > > I suspect it is a real (and long-standing) problem of loss of accuracy > (2.2.1 did a check but did not report the results: it seems to be a > convergence failure looking at qbeta.c). What compiler version is > this? 1 (0) $ gcc --version gcc (GCC) 3.3.5 (Debian 1:3.3.5-13) Copyright (C) 2003 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. -- Bjørn-Helge Mevik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Run package code on R shutdown?
I'm sure I've seen this discussed before, but haven't been able to find it. I'd like some package code to be run when R is shut down (approximately when a user's .Last function would be run), to clean up properly. What is the best way to do this? Duncan Murdoch __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
