It seems that it's an old bug that was found in some other packages, but
at that time not optim:
https://bugs.r-project.org/bugzilla/show_bug.cgi?id=15958
and that Duncan Murdoch posted a patch already last Friday :)
Thomas
Am 06.05.2019 um 16:40 schrieb Ben Bolker:
That's consistent/not
Am 02.09.2016 um 16:02 schrieb Dirk Eddelbuettel:
On 2 September 2016 at 14:54, Thomas Petzoldt wrote:
| Hi,
|
| I have the same problem and, at a first look, the issues reported by the
| CRAN checks seemed easy to fix. However, after checking it again locally
| and on http://win-builder.r
_
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
--
Dr. Thomas Petzoldt
Technische Universitaet Dresden
Faculty of Environmental Sciences
Institute of Hydrobiology
01062 Dresden, Germany
Tel.: +49 351 463 34954
Fax: +49 351 463 37108
E-Mail: tho
functions worked as expected. See example below.
The symptom is that super assignments (<<-) of unmodified variables lead
to "references" instead of copies.
Thomas Petzoldt and Karline Soetaert
## --
## Unexpected behavior:
#
On 13.09.2013 16:44, Prof Brian Ripley wrote:
On 13/09/2013 15:14, Duncan Murdoch wrote:
On 13/09/2013 10:01 AM, Thomas Petzoldt wrote:
Dear R developers,
I found a small issue while plotting contours of data containing both
"usual" and "very small" numbers. It appeared w
YPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
--
Dr. Thomas Petzoldt
Technische Universitaet Dresden
Faculty of Environmental Sciences
Institute of
our help and the great R system!
Thomas P.
--
Thomas Petzoldt
Technische Universitaet Dresden
Faculty of Environmental Sciences
Institute of Hydrobiology
01062 Dresden, Germany
E-Mail: thomas.petzo...@tu-dresden.de
http://tu-dresden.de/Members/thomas.petzo
On 18.04.2013 18:05, José Matos wrote:
On Thursday 18 April 2013 17:38:06 Thomas Petzoldt wrote:
Dear R developers,
I've got an information from Prof. Ripley regarding a bug found
with AdressSanitizer in one of our packages. It is now fixed, thank
you for this information.
Now, I would
ere a recommendation of a suitable Linux distribution with gcc 4.8,
ideally an ISO image or (even better) a virtual appliance for VMware or
VirtalBox? My Debian Wheezy machines have only 4.7.2.
Thank you
Thomas Petzoldt
--
Dr. Thomas Petzoldt
Technische Universitaet Dresden
Faculty of Environm
Thanks to you all for your great work!
Thomas Petzoldt
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On 17.09.2010 20:04, Prof Brian Ripley wrote:
I'm not sure why end users would be using R-devel rather than R-alpha at
this point, but I have already changed R-devel to allow Matrix to get
updated before it fails.
Yes I realized the update and successfully recompiled it. Many thanks.
"End user
On 17.09.2010 19:22, Uwe Ligges wrote:
On 17.09.2010 16:04, Thomas Petzoldt wrote:
Dear R-Devel,
I've just tried to compile the fresh R-devel and found that the install
of package Matrix failed:
-
** help
*** installing help indices
** bui
(save = FALSE)
ERROR: installing package indices failed
-
possible reason: Matrix/data/*.R
News.Rd says:
The \code{save} argument of \code{require()} is defunct.
Thomas Petzoldt
__
R-devel@r-project.org ma
Bill Dunlap,
Matthew Doyle and you (Martyn Plummer). I've also setup a new Linux test
system, so that next time valgrind checks can be performed before
package upload.
Thank you!
Thomas Petzoldt
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On 16.09.2010 17:05, Martyn Plummer wrote:
Dear Thomas,
Is this the deSolve package?
http://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/deSolve-00check.html
I can help you with that. It does pass R CMD check on my OpenSolaris
installation, but I am getting some compiler warnings. I w
to ask about a possibility to run
a few tests on such a system:
r-patched-solaris-x86
An even more recent version of R on the same OS (Solaris 10) and with
the same compiler (Sun Studio 12u1) would help also.
Any assistance is appreciated
Thomas Petzoldt
--
Thomas Petzoldt
Technische Unive
Am 25.02.2010 06:33, wrote Ben:
Wow, thanks for the heads-up. That is horrible behavior. But using
baseenv() doesn't seem like the solution either. I'm new to proto,
but it seems like this is also a big drawback:
z<- 1
proto(baseenv(), expr={a=z})$a
Error in eval(expr, envir, enclos) : obje
if CRAN
would use the \VignetteIndexEntry , but file name ordering (without the
extension) is also ok.
Thomas Petzoldt
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologiethomas.petzo...@tu-dresden.de
01062 Dresden
her special files like NEWS
and LICENSE (as found in MASS) or THANKS (like in Hmisc)?
Thanks for consideration.
Thomas Petzoldt
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Duncan Murdoch wrote:
[...]
The doc directory is known to be visible. It might surprise someone if
arbitrary directories were visible, and readable by any user.
2) The change will introduce additional work for package authors
that used internal links within their packages. I can, of course,
Duncan Murdoch wrote:
Thomas Petzoldt wrote:
[...]
This is fine, but in contrast to older versions (<= 2.9.2) no
automatic index is created for the linked directory, so we now get:
"URL /library/foo/examples/ was not found"
but linking to *individual files* (e.g. examp
would much prefer if a default index would be created for the directory
if no index.html is found.
I very much enjoy the new help system and would be even more happy if
that issue could be fixed.
Thomas Petzoldt
PS: A minimal reproducible example (foo_1.0.tar.gz) can be provided by
mai
package.
The code suggestion was tested with R-devel rev. 49803 and several
contributed packages and we found no negative side effects. Please find
the suggested patch below and please excuse if we overlooked something.
Thanks for your consideration
Best wishes,
Karline Soet
ers use
Fortran). This can be done in a mixed style and even a full C to C
communication is possible (see the deSolve documentation how to do this
with differential equation models).
Thomas P.
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologiethomas.petzo..
"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
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
-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.
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
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
: *** [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
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
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
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
__
R-devel@r-project.o
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
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
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
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
Dear Hadley,
thank you very much for your comments.
hadley wickham wrote:
- there are lots of packages without one, so this would create a lot of
work for people to add them.
No, I don't think that this is too much work. Positively speaking, it's one
small contribution to bring more light into
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
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
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
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
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
Full_Name: Thomas Petzoldt
Version: R 2.8.0 devel, svn version 45389
OS: Linux x86/64 Ubuntu 7.1
Submission from: (NULL) (217.235.62.12)
In contrast to all other tested operating systems a call of Fortran functions on
Linux x86/64 requires an appended underscore.
The problem occured with
MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> Search Path:
>> .GlobalEnv, package:deSolve, package:stats, package:graphics,
>> package:grDevices, package:utils, package:datasets, packag
Thomas Petzoldt schrieb:
Martin Maechler wrote:
"TP" == Thomas Petzoldt <[EMAIL PROTECTED]>
on Sun, 16 Mar 2008 13:50:55 +0100 writes:
TP> Hello, I wonder why the control parameter REPORT is not
TP> supported by method SANN. Looking into optim.c I found
TP
Martin Maechler wrote:
>>>>>> "TP" == Thomas Petzoldt <[EMAIL PROTECTED]>
>>>>>> on Sun, 16 Mar 2008 13:50:55 +0100 writes:
>
> TP> Hello, I wonder why the control parameter REPORT is not
> TP> supported by metho
Ben Bolker wrote:
> optim ignores misspelled control parameters, so that trying
> to set (e.g.) "maxint=1000" in the control argument silently
> does nothing. The patch below (watch out for line breaks! also
> posted at http://www.zoo.ufl.edu/bolker/optim_patch.R , and
> http://www.zoo.ufl.ed
nREPORT to samin and setting
something like:
STEPS = nREPORT / tmax
Thomas P.
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologie[EMAIL PROTECTED]
01062 Dresden http://tu-dresden.de/hydrobiologie/
GERMANY
Hi Gabor,
nice to see you on this thread.
As you see, I'm back with my old problem.
Gabor Grothendieck wrote:
> If the intention is to place fList's contents in the global
> environment
> then you need to specify that in addtoenv or else it assumes
> the parent environment.
No, it was the in
Duncan Murdoch wrote:
> On 1/21/2008 9:58 AM, Thomas Petzoldt wrote:
>> Hello Duncan,
>>
>> thank you very much for your prompt reply. When I interpret your answer
>> correctly there seems to be no alternative than either:
>>
>> A) using lots of (possibly pri
it
requires lots of "obsolete code". I already had this idea but found it
awkward because it would look more like Pascal where one has separate
interface and implementation.
Duncan Murdoch wrote:
> On 1/21/2008 8:30 AM, Thomas Petzoldt wrote:
>> Hello,
>>
>> firs
blem, trivial
m2()
# Error in bar() : could not find function "foo"
m3()
# works, but even in that case we get problems
# if we do this in a package:
# * checking R code for possible problems ... NOTE
# bar: no visible global function definition for 'foo'
## tested with R versio
untb_1.3-2.tar.gz passed the check just now on my system: R 2.7.0
Under development (unstable), svn rev 43092 (5. Oct), i386-pc-mingw32
Thomas P.
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologie[EMAIL PROTECTED]
01062 Dresden
use tryCatch.
>
> Best,
>
> luke
>
> On Mon, 27 Aug 2007, Thomas Petzoldt wrote:
>
>> Hello,
>>
>> is it *really intentional* that the "silent" option of try() does only
>> apply to the outer call in nested try constructs? I would assume that a
>
), silent=TRUE)
Error in exp(NULL) : Non-numeric argument to mathematical function
>
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut fuer Hydrobiologie
01062 Dresden
GERMANY
http://tu-dresden.de/Members/thomas.petzoldt
__
R-devel
Dear Prof.Ripley, Dear Seth,
thank you both, including tcltk in Depends as suggested by Prof. Ripley
immediately helped to silence the tcltk NOTEs, but Seth is also right.
It is in fact not the ultimate solution for the Suggests case, that I
intentionally used like in Seth's code example.
Thom
toplevel'
My question:
- Is this an indication of a serious problem?
- How can one avoid (or if not possible suppress) these messages?
Thanks in advance
Thomas P.
OS: WinXP Prof., German
R 2.6.0, svn-rev. 41910, 2007-06-11
--
Thomas Petzoldt
Technische Universitaet Dresden
Institut
Seth Falcon wrote:
> Thomas Petzoldt <[EMAIL PROTECTED]> writes:
>> One odd thing I found was that initialize does obviously not allow to
>> incorporate additional named parameters which are not slots.
>
> ?! Does for me:
Your example works but one can not a
to lose multiple dispatch when defining
> constructors.
>
> + seth
>
>
> [*1*] The default initialize method interprets named arguments as
> slots which is a reasonable default, but not always sensible. What I
> find quite strange is that an un-named argumen
Hello,
apologies if I missed something well known. I'm just revising an own
package and wonder if it is still common to use "generating
functions" which have the same name as the corresponding S4 class as
suggested by Chambers, 2001. "Classes and Methods in the S Language".
-- or should one conse
Full_Name: Thomas Petzoldt
Version: R 2.2.0 alpha
OS: Windows
Submission from: (NULL) (141.30.20.2)
Symptom:
If one moves a source tree to another drive letter, a following compile will
fail when compiling grDevices.
The bug is found on Windows only.
Reason:
When performing a "make
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