dea that they were designing what became Apple Silicon). I presume it would be
possible to leverage the Apple matrix co-processor for fp128 operations (e.g.,
PowerPC used double-double arithmetics implementation as a precedent), but
given the low priority I have not seen it yet.
Cheers,
Simon
On Ap
As one of original 30-some members of 1985 IEEE 754, I find it discouraging that
we are treating long-double as the exception, when it is the introduction of
"short double" in M1 etc chips that have forced the issue. There are strong
commercial reasons, but they aren't computational ones.
JN
On
I've had an email from CRAN team that the revdep failure with phenofit is a
known issue and
updated optimx package (fixing glitch in computing approximate Hessian when
objective uses dot args)
is on its way to CRAN.
John Nash
__
R-package-devel@r-p
In correcting a minor bug in the optimx package, I submitted a new version
today.
The existing CRAN version (2024-12.2) has all CRAN checks OK, and to my
knowledge
no notifications of bugs. The new version has hit a FAIL with package phenofit
revdep.
Wanting to have output from a "working" syst
This is a question about how things are done rather than a request for a fix.
Yesterday I re-submitted my optimx package with some small but important fixes
(e.g., one place where one solver would miss catching function evaluation
limits).
I'd done a revdepcheck that came up with "Wow, no proble
In answer to my own posting about this, I found the following partially
answers what I need.
The task is to display a file (in my case a pdf, for which 'xdisp' contains
the string for the command to do this. See below for the reason this is a
variable. The displayed file has information I will ne
Hi,
I'm trying to prepare a package to manage some diverse data. It is
extremely convenient to display a PDF derived from the data so the user
can verify information that the R script is going to process (even nicer
if on a 2 monitor system). I've 2 issues:
1) I can display the pdf either with f
On the other hand, Rmpfr did allow me to write an mpfr rootfinder for Martin M.
in 2011
(he modified and streamlined it for use) since one can run R codes on mpfr
objects
as long as one is careful which operators are applied. So one probably could do
something with a very pedestrian eigenvalue m
Yes. An initial space does the trick. Thanks. J
On 2023-11-03 11:48, Serguei Sokol wrote:
Le 03/11/2023 à 15:54, J C Nash a écrit :
I've spent a couple of hours with an Rmarkdown document where I
was describing some spherical coordinates made up of a radius r and
some angles. I wanted t
I've spent a couple of hours with an Rmarkdown document where I
was describing some spherical coordinates made up of a radius r and
some angles. I wanted to fix the radius at 1.
In my Rmarkdown text I wrote
Thus we have `r = 1` ...
This caused failure to render with "unexpected =". I was usi
Thanks. That seems to be the issue. Also vincent's suggestion of checkRd.
JN
On 2023-10-22 10:52, Ivan Krylov wrote:
On Sun, 22 Oct 2023 10:43:08 -0400
J C Nash wrote:
\itemize{
\item{fnchk OK;}{ \code{excode} = 0;
\code{infeasible} = FALSE}
I'm doing a major update of the optimx package and things were going relatively
smoothly until this weekend when files that have passed win-builder gave NOTEs
on r-devel for several manual (.Rd) files.
The NOTE is of the form
* checking Rd files ... NOTE
checkRd: (-1) fnchk.Rd:40-41: Lost braces
his nature. Spencer Graves
On 9/2/23 4:23 PM, Greg Hunt wrote:
The percent encoded characters appear to be valid in that URL, suggesting
that rejecting them is an error. That kind of error could occur when the
software processing them converts them back to a non-unicode character set.
On Sun,
I'm posting this in case it helps some other developers getting build failure.
Recently package nlsr that I maintain got a message that it failed to build on
some platforms. The exact source of the problem is still to be illuminated,
but seems to be in knitr::render and/or pandoc or an unfortunat
My nlsr package was revised mid-February. After CRAN approved it, I got a
message that it was "failing" M1Mac tests. The issue turned out to be ANOTHER
package that was being used in an example in a vignette. Because M1 does not
provide the IEEE 754 80 bit registers, a method in package minqa did
The important information is in the body of the man page for news(),
i.e., found by
?utils::news
and this explains why putting an "o" in front of a line clears the
NOTE. Once I realized that CRAN is running this, I could see the
"why". Thanks.
JN
On 2023-07-26 10:25, Duncan Murdoch wrote:
there are plans to use NEWS for some purpose in
the future i.e., to actually track changes beyond package maintainer's
comments?
Cheers, and thanks again.
JN
On 2023-07-26 10:03, Ivan Krylov wrote:
В Wed, 26 Jul 2023 09:37:38 -0400
J C Nash пишет:
I'd like to avoid NOTEs if pos
In work on an upgrade to my optimx package, I added to my (plain text) NEWS
file.
The lines
VERSION 2023-06-25
o This is a MAJOR revision and overhaul of the optimx package and its
components.
o Fixed CITATION file based on R CMD check --as-cran complaints
regarding requi
In updating my nlsr package, I ran R CMD check --as-cran and got an error
that /usr/lib/R/doc/html/katex/katex.js was not found.
I installed the (large!) r-cran-katex. No joy.
katex.js was in /usr/share/R/doc/html/katex/ so I created a symlink. Then
I got katex-config.js not found (but in 1 dir
Recently I updated my package nlsr and it passed all the usual checks and was
uploaded to CRAN. A few days later I got a message that I should "fix" my
package as it had failed in "M1max" tests.
The "error" was actually a failure in a DIFFERENT package that was used as
an example in a vignette. I
FWIW: optimx::optimx is outdated and only there for legacy use.
Better to use the optimx::optimr() function for single solvers.
JN
On 2022-11-25 05:10, Ivan Krylov wrote:
В Fri, 25 Nov 2022 09:59:10 +
"ROTOLO, Federico /FR" пишет:
When submitting my package parfm, I get the following no
I'd second Uwe's point. I was one of 31 signatories to first IEEE 754 (I didn't
participate in
the two more recent releases, as I already tore my hair out with the details of
low level
bit manipulations). Before the standard, porting code was truly a nightmare. We
did it
because we had to and w
I think this is similar in nature (though not detail) to an issue raised
on StackOverflow where the OP used "x" in dot args and it clashed with the
"x" in a numDeriv call in my optimx package. I've got a very early fix (I
think), though moderators on StackOverflow were unpleasant enough to
delete
> On 12.06.2021 16:39, J C Nash wrote:
>> Two minor notes:
>>
>> 1) The Writing R Extensions manual, as far as I can determine, does not
>> inform package
>> developers that Makevars.win needs to be in the src/ subdirectory. I
>> followed the example
>
install with "makevars.win", I
got a
WARNING on running a CHECK until I replaced it with "Makevars.win", i.e.,
Camel-case
name.
Do these observations merit edits in the manual?
JN
On 2021-06-11 11:16 a.m., J C Nash wrote:
> After some flailing around, discover
2021-06-10 9:37 a.m., Dirk Eddelbuettel wrote:
>
> On 10 June 2021 at 09:22, J C Nash wrote:
> | Thanks to help from Duncan Murdoch, we have extracted the nls()
> functionality to a package nlspkg and are building
> | an nlsalt package. We can then run nlspkg::AFunction() and
>
E=C
> [11] LC_MEASUREMENT=en_CA.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] compiler_4.1.0
>>
On 20
Hi,
I'm mentoring Arkajyoti Bhattacharjee for the Google Summer of Code project
"Improvements to nls()".
Thanks to help from Duncan Murdoch, we have extracted the nls() functionality
to a package nlspkg and are building
an nlsalt package. We can then run nlspkg::AFunction() and nlsalt::AFunctio
.R>,
>>>> is.symmetric.matrix
>>>> <https://rdrr.io/cran/matrixcalc/src/R/is.symmetric.matrix.R>, and
>>>> is.positive.definite
>>>> <https://rdrr.io/cran/matrixcalc/src/R/is.positive.definite.R>) and
>>> there
>>>
I just downloaded the source matrixcalc package to see what it contained. The
functions
I looked at seem fairly straightforward and the OP could likely develop
equivalent features
in his own code, possibly avoiding a function call. Avoiding the function
call means NAMESPACE etc. are not involved,
On 16/04/2021 9:49 a.m., J C Nash wrote:
>> Another approach is to change the responsibility.
>>
>> My feeling is that tests in the TESTING package should be modifiable by the
>> maintainer of
>> the TESTED package, with both packages suspended if the two maintainers
Another approach is to change the responsibility.
My feeling is that tests in the TESTING package should be modifiable by the
maintainer of
the TESTED package, with both packages suspended if the two maintainers cannot
agree. We
need to be able to move forward when legacy behaviour is outdated o
Possibly the "old" site-library is not getting over-written. I had to
manually delete.
See https://www.mail-archive.com/r-help@r-project.org/msg259132.html
JN
On 2020-07-28 7:21 a.m., Dirk Eddelbuettel wrote:
>
> Hi Adelchi,
>
> On 28 July 2020 at 11:46, Adelchi Azzalini wrote:
> | When I upda
Are you sure you want to try to run R etc. under Wine?
- If you have Windows running, either directly or in a VM, you can run R there.
- If you have Windows and want to run R under some other OS, then set up a VM
e.g., Linux Mint, for that. I sometimes test R for Windows in a VirtualBox VM
for Win
I'm seeking some general advice about including vignettes in my packages,
which are largely for nonlinear estimation and function minimization
(optimization).
This means that my packages offer alternatives to many other tools, and the user
then has the chore of deciding which is appropriate. Bad c
ch <mailto:murdoch.dun...@gmail.com>> wrote:
>
> On 07/06/2019 12:32 p.m., William Dunlap wrote:
> > The length-condition-not-equal-to-one checks will cause R to shutdown
> > even if the code in a tryCatch().
>
> That's strange. I'm unable
FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
>>>
>>> The || operator works on length 1 Booleans. Since fval can be of
>> length
>>> greater than 1 at that point, the proper condition seems to be:
>>>
>>> any(is.infinite(fval)) || any(is.
E FALSE FALSE FALSE FALSE FALSE FALSE FALSE
>
> The || operator works on length 1 Booleans. Since fval can be of length
> greater than 1 at that point, the proper condition seems to be:
>
> any(is.infinite(fval)) || any(is.na(fval))
>
> Best regards,
>
> Sebast
ptimization do not violate some conditions e.g., character rather than
numeric etc.
JN
On 2019-06-07 8:44 a.m., J C Nash wrote:
> Uwe Ligges ||gge@ @end|ng |rom @t@t|@t|k@tu-dortmund@de
> Fri Jun 7 11:44:37 CEST 2019
>
> Previous message (by thread): [R-pkg-devel] try() in R C
After making a small fix to my optimx package, I ran my usual R CMD check
--as-cran.
To my surprise, I got two ERRORs unrelated to the change. The errors popped up
in
a routine designed to check the call to the user objective function. In
particular,
one check is that the size of vectors is the
There is a quite well-developed but not terribly large C program
for conjugate gradients and similar approaches to optimization I would
like to wrap in a package for use in R. I would then build this into the
optimx package I maintain. I suspect that the approach may turn out to be
one of the most
very call gives a different environment (but all have the same parent):
>
> ea <- TraceSetup_2(fn = function(x) x^2 - 2*x + 1)
>> ls(ea)
> [1] "fn" "ftrace" "gr" "ifn""igr"
>> ea$fn
> function(x) x^2 - 2*x + 1
ersity
> Hamilton, Ontario, Canada
> Web: https://socialsciences.mcmaster.ca/jfox/
>
>
>
>> -Original Message-
>> From: R-package-devel [mailto:r-package-devel-boun...@r-project.org] On
>> Behalf Of J C Nash
>> Sent: Monday, August 27, 2018 8
> TraceSetup -> -> registerNames
> Execution halted
Also had to use utils::globalVariables( ...
JN
On 2018-08-27 08:40 PM, Richard M. Heiberger wrote:
> Does this solve the problem?
>
> if (getRversion() >= '2.15.1')
> globalVariables(c('envroot
In order to track progress of a variety of rootfinding or optimization
routines that don't report some information I want, I'm using the
following setup (this one for rootfinding).
TraceSetup <- function(ifn=0, igr=0, ftrace=FALSE, fn=NA, gr=NA){
# JN: Define globals here
groot<-list(ifn=ifn, i
Will pending queries to CRAN-submissions about false positives in the check
process be cleared
first, or left pending? I've been waiting quite a while re: new optimx package,
which has 1 so-called "ERROR" (non-convergence, please use a different method
msg)
and 1 WARNING because new optimx subsum
I think several of us have had similar issues lately. You might have seen my
posts on reverse dependencies.
It seems there are some sensitivities in the CRAN test setup, though I think
things are improving.
Last week I submitted optimx again. I don't think I changed anything but the
date and so
Excuses for the length of this, but optimx has a lot of packages
using it.
Over the past couple of months, I have been struggling with checking
a new, and much augmented, optimx package. It offers some serious
improvements:
- parameter scaling on all methods
- two safeguarded Newton methods
For the past few weeks I've been struggling to check a new version of optimx
that gives
a major upgrade to the 2013 version currently on CRAN and subsumes several
other packages.
It seems to work fine, and pass Win-builder, R CMD check etc.
However, both devtools and cran reverse dependency che
It occurs to me that there could be packages developed by early career R
developers that might fit
this prize which is considered quite prestigious (not to mention the cash) in
the numerical methods community.
It is also likely that people may not be aware of the award in the R community.
Cheers
If NOTEs are going to be treated as errors, then a lot of infrastructure (all my
packages for optimization and nonlinear modelling, which are dependencies of
a few dozen other packages etc.) will disappear. This is because they have
version
numbering I've been using in some form that pre-dates R a
> Georgi Boshnakov
>
>
>
>
>
> From: R-package-devel [r-package-devel-boun...@r-project.org] on behalf of J
> C Nash [profjcn...@gmail.com]
> Sent: 11 April 2018 19:05
> To: List r-package-devel
> Subject: [R-pkg-devel] Saving output of check()
utput from these is not capturable/sinkable
> by the master R process. The gist of what's happening is:
>
>> sink("output.log")
>> system("echo hello") ## not sinked/captured
> hello
>> sink()
>> readLines("output.log")
&g
p.
Best, JN
On 2018-04-11 03:24 PM, Henrik Bengtsson wrote:
> R CMD check, which is used internally runs checks in standalone
> background R processes. Output from these is not capturable/sinkable
> by the master R process. The gist of what's happening is:
>
>> sink(
al. I'm running Linux Mint
18.3 Sylvia.
Linux john-j6-18 4.10.0-38-generic #42~16.04.1-Ubuntu SMP Tue Oct 10 16:32:20
UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
john@john-j6-18 ~ $ R
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
J C Nash
___
Duncan's observation is correct. The background work to the standards
I worked on was a big effort, and the content was a lot smaller than R,
though possibly similar in scope to dealing with the current question.
The "voting" was also very late in the process, after the proposals
were developed, di
Having been around a while and part of several programming language and
other standards (see ISO 6373:1984 and IEEE 754-1985), I prefer some democracy
at the
level of getting a standard. Though perhaps at the design level I can agree
with Hadley. However, we're now at the stage of needing to clean
Although I have been working with R for quite a while, I still find some issues
of dependencies troubling. In particular, my optimr package is set up to allow
users to access many function minimization tools via a single wrapper. In the
past
I've had notices from CRAN to fix things when called pa
15.03.2017 18:30, Ben Bolker wrote:
On 17-03-15 11:09 AM, J C Nash wrote:
Possibly tangential, but has there been any effort to set up a Sparc
testbed? It
seems we could use a network-available (virtual?) machine, since this
platform is
often the unfortunate one. Unless, of course, there
Possibly tangential, but has there been any effort to set up a Sparc testbed? It
seems we could use a network-available (virtual?) machine, since this platform
is
often the unfortunate one. Unless, of course, there's a sunset date.
For information, I mentioned SPARC at our local linux group, and
As a way to organize discussion for the session AND for the hopefully
derivative development, I have set up a Github project
https://github.com/nashjc/Rnavpkg
In particular, I've started a small wiki therein, and especially have built a page "Ideas and people" where I have tried
to summari
read the task views and advise others to do so. I
don't know how representative my little corner of the world is,
though.
I have an embryonic task view on mixed models at
https://github.com/bbolker/mixedmodels-misc/blob/master/MixedModels.ctv
but the perfect is the enemy of the good ...
On
Thanks for this. Besides stirring the pot by suggesting this suggestion, my own approach has been to try to do this with
optimr/optimrx for "optimization" (actually function minimization with possibly bounds). Hans Werner Borchers has been
charging ahead with a global optimization wrapper gloptim
We'd be more than happy to have you contribute directly. The goal is not just an
information session, but to get some movement to ways to make the package
collection(s)
easier to use effectively. Note to selves: "effectively" is important -- we
could make
things easy by only recommending a few p
64 matches
Mail list logo
