about that. Is it
still necessary to provide detailed information about all involved
compilers and symbol tables?
Thomas Petzoldt
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologie[EMAIL PROTECTED]
01062 Dresden http://tu-dresden.de/hyd
Excel package.
There is a mailing list for RExcel where this should be discussed. Please
re-post your message to rcom-l.
Please be sure to browse the list archives first. Have a look at the RExcel
documentation for sources of information.
Thomas
__
Not a bug. None of these numbers are exactly representable in binary, so
you can't expect accuracy of better than machine epsilon.
Please don't report things that aren't bugs to r-bugs.
-thomas
On Fri, 8 Aug 2008, [EMAIL PROTECTED] wrote:
Full_Name: Tom Wang
Ve
like antialiasing.
The gap doesn't appear in pdf().
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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On further research it looks as though this has already been fixed (though it
wasn't mentioned in NEWS, so it wasn't immediately obvious).
You could try the patched build from http://r.research.att.com/
-thomas
Thomas Lumley Assoc. Professor, Biostatist
1. This is not a bug (as you seem to realize), so it should not be sent to
r-bugs.
2. You seem to want the drop=FALSE argument to [], as in FAQ 7.5
-thomas
On Wed, 13 Aug 2008 [EMAIL PROTECTED] wrote:
Good Day,
I can understand that after indexing a single column in a matrix, R will
ckage vignette about writing models in
compiled code.
Thomas Petzoldt
Redding, Matthew wrote:
Hello R Developers,
This is my first foray into using c-code with R, so please forgive my
foolishness.
I had a look at the archives and did not find anything on this, so
hopefully I am not doubling u
additional \alias."
My question: what speaks against making this sentence more pronounced
and why not NOTE-ing a missing package alias in the package check?
Thomas Petzoldt
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologie
01062 Dresden
GERMANY
Duncan Murdoch wrote:
Thomas Petzoldt wrote:
Dear R developers,
if one uses package.skeleton() to create a new package, then a file
anRpackage.Rd with the following entries is prepared:
\name{anRpackage-package}
\alias{anRpackage-package}
\alias{anRpackage}
\docType{package}
Packages
Duncan Murdoch wrote:
On 06/10/2008 8:06 AM, Thomas Petzoldt wrote:
Duncan Murdoch wrote:
Thomas Petzoldt wrote:
Dear R developers,
if one uses package.skeleton() to create a new package, then a file
anRpackage.Rd with the following entries is prepared:
\name{anRpackage-package}
\alias
my own pdf + R code file produced using whatever tools I
choose.
> Hadley
I like Sweave, and it is also possible to include your own PDFs and R
files and then to reference them in anRpackage.Rd.
Thomas P.
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ht
hadley wickham wrote:
It may not be much work for you, but I find any additional
requirements to the package format to be a real pain. I have ~10
packages on CRAN and having to go through and add this extra
information all at once is a big hassle. R releases tend to happen in
the middle of the
e the problem of linking to
another package's library (if possible by just using "LinkingTo")
Best regards,
Thomas Baier
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have
explicit objectives on performance or validity have to be avoided.
Thomas Petzoldt
Summary and Wish-list
1 A recommendation to provide a file "foo-package.Rd" and an
\alias{foo} was already given in "Writi
use) Linux, then valgrind is an excellent tool
for this. There's some documentation in 'Writing R Extensions'. Valgrind
runs your code in a virtual machine and tracks all memory accesses, so it
often will even find bugs in C code that are hard to reproduce.
onder why is this mess happening at all?
Moreover, is this behavior considered to be a feature, or a plain bug ?
Thanks,
Thomas
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ask whether it would be possible to change this idiosyncratic behavior?
Tested with:
R version 2.8.0 Patched (2008-11-04 r46830) i386-pc-mingw32
and also
R version 2.9.0 Under development (unstable) (2008-12-03 r47039)
i386-pc-mingw32
Thanks a lot
Thomas Petzoldt
set.seed(3577) # ma
Dear Prof. Ripley,
thank you very much for the fast response. I am very grateful for all
the work that the R Core does and so I try to contribute my humble part
as a tester.
Prof Brian Ripley wrote:
On Wed, 3 Dec 2008, Thomas Petzoldt wrote:
Dear R developers,
I tried to use nlminb
NEWS, rev. 47094 now says:
o nlminb() copies names from 'start' to the parameter vector
used (for consistency with optim()).
Dear Prof. Ripley,
thank you very much for doing this.
Thomas Petzoldt
__
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ible, why is a warning issued, if a
package built with R 2.8.1 is loaded in R 2.8.0?
Thomas
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Simon,
first, I'd like to apologize, that my previous message has been sent to you
directly. I have not checked the receivers list when clicking reply in my
E-mail program.
Simon Urbanek wrote:
> On Jan 7, 2009, at 2:05 , Thomas Baier wrote:
>
>> Simon,
>>
>> Sim
this means that including is
wrong in C++?
I read "Writing R extensions" several times, but was not aware that this
was a mistake. If I replace by then it works on my
systems, but I want to be certain that there are no other side effects.
Thanks in advance for clarificati
CE exports.
I'm almost certainly missing something obvious - please point it out.
Based on the r-forge code it looks like you need library(survival) in R code in
tests/. It doesn't happen automatically like it does for examples.
-thomas
Thomas Lumley Assoc
,]
not work
This is also not a bug. The drop= option to [ controls what happens when the
subset has dimensions of length 1. If you want subset to be a data frame in
this context, use
subset <- data.frame[,'x',drop=FALSE]
and then subset[&#
Thomas Petzoldt wrote:
Prof Brian Ripley schrieb:
We've added a column at
http://cran.r-project.org/web/checks/check_summary.html
of test results using the Sun Studio compiler: it is intended that
these will be updated weekly.
The Sun Studio compiler is that used on Solaris: these
ed some way to make the implementation
easier (money, code, new approaches to the programming,...).
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
__
R-devel@r-
ndard palette isn't ideal, though.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
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he CPU usage to 100%, but
the success of ATLAS suggests that they may really be limited more by cpu
memory bandwidth. I don't know if this counts.
Other people may have different suggestions.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.
: *** [Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’
* Removing ‘/home/user/R/R-devel/library/Matrix’
Can someone help me or give me a pointer what I'm making wrong? How can
I get/include the missing shared library?
Many thanks in advance
Thomas Petzoldt
#file: config.site
t its not an
obvious error in config.site. Maybe it's because I started from a rather
minimal Fedora version, so I'll try to fix my installation.
Thank you
Thomas P.
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologiethomas.petzo...@tu-dresden.d
Just for the record:
Thomas Petzoldt wrote:
Prof Brian Ripley wrote:
This seems to be a problem with your OS installation. I have
I tested compilation on another Fedora 10 installation:
1) fresh installation from the installation DVD
(Fedora-10-x86_64-DVD.iso instead of the harddisk
some version
of the GPL or LGPL?
Also, according to the FSF, the CPL used in Ipopt is technically incompatible
with the GPL because of its choice of law clause.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington
-release-macosx-ix86/simecol-00check.html
or
http://www.r-project.org/nosvn/R.check/r-release-macosx-ix86/fxregime-00check.html
Does anybody know what's wrong here?
Thanks a lot
Thomas Petzoldt
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologiethomas.petzo.
Could you explain what you are seeing that is wrong?
In R 2.7.2, which is what I have here, it looks ok, and the NEWS file doesn't
list any changes since 2.7.1.
-thomas
On Wed, 4 Mar 2009 rha...@stat.purdue.edu wrote:
<>
This is a CRITICAL bug!!! I have verified it in
est
to use accessor functions preferably written as generics working on
returned S3 or S4 objects. I'm strongly against going back to the past S
behaviour and I wonder a little bit about this discussion. I like it to
have a clean workspace with only a few o
n
the evaluation order of the *apply family (eg, does apply process the columns
left to right, or right to left, or however it feels like?).
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUni
works may just be an
inconsistency -- as you can see from previous discussions, R often does not
effectively forbid code that shouldn't work -- or it may be bug-compatibility
with some version of S or S-PLUS.
-thomas
Thomas Lumley Assoc. Professor, Biostatistic
Wacek,
In this case I think the *tmp* dates from the days before backticks, when it
was not a legal name (it still isn't) and it was much, much harder to use
illegal names, so the collision issue really didn't exist.
You're right about the documentation.
-thomas
On S
idn't really
eventuate.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
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Please report bugs in packages to the package maintainer, NOT to r-bugs.
-thomas
On Sun, 15 Mar 2009 sar...@um.ac.ir wrote:
Full_Name: Majid Sarmad
Version: 2.8.1
OS: Linux / Windows
Submission from: (NULL) (194.225.128.135)
With thanks to Alberto Viglione, in HW.tests function of
oes seem from the documentation
that agreement with SAS is intended at least for the Pillai trace and Roy's
largest root.
We do appreciate bug reports, but it shouldn't be necessary to do all this work
to find out what you think the correct answer is.
-thomas
On Mon, 16 Mar 200
"At install time an HTML index for all vignettes is automatically
created from the \VignetteIndexEntry statements unless a file index.html
exists in directory inst/doc. This index is linked into the HTML help
system for each package."
Have I missed something?
Thanks a lot
Th
function; S3 methods will not likely be found
2: In methods("bigglm") : function 'bigglm' appears not to be generic
[This is R 2.7.2, admittedly a little ancient]
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.edu
S3 inheritance on SQLiteConnection (which works, but doesn't
extend to other DBIConnection objects, as you pointed out previously).
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
This is not a bug. You forgot to use the header=TRUE argument to read.table(),
so your variables weren't recognized as numeric.
Please don't use r-bugs unless you are sure there is a bug in R. Use r-help to
ask for help.
-thomas
On Wed, 18 Mar 2009 michael_ka...@earthlink
quot;bigglm", signature=c("formula","data"))
bigglm.data.frame<-function(formula, data, ..., chunksize=5000){
setMethod("bigglm",
c("ANY","DBIConnection"),
function(formula, data, family = gaussian(),
since reported, the 'missing values are
ignored' statement in ?quantile is wrong (or at least incomplete).
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
_
ong-format variable names are x and y and the conditions to be put in the
time variable are Before and After.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
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I've sent a fixed version 2.35-4 to CRAN. It turned out to be a fairly simple
change.
-thomas
On Tue, 31 Mar 2009, Marc Schwartz wrote:
On Mar 30, 2009, at 5:55 PM, Marc Schwartz wrote:
Hi all,
Using:
R version 2.8.1 Patched (2009-03-07 r48068)
on OSX (10.5.6) with sur
The explanation is that quote() is a primitive function and that the argument
matching rules do not apply to primitives. That section of the R Language
definition should say that primitives are excluded; it is documented in
?.Primitive.
-thomas
On Thu, 2 Apr 2009 w...@idi.ntnu.no
ng up quickly is
better than hanging indefinitely.
-thomas
On Fri, 10 Apr 2009, Uwe Ligges wrote:
S Ellison wrote:
I had the same normalizePath error recently on a new laptop, with a fresh
install of R 2.8.1 and an attempt to install lme4. First attempt:
package 'Matrix' succes
users probably don't have /dev/random
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
tlum...@u.washington.eduUniversity of Washington, Seattle
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at the C++ code I've written that is called
> from R.
>
> Primary target is Mac OS X.
Under OS X I use 'sample', which doesn't require any recompiling (or
Sampler.app, which is a GUI version)
-thomas
>
> Thanks.
>
> Ross Boylan
>
>
On Thu, 23 Feb 2006, Prof Brian Ripley wrote:
On Wed, 22 Feb 2006, Fran?ois Pinard wrote:
[...]
So, I was not expecting R, running with that option activated, to
"volunteer" white lines. :-)
But Simon said `with the documentation'. Not doing what you expected is
not a bug. Can you please
On Thu, 23 Feb 2006, Simon Urbanek wrote:
On Feb 23, 2006, at 11:14 AM, Thomas Lumley wrote:
On Thu, 23 Feb 2006, Prof Brian Ripley wrote:
On Wed, 22 Feb 2006, François Pinard wrote:
[...]
So, I was not expecting R, running with that option activated, to
"volunteer" w
ces to MPI and PVM and there is the
possibility of using a parallel BLAS to speed up linear algebra. These
won't help much unless the server is under fairly low load so that a
single program can use more than 100% of a single processor. Our
multiprocessor Opteron servers are rarely that underu
On Mon, 6 Mar 2006, Simone Giannerini wrote:
> On 3/6/06, Thomas Lumley <[EMAIL PROTECTED]> wrote:
>> On Mon, 6 Mar 2006, Simone Giannerini wrote:
>>> The environment will probably be either Unix/Linux or Solaris and the
>>> amount of RAM will be 8-16Gb, depe
Full_Name: Tom Wainwright
Version: 2.2.1 (2005-12-20 r36812)
OS: Linux (SuSE 9.3)
Submission from: (NULL) (161.55.180.38)
The as.Date function returns erroneous result for certain values using a
day-of-year format. First an example that works (last day of 1970):
> as.Date("1970.365", format="%
t;
> I wonder, is there something I should be doing first, to initialize memory?
Yes. Read section 7 of "Writing R Extensions" if you want to write a
different front-end for R.
-thomas
Thomas Lumley Assoc. Professor, B
is in r-devel of March 6, but the problem that was reported to me
involved Windows vs Linux on released versions]
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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change these values.
>
Are you *sure* you want to do this? It seems that you should be able to
use lexical scope to store this information in variables rather than
default arguments and then you can use setVar to change the variables
rather than changing the formals.
-thomas
Thoma
(2) : attempt to apply non-function
>
> but with the new.env(parent=baseenv()) it works fine. The "base"
> environment has the empty environment as a parent. So, I try to do
> the same myself, i.e. new.env(parent=new.env(parent=emptyenv())), but
> once again I get
I don&#x
On Tue, 4 Apr 2006, Andrew Finley wrote:
> Hi Thomas,
>
> Thanks for the note. I'm not sure about a lot of things. Setting the
> formal defaults then calling the function seem straight forward. I just
> assumed it would be like setting list values, or the C equivalent of
it's with other NA's.
>>
All arithmetic operatiosn on *logicals* are coerced to numeric, so if you
have two logical NAs and add them you get a numeric NA.
This isn't anything special about NAs, since you would get the same
conversion for TRUE+TRUE, and you would not get the same
s
"<-" <- function(x,value){
if(tryCatch(is.function(x),error=function(e) FALSE))
stop("assignment to an existing function")
else eval.parent(substitute(.Primitive("<-")(x,value)))
}
-thomas
Th
checked as part of R CMD check?
>
The rationale may be that a demo is entitled to assume it is being run
interactively. Checking demo(tkdensity), for example, would be
unproductive.
-thomas
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Full_Name: Thomas Friedrichsmeier
Version: R 2.2.1
OS: Debian / Linux
Submission from: (NULL) (84.60.123.243)
Wishlist item:
There is a small problem using intall.packages() (and update.packages()):
Typically I want to install packages for system-wide use, not in a user
directory. Obviously
to (and there may well be), I
think adding some convenience option for this particular case may well be
worth while.
Regards
Thomas
pgpsRa2e77DYM.pgp
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:
for (i = 0; i < n; i++)
LOGICAL(ans)[i] = ISNAN(REAL(x)[i]);
break;
and it's hard to see how that can be improved. It does suggest that a
faster anyNA() function would have to not be generic.
-thomas
Thomas Lumley Assoc. Professo
On Mon, 10 Apr 2006, Duncan Murdoch wrote:
> On 4/10/2006 7:22 PM, Thomas Lumley wrote:
>> On Mon, 10 Apr 2006, Henrik Bengtsson wrote:
>>
>>> Suggestion 2:
>>> Create a has.na(x) function to replace any(is.na(x)) that returns TRUE
>>> as soon as a
ckages.
>
> By the way, I think Bill's suggestion of calling it anyMissing makes a
> lot of sense.
>
Here we agree.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
__
rious error
> from an infinite one.)
>
> We could try even harder, but code that is almost never used tends to get
> broken whilst no one is testing it. So if you want to pursue it I think
> we need a comprehensive test suite.
I have actually been working with log-link glms qui
em (for values of N of
> 5000, 25000, 50000 -- should I try others?)
No, it's the C stack, not the R pointer protection stack.
With tcsh this is
limits stacksize 5
or ulimit with bash
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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/check).
>
Also, according to
http://www.cyrusharmon.org/cl/blog/display/49
SBCL uses SIGSEGV as an internal signalling mechanism, which might
conflict with the new segfault catcher.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED]
e a heuristic check somewhat
like
if (abs (R_CStackStart - &i) > 2) {
/* Very unlikely we're this far away from the stack start at
this
point in the code. Disable checking */
R_CStackStart = -1;
}
Regards
T
me for being impatient, but *please* consider this for
inclusion in R 2.3.0.
Regards
Thomas
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riable-length argument lists such as printf's, whether or
not prototypes are in scope), values of type float are promoted to
double, and printf therefore sees only doubles.
I assume this applies to Rprintf as well
-thomas
>
> On Sun, 16 Apr 2006, Kasper Daniel Han
ted
again, below, fixes the problem.
Regards
Thomas
On Monday 17 April 2006 15:20, Thomas Friedrichsmeier wrote:
> Excuse me please, for being impatient, but I'm worried this issue may not
> be considered important enough to be fixed in R 2.3.0 at this late point of
> time. So let
Sorry, I wasn't aware, .c files would be scrubbed. Testcase available for
download here:
http://rkward.sourceforge.net/temp/threadEmbed.c
On Monday 17 April 2006 21:11, Thomas Friedrichsmeier wrote:
> Sorry about all the noise, but I'm slightly irritated by the absence of
> react
ot;
Apparently not so. Then why does an empty string get "split" to a non-existent
string?
Note: I don't really care much about what the behavior is, but if the
described behavior is indeed intended, I think it should be documented. IMO
it's pretty counter intuitive.
Regards
Thomas
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eq(61.56,62,by=0.01) you would have
benefitted from the fact that, although (62-61.56)/0.01 is very slightly
less than 44, seq() still includes the 44th step. In general, though, R
is better off using as much accuracy as possible for a given computation
rather than trying to guess what a user w
available and defines the source as "the preferred form of the work for
making modifications to it." If the .tar.gz packages are not the source,
then, under the GPL, CRAN is required to provide the source as well, which
doesn't seem to be an improvement.
-thomas
Thom
usually prudent to
code as if the garbage collector is out to get you, unless you are doing
deep recursion or other types of coding where running out of pointer
protection stack is a real concern.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTE
n, text, prompt) : syntax error in:
# "print ("hello")
# print ("world")"
Probably there are not too many use cases of parse (n=x) with x not either -1
or 1, so it should not be a grave problem, but it just doesn't look right.
Regards
Thomas
pgpe609NxvQLc
e source code package.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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r C compiler flags on SGI.
If you have a 64bit build then something strange is happening. The message
you quote happens only when malloc() returns NULL, so it is hard to see
how R could be causing it, though.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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ll compiler/linker
flags to work, not just -L/-l
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington, Seattle
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if you use more PROTECTs. On the other hand, R does detect them for you.
If you don't use enough PROTECTs you get bugs that are very hard to track
down [the best bet is probably valgrind + gctorture() to provoke them into
showing themselves early, but that's only available on Linux].
On Wed, 17 May 2006, Michael Dondrup wrote:
> Thank you very much, Thomas!
>
> Thanks to the explanation, I think I could almost track down that bug. May I,
> just for clarification, ask a further bunch of questions (sorry). From what
> you say, did I get it right:
>
>
how to get the output you
wanted.
If R were really giving completely wrong answers for a very simple and
widely used analysis and no-one had noticed, an example would still have
been needed to make this a useful bug report.
-thomas
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rsion server is svn.r-project.org if
you want to check out current code, or there are daily snapshots at
ftp://ftp.stat.math.ethz.ch/Software/R
r-devel is the right place for patches, or r-bugs if it really is a bug fix.
-thomas
Thomas Lumley Assoc. Professor, Biostatis
s
> to add this to DEFS in Makeconf after configuring.
>
> Probably in due course there will be a way to do it via configure and
> config.h, but I do not see one.
>
Yes, adding the -DR_MEMORY_PROFILING to CFLAGS is the intended way to do
it at the moment. In due course there will be
gram.c is part of
the source distribution. Would is not be better to always generate gram.c
from gram.y instead of providing gram.y and gram.c?
Best regards
--
===
Dipl.-Inform. Thomas Dreibholz
Universit
On Wednesday 31 May 2006 15:26, Prof Brian Ripley wrote:
> On Wed, 31 May 2006, Thomas Dreibholz wrote:
> > Hi!
> >
> > Attached to this mail, you find a patch for gram.y setting a #define
> > CONTEXT_STACK_SIZE for the context stack size and replacing the following
collector is a
generational mark-and-sweep collector, not reference counted at all.
NAMED is about preserving the "call-by-value illusion" -- an object with
NAMED=0 or 1 can be modified without copying it -- which seems to be
exactly the problem in PR#7924.
-thomas
> Ke
On Wed, 7 Jun 2006, Kevin B. Hendricks wrote:
>
> Inline is the patch to fix bug 7924.
>
Yes, that seems to fix it. Committed.
-thomas
Thomas Lumley Assoc. Professor, Biostatistics
[EMAIL PROTECTED] University of Washington
Full_Name: Thomas Ruf
Version: 2.3.1
OS: Windows XP home
Submission from: (NULL) (193.154.219.1)
Having created a large Menu with many submenus, R crashed (with an error message
from Windows) when adding another submenu using winMenuAddItem. The problems
seems to be caused by a limit on the
Ruuid is a Bioconductor package; please report bugs to Bioconductor as
they ask.
-thomas
On Mon, 12 Jun 2006, [EMAIL PROTECTED] wrote:
>> source("http://www.bioconductor.org/biocLite.R";)
>> biocLite(c("Ruuid"))
> Running getBioC version 0
> # But fn2() works if n=100
No, it just looks as though it does. I suspect you have a data frame
called data, with 100 rows, in your workspace.
In a clean copy of R I get
> fn2(y ~ x, data=A);
Error in runif(n, min, max) : invalid arguments
-thomas
Thomas
t; predict method?
I would look at bs() and ns() in the splines package.
-thomas
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