[Rd] trigamma for very large arguments (PR#14020)
Full_Name: Jerry W. Lewis Version: 2.9.2 OS: Windows XP Professional Submission from: (NULL) (96.237.55.233) trigamma(x) returns 0 for x>1e152, yet trigamma <- function(x) 1/x gives machine accuracy for any x>1e16 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R Updates or Changes in corporate version of R
> "TV" == Tobias Verbeke > on Wed, 21 Oct 2009 21:20:03 +0200 writes: TV> Hi, >> What is the place to search for *corporate version of R *including >> >> 1) GUI >> >> 2) Documentation >> >> 3) Cloud Computing or HPC TV> R is used *as such* in corporate environments all over the world TV> and TV> 1) it comes with a GUI (on Windows and Mac), TV> 2) comes with extensive documentation and TV> 3) has facilities for HPC using add-on packages most TV> of which are listed here: TV> http://cran.r-project.org/web/views/HighPerformanceComputing.html Indeed! TV> That being said there is a diversity of companies TV> providing commercial services related to R and TV> innumerous initiatives focusing on particular aspects TV> which might be useful to "corporate" contexts as well. TV> Best, TV> Tobias TV> P.S. This is IMO not a subject to be discussed on R-devel. yes, indeed. Ajay, you seem to be *the* person on R-devel to regularly breach R-devel policies. Please don't! Martin Maechler, ETH Zurich with hat 'R-devel List Administrator' __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] source and textConnection
Using todays freshly downloaded compiled version of R-2.10.0 beta
let me pose this question once again:
>> myconn<-textConnection("print(11*11)")
>> source(myconn)
produces
> [1] 121
> Warning message:
> In source(myconn) : argument 'encoding = "native.enc"' will be ignored
So I get a warning about a default parameter value I did not use myself.
This is somewhat strange.
Up to 2.9.2 this warning did not show up,
and 2.9.2 also has the encoding parameter.
source(myconn,encoding="unknown")
does not produce a warning.
Will it remain like this?
I am asking because then I have to adapt a certain mechanism in RExcel.
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Re: [Rd] source and textConnection
On 10/22/2009 7:21 AM, Erich Neuwirth wrote:
Using todays freshly downloaded compiled version of R-2.10.0 beta
let me pose this question once again:
myconn<-textConnection("print(11*11)")
source(myconn)
produces
[1] 121
Warning message:
In source(myconn) : argument 'encoding = "native.enc"' will be ignored
So I get a warning about a default parameter value I did not use myself.
This is somewhat strange.
Up to 2.9.2 this warning did not show up,
and 2.9.2 also has the encoding parameter.
source(myconn,encoding="unknown")
does not produce a warning.
Will it remain like this?
I am asking because then I have to adapt a certain mechanism in RExcel.
I think this is a bug, but it may not be serious enough to fix during
code freeze, so there's a good chance it will remain in 2.10.0, but
hopefully not in later releases.
I'll take a look today.
Duncan Murdoch
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[Rd] Advice on how to arrange fix of buglet
Recently I reported a small bug in optim's SANN method failing to report that it had exceeded the maximum function evaluation limit in the convergence code. This is a small enough matter that I was reluctant to create a full-blown bug report. Indeed in the optimx package Ravi Varadhan and I have been developing on r-forge (under the OptimizeR project) it was a minimal work around to fix the matter in our wrapper that incorporates optim() and a number of other tools. While I don't normally do C code, I could likely figure out a fix for optim too. My query is about how to best get this done without causing a lot of work for others i.e., where to I send patches etc. I expect there are a number of similar issues for different areas of R and its documentation, and a clarification from someone in the core team could streamline things. Maybe the bug system is still the right place? Cheers, JN __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R quits immediately upon start-up (PR#14021)
Full_Name: Gavin Koh Version: 2.9.2 OS: OS X Tiger 10.4.11 Submission from: (NULL) (145.117.52.255) Roughly two weeks ago, it became impossible to start-up R. The console window would appear for a fraction of a second and then the programme would exit with no error message. The symptoms are not specific and do not specifically point to Mozy being the culprit. Users will notice that they are unable to sync their iPhones or cameras. They will be unable to print from any application and some programmes will refuse to uninstall; file sharing cannot be started and you cannot burn discs. Stata will run but will not draw graphs or use any other function that requires creating temporary files. The problem started in the second week of October and is due to a faulty update of the popular off-site back-up programme, Mozy. Version 1.5.0 is accidentally overwriting an hidden symbolic link (./tmp -> private/tmp) which causes the operating system to seize up. Because Mozy updates itself silently, most users will not have noticed the problem only started after the last software update. This is the fix: 1. Open the Mozy Preferences menu. 2. Change the Temporary Files Location from "Default" to "Custom" and specify something like "/Applications/Mozy Temp/" 3. Now go to "/Applications/Utilities/Disk Utility.app" and select the hard disk your operating system is running from. Tell it to "Repair Disk Permissions" This will repair the symbolic link that Mozy broke, and should prevent the problem from re-occurring. Read these threads on the Apple message boards for more information: http://discussions.apple.com/thread.jspa?threadID=2193927&start=30&tstart=0 http://discussions.apple.com/thread.jspa?messageID=10440090#10440090 If this solves your problem, please write to customer service at Mozy and give them hell. The e-mail address is macsupp...@mozy.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Error in link in Rd file stops package installation
With a pretty recent version of R 2.11.0 (devel,unstable,
svn 50178) on Linux I could not install version 1.5-8 of zoo (the
current on on CRAN):
% R-devel CMD INSTALL -l Rlib3 zoo
* installing *source* package 'zoo' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'zoo'
finding HTML links ... done
MATCH html
ORDER html
aggregate.zoo html
as.Date.ts html
as.zoo html
coredatahtml
frequency html
index html
is.regular html
lag.zoo html
Error: argument is of length zero
* removing
'/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
The tryCatch calls in the installer code obliterate
most traces of where this 'argument is of length zero'
comes from. If I run the install from a directory containing
the .Rprofile file containing the line
utils::assignInNamespace("tryCatch", function(expr, ...) expr,
ns="base")
then I get:
...
is.regular html
lag.zoo html Error in if
(nzchar(file)) { : argument is of length zero
* removing
'/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
* restoring previous
'/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
and I can grep around for 'if (nzchar(file))'. (Redefining q() in
.Rprofile to give a traceback can help in the search also.)
After the attached change to Rd2HTML I get
...
index html
is.regular html
lag.zoo html
Rd warning: ./man/lag.zoo.Rd:54: missing file link 'diff'
make.par.list html
merge.zoo html
...
Line 54 of that help file is
\seealso{\code{\link{zoo}}, \code{\link[stats]{lag}},
\code{\link[stats]{diff}}}
and I think the [stats]{diff} should be [base]{diff}.
The change I made (which isn't quite right but avoids
mysteriously killing the installation for what turns out
to be a minor error) was
Index: src/library/tools/R/Rd2HTML.R
===
--- src/library/tools/R/Rd2HTML.R (revision 50178)
+++ src/library/tools/R/Rd2HTML.R (working copy)
@@ -305,7 +305,7 @@
if (!OK) {
## so how about as a topic?
file <- utils:::index.search(parts$targetfile,
pkgpath)
-if (nzchar(file)) {
+if (length(file)>0 && nzchar(file)) {
warnRd(block, Rdfile,
"file link ", sQuote(parts$targetfile),
" in package ", sQuote(parts$pkg),
A longer range fix would be to print more contextual
information with the error messages from INSTALL.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
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[Rd] Goto memory alignment query...
Several days back, I posted a comment/question from Kazushige Goto (the developer and maintainer of Goto BLAS) - "By the way, please ask your R developer to rewrite memory allocation function including garbage collection. They give 4 byte offset memory region and never perform well (or it will cause segmentation fault. 4 byte offset is fatal). Since R use complex double precision, memory alignment should be at least 16 bytes..." Goto obviously has thought an awful lot about such things, and (apparently) wrt to R (and he is extremely well-known in programming circles - you don't write a BLAS unless you know a thing or two). Since a number of R users (like me) make use of Goto BLAS, I'd hope that on the devel group could comment/reply. I'll forward to Goto. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] Error in link in Rd file stops package installation
The following patch seems to get the warning message right
lag.zoo html
Rd warning: ./man/lag.zoo.Rd:54: file link 'diff' in package 'stats'
does not exist and so has been treated as a topic
Index: src/library/tools/R/Rd2HTML.R
===
--- src/library/tools/R/Rd2HTML.R (revision 50178)
+++ src/library/tools/R/Rd2HTML.R (working copy)
@@ -305,7 +305,7 @@
if (!OK) {
## so how about as a topic?
file <- utils:::index.search(parts$targetfile,
pkgpath)
-if (nzchar(file)) {
+if (length(file)==0 || nzchar(file)) {
warnRd(block, Rdfile,
"file link ", sQuote(parts$targetfile),
" in package ", sQuote(parts$pkg),
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
> -Original Message-
> From: r-devel-boun...@r-project.org
> [mailto:r-devel-boun...@r-project.org] On Behalf Of William Dunlap
> Sent: Thursday, October 22, 2009 1:54 PM
> To: R-devel@r-project.org
> Subject: [Rd] Error in link in Rd file stops package installation
>
> With a pretty recent version of R 2.11.0 (devel,unstable,
> svn 50178) on Linux I could not install version 1.5-8 of zoo (the
> current on on CRAN):
>
>% R-devel CMD INSTALL -l Rlib3 zoo
>* installing *source* package 'zoo' ...
>** R
>** inst
>** preparing package for lazy loading
>** help
>*** installing help indices
> converting help for package 'zoo'
>finding HTML links ... done
>MATCH html
>ORDER html
>aggregate.zoo html
>as.Date.ts html
>as.zoo html
>coredatahtml
>frequency html
>index html
>is.regular html
>lag.zoo html
>Error: argument is of length zero
>* removing
> '/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
>
> The tryCatch calls in the installer code obliterate
> most traces of where this 'argument is of length zero'
> comes from. If I run the install from a directory containing
> the .Rprofile file containing the line
>utils::assignInNamespace("tryCatch", function(expr, ...) expr,
> ns="base")
> then I get:
>...
>is.regular html
>lag.zoo html Error in if
> (nzchar(file)) { : argument is of length zero
>* removing
> '/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
>* restoring previous
> '/a/seafiler01.na.tibco.com/vol/vol2/users/bill/packages/Rlib3/zoo'
> and I can grep around for 'if (nzchar(file))'. (Redefining q() in
> .Rprofile to give a traceback can help in the search also.)
>
> After the attached change to Rd2HTML I get
>...
>index html
>is.regular html
>lag.zoo html
>Rd warning: ./man/lag.zoo.Rd:54: missing file link 'diff'
>make.par.list html
>merge.zoo html
>...
> Line 54 of that help file is
> \seealso{\code{\link{zoo}}, \code{\link[stats]{lag}},
> \code{\link[stats]{diff}}}
> and I think the [stats]{diff} should be [base]{diff}.
>
> The change I made (which isn't quite right but avoids
> mysteriously killing the installation for what turns out
> to be a minor error) was
>
> Index: src/library/tools/R/Rd2HTML.R
> ===
> --- src/library/tools/R/Rd2HTML.R (revision 50178)
> +++ src/library/tools/R/Rd2HTML.R (working copy)
> @@ -305,7 +305,7 @@
> if (!OK) {
> ## so how about as a topic?
> file <- utils:::index.search(parts$targetfile,
> pkgpath)
> -if (nzchar(file)) {
> +if (length(file)>0 && nzchar(file)) {
> warnRd(block, Rdfile,
> "file link ",
> sQuote(parts$targetfile),
> " in package ", sQuote(parts$pkg),
>
> A longer range fix would be to print more contextual
> information with the error messages from INSTALL.
>
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
> __
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>
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[Rd] mysteriously persistent generic definition
Originally I made a function yearStop that took an argument "object". I
made a generic, but later changed the argument to "x". R keeps
resurrecting the old definition. Could anyone explain what is going on,
or how to fix it? Note particularly the end of the transcript below: I
remove the generic, verify that the symbol is undefined, make a new
function, and then make a generic. But the generic does not use the
argument of the new function definition.
> args(yearStop)
function (obj)
NULL
> yearStop <- function(x) x...@yearstop
> args(yearStop)
function (x)
NULL
> setGeneric("yearStop")
[1] "yearStop"
> args(yearStop)
function (obj)
NULL
> removeGeneric("yearStop")
[1] TRUE
> args(yearStop)
Error in args(yearStop) : object "yearStop" not found
> yearStop <- function(x) x...@yearstop
> setGeneric("yearStop")
[1] "yearStop"
> args(yearStop)
function (obj)
NULL
R 2.7.1. I originally read the definitions in from a file with ^c^l in
ESS; however, I typed the commands above by hand.
Thanks.
Ross Boylan
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Re: [Rd] mysteriously persistent generic definition
Ross Boylan wrote:
> Originally I made a function yearStop that took an argument "object". I
> made a generic, but later changed the argument to "x". R keeps
> resurrecting the old definition. Could anyone explain what is going on,
> or how to fix it? Note particularly the end of the transcript below: I
> remove the generic, verify that the symbol is undefined, make a new
> function, and then make a generic. But the generic does not use the
> argument of the new function definition.
>
>
>> args(yearStop)
> function (obj)
> NULL
>> yearStop <- function(x) x...@yearstop
>> args(yearStop)
> function (x)
> NULL
>> setGeneric("yearStop")
> [1] "yearStop"
>> args(yearStop)
> function (obj)
> NULL
>> removeGeneric("yearStop")
> [1] TRUE
>> args(yearStop)
> Error in args(yearStop) : object "yearStop" not found
>> yearStop <- function(x) x...@yearstop
>> setGeneric("yearStop")
> [1] "yearStop"
>> args(yearStop)
> function (obj)
> NULL
>
>
> R 2.7.1. I originally read the definitions in from a file with ^c^l in
I don't see this behavior in R-2.9.2, or in the release candidate.
Martin
> ESS; however, I typed the commands above by hand.
>
> Thanks.
> Ross Boylan
>
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Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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