[Rd] 'make check' fails on d-p-q-r-tests (PR#9326)

2006-10-31 Thread p . c . j . kleiweg 

'make check' fails on d-p-q-r-tests:

> ##-- non central Chi^2 :
> xB <- c(2000,1e6,1e50,Inf)
> for(df in c(0.1, 1, 10))
+ for(ncp in c(0, 1, 10, 100)) stopifnot(pchisq(xB, df=df, ncp=ncp) == 1)
Error: pchisq(xB, df = df, ncp = ncp) == 1 is not all TRUE
Execution halted


Here is some more testing:

xB <- c(2000,1e6,1e50,Inf)
for(df in c(0.1, 1, 10)) for(ncp in c(0, 1, 10, 100)) { print(pchisq(xB, df=df, 
ncp=ncp)); print(pchisq(xB, df=df, ncp=ncp) == 1) }
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] FALSE FALSE FALSE  TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] FALSE FALSE FALSE  TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] FALSE FALSE FALSE  TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE

options(digits=22)
for(df in c(0.1, 1, 10)) for(ncp in c(0, 1, 10, 100)) { print(pchisq(xB, df=df, 
ncp=ncp)); print(pchisq(xB, df=df, ncp=ncp) == 1) }
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 0.9998889777 0.9998889777 0.9998889777 
1.00
[1] FALSE FALSE FALSE  TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 0.9998889777 0.9998889777 0.9998889777 
1.00
[1] FALSE FALSE FALSE  TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE
[1] 0.9998889777 0.9998889777 0.9998889777 
1.00
[1] FALSE FALSE FALSE  TRUE
[1] 1 1 1 1
[1] TRUE TRUE TRUE TRUE



--please do not edit the information below--

Version:
 platform = i686-pc-linux-gnu
 arch = i686
 os = linux-gnu
 system = i686, linux-gnu
 status = 
 major = 2
 minor = 4.0
 year = 2006
 month = 10
 day = 03
 svn rev = 39566
 language = R
 version.string = R version 2.4.0 (2006-10-03)

Locale:
[EMAIL PROTECTED];LC_NUMERIC=C;[EMAIL PROTECTED];LC_COLLATE=C;[EMAIL 
PROTECTED];[EMAIL PROTECTED];[EMAIL 
PROTECTED];LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;[EMAIL 
PROTECTED];LC_IDENTIFICATION=C

Search Path:
 .GlobalEnv, package:methods, package:stats, package:utils, package:datasets, 
package:graphics, package:grDevices, Autoloads, package:base

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[Rd] malformed manual page with 'man R' (PR#9327)

2006-10-31 Thread p . c . j . kleiweg 

I get a malformed manual page with 'man R':


WARNING:(1)FSFWARNING:(1)

NAME
   WARNING: - a language for data analysis and graphics

SYNOPSIS
   R [options] [< infile] [> outfile]
   R CMD command [arguments]

DESCRIPTION
   WARNING: ignoring environment value of R_HOME

   Start  R, a system for statistical computation and graphics, with the 
specified options, or invoke an
   R tool via the 'R CMD' interface.

(more deleted)


--please do not edit the information below--

Version:
 platform = i686-pc-linux-gnu
 arch = i686
 os = linux-gnu
 system = i686, linux-gnu
 status = 
 major = 2
 minor = 4.0
 year = 2006
 month = 10
 day = 03
 svn rev = 39566
 language = R
 version.string = R version 2.4.0 (2006-10-03)

Locale:
[EMAIL PROTECTED];LC_NUMERIC=C;[EMAIL PROTECTED];LC_COLLATE=C;[EMAIL 
PROTECTED];[EMAIL PROTECTED];[EMAIL 
PROTECTED];LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;[EMAIL 
PROTECTED];LC_IDENTIFICATION=C

Search Path:
 .GlobalEnv, package:methods, package:stats, package:utils, package:datasets, 
package:graphics, package:grDevices, Autoloads, package:base

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[Rd] lme4 install, was Re: [R] Which executable is associated with R CMD INSTALL?

2006-10-31 Thread Peter Dalgaard 

[move to r-devel, put maintainer in loop]

Patrick Connolly <[EMAIL PROTECTED]> writes:

> On Mon, 30-Oct-2006 at 04:44PM -0500, Duncan Murdoch wrote:
> 
>  
> |> Try "R CMD printenv R_HOME" and you'll find which R home directory it is 
> |> using.  You can see a lot more with "R CMD printenv" or various options 
> |> to "R CMD config".
> 
> Thanks for that information.  It knocks my theory on the head.  Pity
> that, because I might have been able to do something about it if that
> was the problem.  Now I'm at a loss to work out why lme4 installation
> cannot find Matrix, and more strangely, why nothing else gave a
> similar problem.  I think I've tried every version of lme4 and Matrix
> that has emerged since R-2.4.0 has been released.
> 
> The fact that no other Red hat user has a problem indicates the
> problem is this end; but I'm short of ideas about where to look.
> Looks like it's back to versions 6 months old -- like proprietary
> software users have to put up with. :-(

Hmmm, I can provoke this on SUSE too (I was going to ask you to try
this!):

mkdir foo
MY_R=~/misc/r-release-branch/BUILD/bin/R
R_LIBS=foo $MY_R --vanilla << EOF
 options(repos=c(CRAN="http://cran.dk.r-project.org";))
 install.packages("lme4", depend=TRUE)
EOF

This installs Matrix alright, then dies with

Warning in install.packages("lme4", depend = TRUE) :
 argument 'lib' is missing: using foo
trying URL 'http://cran.dk.r-project.org/src/contrib/lme4_0.9975-8.tar.gz'
Content type 'application/x-tar' length 235617 bytes
opened URL
==
downloaded 230Kb

* Installing *source* package 'lme4' ...
** libs

gcc -I/usr/local/src/pd/r-release-branch/BUILD/include
  -I/usr/local/src/pd/r-release-branch/BUILD/include
  -I/usr/local/include -fpic -g -O2 -std=gnu99 -c Wishart.c -o Wishart.o

In file included from Wishart.h:4,
 from Wishart.c:1:
lme4_utils.h:9:20: Matrix.h: No such file or directory
In file included from Wishart.h:4,
 from Wishart.c:1:
lme4_utils.h:25: error: syntax error before "c"
lme4_utils.h:25: warning: type defaults to `int' in declaration of `c'
lme4_utils.h:25: warning: data definition has no type or storage class
lme4_utils.h:163: error: syntax error before "cholmod_factor"
lme4_utils.h:177: error: syntax error before "cholmod_factor"
make: *** [Wishart.o] Error 1
ERROR: compilation failed for package 'lme4'

And Matrix.h is sitting happily in foo/Matrix/include/ but obviously
not getting included. Should there have been a copy inside lme4?

What is not obvious to me is how this can work anywhere...

I also tried unpacking the lme4 directory from its tarball, dropping
all files from the Matrix installed include dir into lme4/src and then

$MY_R CMD INSTALL -l foo lme4

but no go

gcc -shared -L/usr/local/lib64 -o lme4.so Matrix_stubs.o Wishart.o
glmer.o init.o lme4_utils.o lmer.o local_stubs.o pedigree.o
-L/usr/local/src/pd/r-release-branch/BUILD/lib -lRlapack
-L/usr/local/src/pd/r-release-branch/BUILD/lib -lRblas -lg2c -lm
-lgcc_s

local_stubs.o(.text+0x0): In function `M_numeric_as_chm_dense':
/home/bs/pd/tmp/lme4/src/Matrix_stubs.c:420: multiple definition of 
`M_numeric_as_chm_dense'
Matrix_stubs.o(.text+0x0):/home/bs/pd/tmp/lme4/src/Matrix_stubs.c:420: first 
defined here

local_stubs.o(.text+0x70): In function `M_dpoMatrix_chol':
/home/bs/pd/tmp/lme4/src/Matrix_stubs.c:412: multiple definition of 
`M_dpoMatrix_chol'
Matrix_stubs.o(.text+0x70):/home/bs/pd/tmp/lme4/src/Matrix_stubs.c:412: first 
defined here
..etc..

-- 
   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

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Re: [Rd] 'make check' fails on d-p-q-r-tests (PR#9326)

2006-10-31 Thread Peter Dalgaard 
[EMAIL PROTECTED] writes:

> 'make check' fails on d-p-q-r-tests:
...
> --please do not edit the information below--
> 
> Version:
>  platform = i686-pc-linux-gnu
>  arch = i686
>  os = linux-gnu
>  system = i686, linux-gnu
>  status = 
>  major = 2
>  minor = 4.0
>  year = 2006
>  month = 10
>  day = 03
>  svn rev = 39566
>  language = R
>  version.string = R version 2.4.0 (2006-10-03)
> 
> Locale:
> [EMAIL PROTECTED];LC_NUMERIC=C;[EMAIL PROTECTED];LC_COLLATE=C;[EMAIL 
> PROTECTED];[EMAIL PROTECTED];[EMAIL 
> PROTECTED];LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;[EMAIL 
> PROTECTED];LC_IDENTIFICATION=C


You need to be more specific (yes, it is unfortunate that we cannot
extract all details about Linuxen from the Version: listing). Which
distribution, did you compile youself or use a binary, and if the
former: did you set any special compiler flags?

-- 
   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

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Re: [Rd] 'make check' fails on d-p-q-r-tests (PR#9326)

2006-10-31 Thread Peter Dalgaard 
Peter Kleiweg <[EMAIL PROTECTED]> writes:

> Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 2006:
> 
> > [EMAIL PROTECTED] writes:
> > 
> > > 'make check' fails on d-p-q-r-tests:
> > ...
> > > --please do not edit the information below--
> > > 
> > > Version:
> > >  platform = i686-pc-linux-gnu
> > >  arch = i686
> > >  os = linux-gnu
> > >  system = i686, linux-gnu
> > >  status = 
> > >  major = 2
> > >  minor = 4.0
> > >  year = 2006
> > >  month = 10
> > >  day = 03
> > >  svn rev = 39566
> > >  language = R
> > >  version.string = R version 2.4.0 (2006-10-03)
> > > 
> > > Locale:
> > > [EMAIL PROTECTED];LC_NUMERIC=C;[EMAIL PROTECTED];LC_COLLATE=C;[EMAIL 
> > > PROTECTED];[EMAIL PROTECTED];[EMAIL 
> > > PROTECTED];LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;[EMAIL 
> > > PROTECTED];LC_IDENTIFICATION=C
> > 
> > 
> > You need to be more specific (yes, it is unfortunate that we cannot
> > extract all details about Linuxen from the Version: listing). Which
> > distribution, did you compile youself or use a binary, and if the
> > former: did you set any special compiler flags?
> 
> config.log:

11000 lines or so deleted, and you still didn't answer the questions

(well, I can tell that it is SUSE, and it must be an old version since
you are using the ancient 2.95.3 compilers...)

-- 
   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

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Re: [Rd] 'make check' fails on d-p-q-r-tests (PR#9326)

2006-10-31 Thread p . dalgaard 
Peter Kleiweg <[EMAIL PROTECTED]> writes:

> Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 2006:
>=20
> > [EMAIL PROTECTED] writes:
> >=20
> > > 'make check' fails on d-p-q-r-tests:
> > ...
> > > --please do not edit the information below--
> > >=20
> > > Version:
> > >  platform =3D i686-pc-linux-gnu
> > >  arch =3D i686
> > >  os =3D linux-gnu
> > >  system =3D i686, linux-gnu
> > >  status =3D=20
> > >  major =3D 2
> > >  minor =3D 4.0
> > >  year =3D 2006
> > >  month =3D 10
> > >  day =3D 03
> > >  svn rev =3D 39566
> > >  language =3D R
> > >  version.string =3D R version 2.4.0 (2006-10-03)
> > >=20
> > > Locale:
> > > [EMAIL PROTECTED];LC_NUMERIC=3DC;[EMAIL PROTECTED];LC_COLLATE=
=3DC;[EMAIL PROTECTED];[EMAIL PROTECTED];[EMAIL PROTECTED]
o;LC_NAME=3DC;LC_ADDRESS=3DC;LC_TELEPHONE=3DC;[EMAIL PROTECTED];L=
C_IDENTIFICATION=3DC
> >=20
> >=20
> > You need to be more specific (yes, it is unfortunate that we cannot
> > extract all details about Linuxen from the Version: listing). Which
> > distribution, did you compile youself or use a binary, and if the
> > former: did you set any special compiler flags?
>=20
> config.log:

11000 lines or so deleted, and you still didn't answer the questions

(well, I can tell that it is SUSE, and it must be an old version since
you are using the ancient 2.95.3 compilers...)

--=20
   O__   Peter Dalgaard =C3=98ster 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

__
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Re: [Rd] 'make check' fails on d-p-q-r-tests (PR#9326)

2006-10-31 Thread Peter Kleiweg 
Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 2006:

> Peter Kleiweg <[EMAIL PROTECTED]> writes:
> 
> > Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 2006:
> > 
> > > [EMAIL PROTECTED] writes:
> > > 
> > > > 'make check' fails on d-p-q-r-tests:
> > > ...
> > > > --please do not edit the information below--
> > > > 
> > > > Version:
> > > >  platform = i686-pc-linux-gnu
> > > >  arch = i686
> > > >  os = linux-gnu
> > > >  system = i686, linux-gnu
> > > >  status = 
> > > >  major = 2
> > > >  minor = 4.0
> > > >  year = 2006
> > > >  month = 10
> > > >  day = 03
> > > >  svn rev = 39566
> > > >  language = R
> > > >  version.string = R version 2.4.0 (2006-10-03)
> > > > 
> > > > Locale:
> > > > [EMAIL PROTECTED];LC_NUMERIC=C;[EMAIL PROTECTED];LC_COLLATE=C;[EMAIL 
> > > > PROTECTED];[EMAIL PROTECTED];[EMAIL 
> > > > PROTECTED];LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;[EMAIL 
> > > > PROTECTED];LC_IDENTIFICATION=C
> > > 
> > > 
> > > You need to be more specific (yes, it is unfortunate that we cannot
> > > extract all details about Linuxen from the Version: listing). Which
> > > distribution, did you compile youself or use a binary, and if the
> > > former: did you set any special compiler flags?
> > 
> > config.log:
> 
> 11000 lines or so deleted, and you still didn't answer the questions
>
> (well, I can tell that it is SUSE, and it must be an old version since
> you are using the ancient 2.95.3 compilers...)

Let me see...

> Which distribution

SuSE. It's right there in config.log.
And there is nothing ancient about 2.95.3 compilers. 

> did you compile youself or use a binary

I sent you config.log. That should give you a clue. 

> did you set any special compiler flags?

Did you read the first few lines of config.log?


Any questions I missed?

-- 
Peter Kleiweg
http://www.let.rug.nl/~kleiweg/

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Re: [Rd] 'make check' fails on d-p-q-r-tests (PR#9326)

2006-10-31 Thread Peter Dalgaard 
Peter Kleiweg <[EMAIL PROTECTED]> writes:

> Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 2006:
> 
> > Peter Kleiweg <[EMAIL PROTECTED]> writes:
> > 
> > > Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 2006:
> > > 
> > > > [EMAIL PROTECTED] writes:
> > > > 
> > > > > 'make check' fails on d-p-q-r-tests:
> > > > ...
> > > > > --please do not edit the information below--
> > > > > 
> > > > > Version:
> > > > >  platform = i686-pc-linux-gnu
> > > > >  arch = i686
> > > > >  os = linux-gnu
> > > > >  system = i686, linux-gnu
> > > > >  status = 
> > > > >  major = 2
> > > > >  minor = 4.0
> > > > >  year = 2006
> > > > >  month = 10
> > > > >  day = 03
> > > > >  svn rev = 39566
> > > > >  language = R
> > > > >  version.string = R version 2.4.0 (2006-10-03)
> > > > > 
> > > > > Locale:
> > > > > [EMAIL PROTECTED];LC_NUMERIC=C;[EMAIL PROTECTED];LC_COLLATE=C;[EMAIL 
> > > > > PROTECTED];[EMAIL PROTECTED];[EMAIL 
> > > > > PROTECTED];LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;[EMAIL 
> > > > > PROTECTED];LC_IDENTIFICATION=C
> > > > 
> > > > 
> > > > You need to be more specific (yes, it is unfortunate that we cannot
> > > > extract all details about Linuxen from the Version: listing). Which
> > > > distribution, did you compile youself or use a binary, and if the
> > > > former: did you set any special compiler flags?
> > > 
> > > config.log:
> > 
> > 11000 lines or so deleted, and you still didn't answer the questions
> >
> > (well, I can tell that it is SUSE, and it must be an old version since
> > you are using the ancient 2.95.3 compilers...)
> 
> Let me see...
> 
> > Which distribution
> 
> SuSE. It's right there in config.log.
> And there is nothing ancient about 2.95.3 compilers. 
> 
> > did you compile youself or use a binary
> 
> I sent you config.log. That should give you a clue. 
> 
> > did you set any special compiler flags?
> 
> Did you read the first few lines of config.log?
> 
> 
> Any questions I missed?

Why should we care? It's your problem and your job to make it easier
for maintainers to track down problems. Copying config.log to a public
mailing list could be considered thoughtless, the above is plainly
insulting. 

Maybe someone else will help you, but I have definitely lost all
interest. For your information, the problem does not occur in SUSE 9.3
and 10.0.


-- 
   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

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Re: [Rd] 'make check' fails on d-p-q-r-tests (PR#9326)

2006-10-31 Thread p . dalgaard 
Peter Kleiweg <[EMAIL PROTECTED]> writes:

> Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 2006:
>=20
> > Peter Kleiweg <[EMAIL PROTECTED]> writes:
> >=20
> > > Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 20=
06:
> > >=20
> > > > [EMAIL PROTECTED] writes:
> > > >=20
> > > > > 'make check' fails on d-p-q-r-tests:
> > > > ...
> > > > > --please do not edit the information below--
> > > > >=20
> > > > > Version:
> > > > >  platform =3D i686-pc-linux-gnu
> > > > >  arch =3D i686
> > > > >  os =3D linux-gnu
> > > > >  system =3D i686, linux-gnu
> > > > >  status =3D=20
> > > > >  major =3D 2
> > > > >  minor =3D 4.0
> > > > >  year =3D 2006
> > > > >  month =3D 10
> > > > >  day =3D 03
> > > > >  svn rev =3D 39566
> > > > >  language =3D R
> > > > >  version.string =3D R version 2.4.0 (2006-10-03)
> > > > >=20
> > > > > Locale:
> > > > > [EMAIL PROTECTED];LC_NUMERIC=3DC;[EMAIL PROTECTED];LC_COLL=
ATE=3DC;[EMAIL PROTECTED];[EMAIL PROTECTED];[EMAIL PROTECTED]
euro;LC_NAME=3DC;LC_ADDRESS=3DC;LC_TELEPHONE=3DC;[EMAIL PROTECTED]
o;LC_IDENTIFICATION=3DC
> > > >=20
> > > >=20
> > > > You need to be more specific (yes, it is unfortunate that we cannot
> > > > extract all details about Linuxen from the Version: listing). Which
> > > > distribution, did you compile youself or use a binary, and if the
> > > > former: did you set any special compiler flags?
> > >=20
> > > config.log:
> >=20
> > 11000 lines or so deleted, and you still didn't answer the questions
> >
> > (well, I can tell that it is SUSE, and it must be an old version since
> > you are using the ancient 2.95.3 compilers...)
>=20
> Let me see...
>=20
> > Which distribution
>=20
> SuSE. It's right there in config.log.
> And there is nothing ancient about 2.95.3 compilers.=20
>=20
> > did you compile youself or use a binary
>=20
> I sent you config.log. That should give you a clue.=20
>=20
> > did you set any special compiler flags?
>=20
> Did you read the first few lines of config.log?
>=20
>=20
> Any questions I missed?

Why should we care? It's your problem and your job to make it easier
for maintainers to track down problems. Copying config.log to a public
mailing list could be considered thoughtless, the above is plainly
insulting.=20

Maybe someone else will help you, but I have definitely lost all
interest. For your information, the problem does not occur in SUSE 9.3
and 10.0.


--=20
   O__   Peter Dalgaard =C3=98ster 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

__
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[Rd] Syntax Error in Rcmd check on Windows

2006-10-31 Thread Michael Hoehle 
Dear R-developers,

I am currently developing an R package called RLadyBug. When
developing under Linux "R CMD check ." works fine without a warning.
However, when I do "Rcmd check ." under Windows (version 2.4.0 and
earlier)  I get a „syntax error" when checking the examples.

This puzzles me somewhat, because a manual source("RLadyBug-Ex.R") on
Windows works fine. On the other hand, a "Rterm.exe --no-save <
RLadyBug-Ex.R" in a command shell under Windows reproduces the error.
My first guess was that the very long line was causing the problem,
but when I open RLadyBug-Ex.R in Emacs, change the coding system from
"undecided-dos" to "undecided-unix" and save the file "Rterm.exe
--no-save < RLadyBug-Ex.R" works fine

Does anybody has an idea what is causing the error and how to fix this?

Best regards,

Michael Höhle

--

---
* checking for working latex ... OK
* using log directory 'z:/Transmission/RLadyBug/..Rcheck'
* using R version 2.4.0 (2006-10-03)
* checking for file './DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RLadyBug' version '0.4-1'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'RLadyBug' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for syntax errors ... OK
* checking R files for non-ASCII characters ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* creating RLadyBug-Ex.R ... OK
* checking examples ... ERROR
Running examples in 'RLadyBug-Ex.R' failed.
The error most likely occurred in:

> ### * LBExperiment-class
>
> flush(stderr()); flush(stdout())
>
> ### Name: LBExperiment-class
> ### Title: Class "LBExperiment"
> ### Aliases: LBExperiment-class show,LBExperiment-method
> ###   plot,LBExperiment-method plot,LBExperiment,missing-method
> ###   summary,LBExperiment-method data2events,LBExperiment-method
> ###   data2events
> ### Keywords: classes
>
> ### ** Examples
>
> sim.layout <- new( "LBLayout", S0=matrix( c( 13, rep( 14, 7 ) ), ncol=4 ),
+   E0=matrix( c(  1, rep(  0, 7 ) ), ncol=4 ) )
> sim.opts <- new( "LBOptions", seed=2006,
+ LBmodel=c( "gamma", "gamma", "gamma", FALSE ),
+ ignoreData=c( FALSE, FALSE, FALSE ),
+ initBeta =list( init=0.125,
+ gamma=0.001, delta=0.001 ),
+ initBetaN=list( init=0.018,
+ gamma=0.001, delta=0.001 ),
+ initIncu=list( asis=FALSE, const=FALSE,
+ g=6.697, g.gamma=0.001, g.delta=0.001,
+ d=0.84, d.gamma=0.001,d.delta=0.001 ),
+ initInf=list( 1.772, 0.001, 0.001,
0.123, 0.001, 0.001 ),
+ initDia=list( 149.126, 0.001, 0.001,
+ 8.737, 0.001, 0.001 ) )
Error: syntax error in:
"a=list( 149.126, 0.001, 0.001,
"   8.737, 0.001, 0.001 ) )
Execution halted

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Re: [Rd] Syntax Error in Rcmd check on Windows

2006-10-31 Thread Duncan Murdoch 
On 10/31/2006 8:38 AM, Michael Hoehle wrote:
> Dear R-developers,
> 
> I am currently developing an R package called RLadyBug. When
> developing under Linux "R CMD check ." works fine without a warning.
> However, when I do "Rcmd check ." under Windows (version 2.4.0 and
> earlier)  I get a „syntax error" when checking the examples.
> 
> This puzzles me somewhat, because a manual source("RLadyBug-Ex.R") on
> Windows works fine. On the other hand, a "Rterm.exe --no-save <
> RLadyBug-Ex.R" in a command shell under Windows reproduces the error.
> My first guess was that the very long line was causing the problem,
> but when I open RLadyBug-Ex.R in Emacs, change the coding system from
> "undecided-dos" to "undecided-unix" and save the file "Rterm.exe
> --no-save < RLadyBug-Ex.R" works fine
> 
> Does anybody has an idea what is causing the error and how to fix this?

No. Could you send me the RLadyBug-Ex.R file?  I'd like to get an exact 
copy of what you have, so please put it in a .zip or other archive.  If 
you use .zip, you'll need to rename it when mailing (or just put it on a 
web page somewhere), because our mail server doesn't accept emailed .zip 
files.

Duncan Murdoch

> 
> Best regards,
> 
> Michael Höhle
> 
> --
> 
> ---
> * checking for working latex ... OK
> * using log directory 'z:/Transmission/RLadyBug/..Rcheck'
> * using R version 2.4.0 (2006-10-03)
> * checking for file './DESCRIPTION' ... OK
> * checking extension type ... Package
> * this is package 'RLadyBug' version '0.4-1'
> * checking package dependencies ... OK
> * checking if this is a source package ... OK
> * checking whether package 'RLadyBug' can be installed ... OK
> * checking package directory ... OK
> * checking for portable file names ... OK
> * checking DESCRIPTION meta-information ... OK
> * checking top-level files ... OK
> * checking index information ... OK
> * checking package subdirectories ... OK
> * checking R files for syntax errors ... OK
> * checking R files for non-ASCII characters ... OK
> * checking whether the package can be loaded ... OK
> * checking whether the package can be loaded with stated dependencies ... OK
> * checking whether the name space can be loaded with stated dependencies ... 
> OK
> * checking S3 generic/method consistency ... OK
> * checking replacement functions ... OK
> * checking foreign function calls ... OK
> * checking R code for possible problems ... OK
> * checking Rd files ... OK
> * checking Rd cross-references ... OK
> * checking for missing documentation entries ... OK
> * checking for code/documentation mismatches ... OK
> * checking Rd \usage sections ... OK
> * creating RLadyBug-Ex.R ... OK
> * checking examples ... ERROR
> Running examples in 'RLadyBug-Ex.R' failed.
> The error most likely occurred in:
> 
>> ### * LBExperiment-class
>>
>> flush(stderr()); flush(stdout())
>>
>> ### Name: LBExperiment-class
>> ### Title: Class "LBExperiment"
>> ### Aliases: LBExperiment-class show,LBExperiment-method
>> ###   plot,LBExperiment-method plot,LBExperiment,missing-method
>> ###   summary,LBExperiment-method data2events,LBExperiment-method
>> ###   data2events
>> ### Keywords: classes
>>
>> ### ** Examples
>>
>> sim.layout <- new( "LBLayout", S0=matrix( c( 13, rep( 14, 7 ) ), ncol=4 ),
> +   E0=matrix( c(  1, rep(  0, 7 ) ), ncol=4 ) )
>> sim.opts <- new( "LBOptions", seed=2006,
> + LBmodel=c( "gamma", "gamma", "gamma", FALSE ),
> + ignoreData=c( FALSE, FALSE, FALSE ),
> + initBeta =list( init=0.125,
> + gamma=0.001, delta=0.001 ),
> + initBetaN=list( init=0.018,
> + gamma=0.001, delta=0.001 ),
> + initIncu=list( asis=FALSE, const=FALSE,
> + g=6.697, g.gamma=0.001, g.delta=0.001,
> + d=0.84, d.gamma=0.001,d.delta=0.001 ),
> + initInf=list( 1.772, 0.001, 0.001,
> 0.123, 0.001, 0.001 ),
> + initDia=list( 149.126, 0.001, 0.001,
> + 8.737, 0.001, 0.001 ) )
> Error: syntax error in:
> "a=list( 149.126, 0.001, 0.001,
> "   8.737, 0.001, 0.001 ) )
> Execution halted

Is there a closing parenthesis not shown?  Because they don't balance in 
that expression.

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Re: [Rd] Syntax Error in Rcmd check on Windows

2006-10-31 Thread Peter Dalgaard 
"Michael Hoehle" <[EMAIL PROTECTED]> writes:

> Dear R-developers,
> 
> I am currently developing an R package called RLadyBug. When
> developing under Linux "R CMD check ." works fine without a warning.
> However, when I do "Rcmd check ." under Windows (version 2.4.0 and
> earlier)  I get a „syntax error" when checking the examples.
> 
> This puzzles me somewhat, because a manual source("RLadyBug-Ex.R") on
> Windows works fine. On the other hand, a "Rterm.exe --no-save <
> RLadyBug-Ex.R" in a command shell under Windows reproduces the error.
> My first guess was that the very long line was causing the problem,
> but when I open RLadyBug-Ex.R in Emacs, change the coding system from
> "undecided-dos" to "undecided-unix" and save the file "Rterm.exe
> --no-save < RLadyBug-Ex.R" works fine
> 
> Does anybody has an idea what is causing the error and how to fix this?
> 
> Best regards,
> 
> Michael H�hle


> > sim.opts <- new( "LBOptions", seed=2006,
> + LBmodel=c( "gamma", "gamma", "gamma", FALSE ),
> + ignoreData=c( FALSE, FALSE, FALSE ),
> + initBeta =list( init=0.125,
> + gamma=0.001, delta=0.001 ),
> + initBetaN=list( init=0.018,
> + gamma=0.001, delta=0.001 ),
> + initIncu=list( asis=FALSE, const=FALSE,
> + g=6.697, g.gamma=0.001, g.delta=0.001,
> + d=0.84, d.gamma=0.001,d.delta=0.001 ),
> + initInf=list( 1.772, 0.001, 0.001,
> 0.123, 0.001, 0.001 ),
> + initDia=list( 149.126, 0.001, 0.001,
> + 8.737, 0.001, 0.001 ) )
> Error: syntax error in:
> "a=list( 149.126, 0.001, 0.001,
> "   8.737, 0.001, 0.001 ) )
> Execution halted


It's a longshot, but could some funny characters have crept in around
"initDia"?? (There's a way to open it in Hex from inside Emacs, isn't
there?)

-- 
   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

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Re: [Rd] Syntax Error in Rcmd check on Windows

2006-10-31 Thread Michael Hoehle 
Hello again,

Thank you for the feedback. I put the source File on the net as

http://www.statistik.lmu.de/~hoehle/software/RLadyBug/RLadyBug-Ex.zip

In case you need the entire "..Rcheck" directory I put this as

http://www.statistik.lmu.de/~hoehle/software/RLadyBug/Rcheck.zip

The "("  ")" should balance as it runs through source without
problems. I tried to use "hexl-mode" in Emacs to look for funny
characters, but didn't find any. If I delete the "initDia" line I just
get an syntax error a few lines later...

Probably its something very stupid thats wrong, but atm I fail to see it.

Best regards,

Michael Höhle

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[Rd] setReplaceMethod

2006-10-31 Thread Robin Hankin 
Hi

If x <- 1:10then  x[5] <- 1iwill promote
x to be a complex vector.

Suppose I  have an S4 class "brob", and have functions
is.brob(), as.brob(), as.numeric() and so forth (minimal self-contained
code below).

If x is numeric (1:10, say) and y is a brob, what
is the best way to make

x[5] <- y

promote x to a brob in the same way as the complex example?

Or is this not desirable for some reason?


My first idea was to use

setReplaceMethod("[",signature("ANY","brob"), ...)

but this gives a seal error:

Error in setMethod(paste(f, "<-", sep = ""), ..., where = where) :
the method for function "[<-" and signature x="ANY", i="brob" is  
sealed and cannot be re-defined




so this can't be right.











setClass("swift",
  representation = "VIRTUAL"
  )

setClass("brob",
  representation = representation 
(x="numeric",positive="logical"),
  prototype  = list(x=numeric(),positive=logical()),
  contains   = "swift"
  )

setAs("brob", "numeric", function(from){
   out <- exp([EMAIL PROTECTED])
   [EMAIL PROTECTED] <- [EMAIL PROTECTED]
   return(out)
} )

setMethod("as.numeric",signature(x="brob"),function(x){as(x,"numeric")})
is.brob <- function(x){is(x,"brob")}

"brob" <- function(x=double(),positive){
   if(missing(positive)){
 positive <- rep(TRUE,length(x))
   }
   if(length(positive)==1){
 positive <- rep(positive,length(x))
   }
   new("brob",x=as.numeric(x),positive=positive)
}

"as.brob" <- function(x){
   if(is.brob(x)){
 return(x)
   } else if(is.complex(x)) {
 warning("imaginary parts discarded")
 return(Recall(Re(x)))
   } else if(is.glub(x)){
 warning("imaginary parts discarded")
 return(Re(x))
   } else {
 return(brob(log(abs(x)), x>=0))
   }
}

setMethod("[", "brob",
   function(x, i, j, drop){
 brob([EMAIL PROTECTED], [EMAIL PROTECTED])
   } )

setReplaceMethod("[",signature(x="brob"),
  function(x,i,j,value){
jj.x <- [EMAIL PROTECTED]
jj.pos <- [EMAIL PROTECTED]
if(is.brob(value)){
  jj.x[i] <- [EMAIL PROTECTED]
  jj.pos[i] <- [EMAIL PROTECTED]
  return(brob(x=jj.x,positive=jj.pos))
} else {
  x[i] <- as.brob(value)
  return(x)
}
  } )


setReplaceMethod("[",signature("ANY","brob"),

  function(x,i,j,value){
x <- as.brob(x)
x[i] <- as.brob(value)
return(x)
  }
  )




--
Robin Hankin
Uncertainty Analyst
National Oceanography Centre, Southampton
European Way, Southampton SO14 3ZH, UK
  tel  023-8059-7743

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[Rd] help with extended mle package?

2006-10-31 Thread Ben Bolker 

  A while back, I wrote to the list/engaged in some debate with
Peter Dalgaard about the mle() function in the stats4 package --
in particular, I wanted it to have a data= argument so that
parameters could be estimated for different sets of data with
the same minuslogl function: Peter disagreed, suggesting that
a function-defining-function (e.g. something like

minusloglfun <- function(data) {
   with(data,
  function(param1,param2) {
 [negative log-likelihood expression]
  })
) was a good solution.

  I also had some confusion/misunderstanding about the differences
between the fullcoef and coef slots within the mle object.

  Since then I've done a fair amount with my version
of mle()  [bbmle, available from
http://www.zoo.ufl.edu/bolker/R/src/bbmle_0.3.0.tar.gz ] ;


 - confidence limits estimated by spline back-fitting
(as in base mle package) OR uniroot (for higher precision/
models with non-smooth profiles) OR quadratic approximation

 - allows parameters to be specified as a named vector
rather than a named list (so you can in principle use the
same objective function for optim() or mle())

 - options for profile plots

 - anova method for mle to produce Likelihood Ratio Test
tables

 - AIC, BIC methods for single and multiple models

 - some robustness -- e.g. continues with more informative
messages if (e.g.) Hessian can't be inverted or profile
finds better fit

  I'm afraid, however, that my code is now getting somewhat
idiosyncratic and spaghetti-ish -- I ran into this particularly
when trying to add some options to the AIC method to allow
(e.g.) small-sample corrections or calculation of AIC weights
a la Burnham and Anderson.

  I did have the original goal of also extending mle in the
direction of allowing more analytic expressions for parameters
of known distributions (like Jim Lindsey's packages, but ideally (?)
more robust), but I haven't gotten there yet.  My main goal
is to make mle a practical, robust and convenient tool for
analysis ... in the long run I would love it if at least
some of my changes got rolled back into stats4.

   Anyone out there interesting in hacking on this a bit more
with me/providing some perspective on which bells and whistles
are really necessary and which are unnecessary complications?

  cheers
Ben Bolker




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Re: [Rd] Syntax Error in Rcmd check on Windows

2006-10-31 Thread Duncan Murdoch 
On 10/31/2006 8:38 AM, Michael Hoehle wrote:
> Dear R-developers,
> 
> I am currently developing an R package called RLadyBug. When
> developing under Linux "R CMD check ." works fine without a warning.
> However, when I do "Rcmd check ." under Windows (version 2.4.0 and
> earlier)  I get a „syntax error" when checking the examples.

Thanks for pointing me to the source.  I can reproduce the problem, and 
I'm fairly sure it's an R bug, not a problem in your source.  I need to 
trace through at a low level to confirm this and to work out the fix.

Duncan Murdoch

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[Rd] Some R questions

2006-10-31 Thread Vladimir Dergachev 
Hi all, 

   I am working with some large data sets (1-4 GB) and have some questions 
that I hope someone can help me with:

   1.  Is there a way to turn off garbage collector from within C interface ?
what I am trying to do is suck data from mysql (using my own C
functions) and I see that allocating each column (with about 1-4 million
items) takes between 0.5 and 1 seconds. My first thought was that it
would be nice to turn off garbage collector, allocate all the data, 
copy values and then turn the garbage collector back on.

   2.  For creating STRSXP should I be using mkChar() or mkString() to create
element values ? Is there a way to do it without allocating a cons cell 
?
(otherwise a single STRSXP with 1e6 length slows down garbage collector)

   3.   Is "row.names" attribute required for data frames and, if so, can I
use some other type besides STRSXP ?

   4.   While poking around to find out why some of my code is excessively slow
I have come upon definition of `[.data.frame` - subscription operator
for data frames, which appears to be written in R. I am wondering 
whether
I am looking at the right place and whether anyone would be interested 
in
a piece of C code optimizing it - in particular extraction of single 
element
is quite slow (i.e. calls like T[i, j]).

   thank you very much !

 Vladimir Dergachev

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[Rd] missing SIGWINCH?

2006-10-31 Thread Jon Stearley 
I have an R library which uses identify() and system(com="xterm -e  
less /a/corresponding/file") to view files when I click on an x11()  
plot.  I can successfully resize the xterm on Linux (i486) and Macos  
10.4 (G4 and G5), but NOT Macos 10.4 (Intel).  For example, on a new  
mac pro:

# in a terminal,xterm,iterm,etc:
xterm -e "printenv | less"
# the resulting xterm resizes fine - eg text wraps at resized window  
boundaries.  so i don't think the problem is in xterm (?)

# BUT, in R:
system(com="xterm -e 'printenv | less'")
# the resulting xterm DOES NOT resize fine - eg text does not wrap at  
resized window boundaries.

these both work fine on the other platforms, and i don't see any  
obviously important differences in the environment variables.  i have  
confirmed this behaviour on two different out-of-the-box mac pros.   
perhaps there is a peculiarity with R's system() on macos/intel (i  
have no idea)?

not being able to resize the resulting xterm turns out to be a major  
bummer for my application - any help towards debugging this would be  
much appreciated.  thank you!

-- 
+--+
| Jon Stearley  (505) 845-7571  (FAX 844-9297) |
| Sandia National Laboratories  Scalable Systems Integration   |
+--+

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Re: [Rd] missing SIGWINCH?

2006-10-31 Thread Simon Urbanek 
Jon,

I don't have access to a Mac Pro, so I can't test anything, but based  
on your report I found a bug in R_system that affects signal handling  
during "system" calls on Macs. Please test the current R-devel  
(39754) or R-2-4-branch (39755) to see if it solves your problem.

Thanks,
Simon

On Oct 31, 2006, at 2:48 PM, Jon Stearley wrote:

> I have an R library which uses identify() and system(com="xterm -e   
> less /a/corresponding/file") to view files when I click on an x11 
> ()  plot.  I can successfully resize the xterm on Linux (i486) and  
> Macos  10.4 (G4 and G5), but NOT Macos 10.4 (Intel).  For example,  
> on a new  mac pro:
> [...]
>

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Re: [Rd] setReplaceMethod

2006-10-31 Thread John Chambers 
There's a two-level issue here, principle and practice.

The principle is that the behavior of basic R functions on basic R data 
types is considered "sealed".  Math functions, arithmetic, etc. on basic 
vectors are not supposed to be alterable.

The function "[<-" is one of those functions.  If x is a basic vector 
type, then x[i] <- value is considered sealed.  That's what the error 
message is telling you.  (By the way setReplaceMethod() has nothing to 
do with the issue; it's just a way of relieving the programmer from 
knowing that x[i]<-value is really a call to the function "[<-"; again, 
the error message shows that.)

Since you are writing the method for x having class "ANY", that is even 
stronger than changing the behavior for a specific basic type.

If you were to convince the R management that in principle having a 
special class on the right side justified breaking the seal (and that 
would take some arguing), then there is a practical problem.

The current implementation of primitives in C code examines the first 
argument only (except for binary operators, where both arguments are 
examined).  The object is examined for having a non-basic class.  If 
it's a basic data type, no further checking for methods occurs.  So even 
if you were allowed to define the method, it wouldn't get called if x 
was a numeric vector, for example.  Changing that would require changes 
at a low level, and almost certainly add some overhead to all calls.  
Expect opposition.

Otherwise, you must define some class and only expect your assignment to 
promote x if x  inherits from that class.  Or have another function, not 
"[<-", as the generic.

By the way, your method definition is not what you wanted in any case.  
The signature you meant to have was signature(x="ANY", value = "brob").  
At least I assume it was the  right-hand side and not argument "i" that 
you meant to have class "brob".  You don't actually need the x="ANY" 
part, that is the default for omitted arguments--but it's clearer in 
this case to be explicit.



Robin Hankin wrote:
> Hi
>
> If x <- 1:10then  x[5] <- 1iwill promote
> x to be a complex vector.
>
> Suppose I  have an S4 class "brob", and have functions
> is.brob(), as.brob(), as.numeric() and so forth (minimal self-contained
> code below).
>
> If x is numeric (1:10, say) and y is a brob, what
> is the best way to make
>
> x[5] <- y
>
> promote x to a brob in the same way as the complex example?
>
> Or is this not desirable for some reason?
>
>
> My first idea was to use
>
> setReplaceMethod("[",signature("ANY","brob"), ...)
>
> but this gives a seal error:
>
> Error in setMethod(paste(f, "<-", sep = ""), ..., where = where) :
>   the method for function "[<-" and signature x="ANY", i="brob" is  
> sealed and cannot be re-defined
>
>
>
>
> so this can't be right.
>
>
>
>
>
>
>
>
>
>
>
> setClass("swift",
>   representation = "VIRTUAL"
>   )
>
> setClass("brob",
>   representation = representation 
> (x="numeric",positive="logical"),
>   prototype  = list(x=numeric(),positive=logical()),
>   contains   = "swift"
>   )
>
> setAs("brob", "numeric", function(from){
>out <- exp([EMAIL PROTECTED])
>[EMAIL PROTECTED] <- [EMAIL PROTECTED]
>return(out)
> } )
>
> setMethod("as.numeric",signature(x="brob"),function(x){as(x,"numeric")})
> is.brob <- function(x){is(x,"brob")}
>
> "brob" <- function(x=double(),positive){
>if(missing(positive)){
>  positive <- rep(TRUE,length(x))
>}
>if(length(positive)==1){
>  positive <- rep(positive,length(x))
>}
>new("brob",x=as.numeric(x),positive=positive)
> }
>
> "as.brob" <- function(x){
>if(is.brob(x)){
>  return(x)
>} else if(is.complex(x)) {
>  warning("imaginary parts discarded")
>  return(Recall(Re(x)))
>} else if(is.glub(x)){
>  warning("imaginary parts discarded")
>  return(Re(x))
>} else {
>  return(brob(log(abs(x)), x>=0))
>}
> }
>
> setMethod("[", "brob",
>function(x, i, j, drop){
>  brob([EMAIL PROTECTED], [EMAIL PROTECTED])
>} )
>
> setReplaceMethod("[",signature(x="brob"),
>   function(x,i,j,value){
> jj.x <- [EMAIL PROTECTED]
> jj.pos <- [EMAIL PROTECTED]
> if(is.brob(value)){
>   jj.x[i] <- [EMAIL PROTECTED]
>   jj.pos[i] <- [EMAIL PROTECTED]
>   return(brob(x=jj.x,positive=jj.pos))
> } else {
>   x[i] <- as.brob(value)
>   return(x)
> }
>   } )
>
>
> setReplaceMethod("[",signature("ANY","brob"),
>
>   function(x,i,j,value){
> x <- as.brob(x)
> x[i] <- as.brob(value)
> return(x)
>   }
>   )
>
>
>
>
> --
> Robin Hankin
> Unc

Re: [Rd] 'make check' fails on d-p-q-r-tests (PR#9326)

2006-10-31 Thread Peter Kleiweg 
Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 2006:

> Peter Kleiweg <[EMAIL PROTECTED]> writes:
> 
> > Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 2006:
> > 
> > > Peter Kleiweg <[EMAIL PROTECTED]> writes:
> > > 
> > > > Peter Dalgaard schreef op de 31e dag van de wijnmaand van het jaar 2006:
> > > > 
> > > > > [EMAIL PROTECTED] writes:
> > > > > 
> > > > > > 'make check' fails on d-p-q-r-tests:
> > > > > ...
> > > > > > --please do not edit the information below--
> > > > > > 
> > > > > > Version:
> > > > > >  platform = i686-pc-linux-gnu
> > > > > >  arch = i686
> > > > > >  os = linux-gnu
> > > > > >  system = i686, linux-gnu
> > > > > >  status = 
> > > > > >  major = 2
> > > > > >  minor = 4.0
> > > > > >  year = 2006
> > > > > >  month = 10
> > > > > >  day = 03
> > > > > >  svn rev = 39566
> > > > > >  language = R
> > > > > >  version.string = R version 2.4.0 (2006-10-03)
> > > > > > 
> > > > > > Locale:
> > > > > > [EMAIL PROTECTED];LC_NUMERIC=C;[EMAIL 
> > > > > > PROTECTED];LC_COLLATE=C;[EMAIL PROTECTED];[EMAIL PROTECTED];[EMAIL 
> > > > > > PROTECTED];LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;[EMAIL 
> > > > > > PROTECTED];LC_IDENTIFICATION=C
> > > > > 
> > > > > 
> > > > > You need to be more specific (yes, it is unfortunate that we cannot
> > > > > extract all details about Linuxen from the Version: listing). Which
> > > > > distribution, did you compile youself or use a binary, and if the
> > > > > former: did you set any special compiler flags?
> > > > 
> > > > config.log:
> > > 
> > > 11000 lines or so deleted, and you still didn't answer the questions
> > >
> > > (well, I can tell that it is SUSE, and it must be an old version since
> > > you are using the ancient 2.95.3 compilers...)
> > 
> > Let me see...
> > 
> > > Which distribution
> > 
> > SuSE. It's right there in config.log.
> > And there is nothing ancient about 2.95.3 compilers. 
> > 
> > > did you compile youself or use a binary
> > 
> > I sent you config.log. That should give you a clue. 
> > 
> > > did you set any special compiler flags?
> > 
> > Did you read the first few lines of config.log?
> > 
> > 
> > Any questions I missed?
> 
> Why should we care? It's your problem and your job to make it easier
> for maintainers to track down problems. Copying config.log to a public
> mailing list could be considered thoughtless, the above is plainly
> insulting. 

My problem? It is YOUR software. I guess it is your job not to 
give a fuck when people take the trouble of pointing out bugs.

> Maybe someone else will help you, but I have definitely lost all
> interest. For your information, the problem does not occur in SUSE 9.3
> and 10.0.

I am not the one in need of help. 


-- 
Peter Kleiweg
http://www.let.rug.nl/~kleiweg/

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[Rd] Error in optim(...) non-finite finite-difference value (PR#9328)

2006-10-31 Thread avbell 
Full_Name: Adrian Bell
Version: 2.2.0
OS: Windows XP Prof
Submission from: (NULL) (169.237.62.194)


Mysterious error that I do not know how to get around.

Error in optim(...) 
non-finite finite-difference value 

For me, this has occurred for methods Nelder-Mead and L-BFGS-B.

What does it mean? Is it a bug? I have tried several things including coercing
the function being optimized to be finite.

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[Rd] Argument error reporting slowness

2006-10-31 Thread McGehee, Robert 
Hello,
My work with large datasets slows down a fair amount in R 2.4.0 when I
mistakenly pass in a large dataset using an incorrect argument. That is,
the same error message for reporting an incorrect argument usage when I
pass in a 1e8 length matrix takes 3 minutes on R 2.4.0 versus 0.01
seconds on R 2.3.1 This slowness may be an unintentional side effect of
a creating a better error message for reporting bad arguments. For even
larger data sets, I have chosen to kill my R session rather than wait
out this error if mis-typing an argument name.

For instance,
## In R 2.3.1, immediate reporting
> system.time(cor(badArg = matrix(1:1e8)))
Error in cor(badArg = matrix(1:1e+07)) : unused argument(s) (badArg ...)
Timing stopped at: 0 0.01 0.02 NA NA

## In R 2.4.0, extremely slow
> system.time(cor(badArg = matrix(1:1e8)))
Error in cor(badArg = matrix(1:1e+08)) : unused argument(s) (badArg =
c(1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20,
21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56,
57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108,
109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 
Timing stopped at: 175.84 1.546 177.423 0 0

Best,
Robert

platform   x86_64-unknown-linux-gnu   
arch   x86_64 
os linux-gnu  
system x86_64, linux-gnu  
status Patched
major  2  
minor  4.0
year   2006   
month  10 
day03 
svn rev39576  
language   R  
version.string R version 2.4.0 Patched (2006-10-03 r39576)

Robert McGehee
Quantitative Analyst
Geode Capital Management, LLC
1 Post Office Square, 28th Floor | Boston, MA | 02109
Tel: 617/392-8396Fax:617/476-6389
mailto:[EMAIL PROTECTED]



This e-mail, and any attachments hereto, are intended for us...{{dropped}}

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[Rd] fields appearing in cran descriptions pages

2006-10-31 Thread Gabor Grothendieck 
What determines which fields appear in CRAN descriptions pages.
For example, for doBy there is no Date: but there is a vignette listed:

   http://cran.r-project.org/src/contrib/Descriptions/doBy.html

whereas for gsubfn there is a Date: but there is no vignette listed
(even though it has one).

  http://cran.r-project.org/src/contrib/Descriptions/gsubfn.html

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Re: [Rd] Some R questions

2006-10-31 Thread miguel manese 
Hi,

Had experience with this on doing SQLiteDF...

On 11/1/06, Vladimir Dergachev <[EMAIL PROTECTED]> wrote:
> Hi all,
>
>I am working with some large data sets (1-4 GB) and have some questions
> that I hope someone can help me with:
>
>1.  Is there a way to turn off garbage collector from within C interface ?
> what I am trying to do is suck data from mysql (using my own C
> functions) and I see that allocating each column (with about 1-4 
> million
> items) takes between 0.5 and 1 seconds. My first thought was that it
> would be nice to turn off garbage collector, allocate all the data,
> copy values and then turn the garbage collector back on.
I believe not. FWIW a numeric() vector is a chunk of memory with a
VECTOR_SEXP header and then your data contiguously allocated. If you
are desparate enough and assuming the garbage collector is indeed the
culprit, you may want to implement your own  lightweight allocVector
(the function expanded to by NEW_NUMERIC(), etc.)


>2.  For creating STRSXP should I be using mkChar() or mkString() to create
> element values ? Is there a way to do it without allocating a cons 
> cell ?
> (otherwise a single STRSXP with 1e6 length slows down garbage 
> collector)
A string vector (STRSXP) is composed of CHARSXP's. mkChar makes ar
CHARSXP, and mkString makes a STRSXP with 1 CHARSXP, more like a
shorthand for

SEXP str = NEW_CHARACTER(1);
SET_STRING_ELT(str, 0, mkChar("foo"));


>3.   Is "row.names" attribute required for data frames and, if so, can I
> use some other type besides STRSXP ?
It is required. It can be integers, for 2.4.0+


>4.   While poking around to find out why some of my code is excessively 
> slow
> I have come upon definition of `[.data.frame` - subscription operator
> for data frames, which appears to be written in R. I am wondering 
> whether
> I am looking at the right place and whether anyone would be 
> interested in
> a piece of C code optimizing it - in particular extraction of single 
> element
> is quite slow (i.e. calls like T[i, j]).
[.data.frame is such a pain to implement because there is just too
many ways to index a data frame. You may want to do a specialized
index-er that just considers the index-ing styles you use. But I think
you are not just vectorizing enough. If you have to access your data
frames like that then it must be inside some loop, which would kill
your social life.


Or, you may just use (and pour your effort on improving) SQLiteDF
http://cran.r-project.org/src/contrib/Descriptions/SQLiteDF.html


M. Manese

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Re: [Rd] (PR#9328) Error in optim(...) non-finite finite-difference

2006-10-31 Thread ripley 
No, this is not a bug in R, but a report to you by R of a problem with 
your code.  It means that the difference of two values of your function 
evaluated to a non-finite value when doing finite-differencing. 
Non-finite values are Inf, -Inf or NaN.

There is nothing to reproduce here, your version of R is long obsolete and 
you are asking a question.  Please do study the FAQ *before* posting an 
unhelpful non-bug report like this.

On Wed, 1 Nov 2006, [EMAIL PROTECTED] wrote:

> Full_Name: Adrian Bell
> Version: 2.2.0
> OS: Windows XP Prof
> Submission from: (NULL) (169.237.62.194)
>
>
> Mysterious error that I do not know how to get around.
>
> Error in optim(...)
> non-finite finite-difference value
>
> For me, this has occurred for methods Nelder-Mead and L-BFGS-B.
>
> What does it mean? Is it a bug? I have tried several things including coercing
> the function being optimized to be finite.
>
> __
> R-devel@r-project.org mailing list
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>

-- 
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

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