[Rd] Wish for arima function: add a data argument and a formula-type for regressors

2017-05-16 Thread Olivier Renaud
intercept trait01 mesure0 interact 0.271534.1363 -5.5777 0.0075 -0.1809 s.e. 0.1211 0.6685 0.9009 0.03420.0490 -- Prof. Olivier Renaud http://www.unige.ch/fapse/mad/ Methodology & Data Analysis - Psychology Dept - University of Geneva UniM

[Rd] .S3methods: issue in content of info data.frame

2016-11-11 Thread Renaud Gaujoux
r ..." except for visible methods. Is this the expected behavior? See code and output below. Thank you. Bests, Renaud $ Rscript -e "library(xtable); attr(.S3methods('plot'), 'info'); sessionInfo()" visible from generic

[Rd] Ubuntu console weird behaviour

2016-03-03 Thread Renaud Gaujoux
ter-a-res Thank you. Bests, Renaud My settings are: R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 15.10 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_ZA.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_ZA.UTF-8LC_MES

[Rd] Method from package dependency is not updated due to lazy load?

2016-02-10 Thread Renaud Gaujoux
the user that there could be issues due to version discrepancy. Thank you. Bests, Renaud ## Code library(devtools) unlink('test', recursive = TRUE) dir.create('test/lib', recursive = TRUE) # create packages createA <- function(version){ dir.create(file.path('test&

Re: [Rd] List S3 methods and defining packages

2015-07-08 Thread Renaud Gaujoux
; Kevin Wright > > > On Wed, Jul 8, 2015 at 5:09 AM, Renaud Gaujoux > wrote: >> Thank you for your reply Martin. >> Your code made me realize that S3 methods are added to the >> .__S3MethodsTable__. of the package that defines the generic, not to >> the ones defi

Re: [Rd] List S3 methods and defining packages

2015-07-08 Thread Renaud Gaujoux
A? I don't get any warning message and there seems to be only one entry in the relevant .__S3MethodsTable__. Aren't these tables updated when the masking package B is detached? On 7 July 2015 at 21:01, Martin Morgan wrote: > On 07/07/2015 02:05 AM, Renaud Gaujoux wrote: >> &g

[Rd] List S3 methods and defining packages

2015-07-07 Thread Renaud Gaujoux
od for print", instead of the actual package name (see below for the first rows). Is this normal behaviour? If so, is there a way to get what I want: a character vector mapping class to package (ideally in loading order, but this I can re-order from search

Re: [Rd] install.packages deletes PACKAGES file in local repo

2014-12-05 Thread Renaud Gaujoux
t happened. Closing the thread. Thanks. On 6 December 2014 at 02:23, Gabriel Becker wrote: > Can you post exact code, i have not seen this behavior, and I work with > local repositories quite extensively on my current project. > > ~G > > On Fri, Dec 5, 2014 at 7:4

[Rd] install.packages deletes PACKAGES file in local repo

2014-12-05 Thread Renaud Gaujoux
. Subsequent calls to install.packages() complain about src/contrib/PACKAGES not existing, although there still is a src/contrib/PACKAGES.gz file. Is this a know issue? Thank you. Bests, Renaud [[alternative HTML version deleted]] __ R-devel@r

Re: [Rd] Is it possible to make install.packages compile source code on Unix but use shipped binary on Windows?

2014-06-19 Thread Renaud Gaujoux
greed completely. I really like R cross-platform packaging and checking system, and was just wondering if this conditional compilation option was possible using the flexibility of this very system. Renaud __ R-devel@r-project.org mailing list https://sta

Re: [Rd] Is it possible to make install.packages compile source code on Unix but use shipped binary on Windows?

2014-06-18 Thread Renaud Gaujoux
-- and in PATH. Renaud __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Is it possible to make install.packages compile source code on Unix but use shipped binary on Windows?

2014-06-18 Thread Renaud Gaujoux
ile, although in may case users actually get it through a personal CRAN-like repository, using argument type='both'. Thank you. Bests, Renaud __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Is it possible to make install.packages compile source code on Unix but use shipped binary on Windows?

2014-06-13 Thread Renaud Gaujoux
. Thank you. Bests, Renaud __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] traceback does not show source line number of long calls when truncating output

2014-05-12 Thread Renaud Gaujoux
intended. Thank you. Bests, Renaud ## File: traceback.R a <- function(...){ stop('this is an error') } # code to generate the long call # set.seed(123) # v <- unique(replicate(10, { paste0(sample(letters[1:26]), collapse = "") })) # sprintf("a(%

Re: [Rd] Proxy settings not honoured anymore

2014-03-27 Thread Renaud Gaujoux
All right, just ignore this silly post, things magically came back into place... :| On 27 March 2014 17:28, Renaud Gaujoux wrote: > Hi, > > it seems that my proxy settings are not picked up by the R console any > longer, although the environment variable http_proxy is set and >

[Rd] Proxy settings not honoured anymore

2014-03-27 Thread Renaud Gaujoux
Hi, it seems that my proxy settings are not picked up by the R console any longer, although the environment variable http_proxy is set and exported. Is anybody experiencing this issue as well? Thank you. Bests, Renaud # System info (from R --vanilla) > sessionInfo() R version 3.0.3 (2014-03

[Rd] contrib.url in non-interactive mode

2014-02-14 Thread Renaud Gaujoux
Hi, is it intended that one cannot install packages in non-interactive mode, without explicitly setting a CRAN mirror (see below)? Couldn't a default mirror be used in that case? Thank you. Bests, Renaud $ Rscript --vanilla -e "install.packages('whatever')" Installing p

[Rd] S4 method for '[' with extra arguments: distinguishing between x[i] and x[i, ]

2013-12-05 Thread Renaud Gaujoux
definition) but could not find its definition, and can't see how setMethod will know for which '[' to define the method. Defining a method for signature(x = 'A', j = 'missing') has the same issue. Is there actually a way to do this? Thank you. Bests, Renaud

Re: [Rd] cat with backspace and newline characters

2013-11-06 Thread Renaud Gaujoux
inly not worth the effort anyway! I guess we can happily close this thread :D Many thanks. Bests, Renaud __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] How to do package cleanup: hooks .onUnload, R_unload_mylib, .onDetach are not called on quit

2013-11-06 Thread Renaud Gaujoux
Many thanks for all responses and clarification! It worked great by defining a dummy environment in the package namespace and calling reg.finalizer to "attach" the cleanup function to it. Bests, Renaud On 6 November 2013 13:54, Prof Brian Ripley wrote: > On 06/11/2013 11:36, D

[Rd] How to do package cleanup: hooks .onUnload, R_unload_mylib, .onDetach are not called on quit

2013-11-06 Thread Renaud Gaujoux
= TRUE)? * is there a reason why the hooks are not called on quit? Thank you. Bests, Renaud ### > Sys.info() sysname release version "Linux" "3.11.0-12-generic" "

Re: [Rd] cat with backspace and newline characters

2013-11-06 Thread Renaud Gaujoux
> Anyway, > thanks for all the experiments, and (to Renaud) support.rstudio.org is > the place to report such problems. > Funny how the post diverged to an RStudio-related issue. Anyway, I posted a link to this post at support.rstudio.org: http://support.rstudio.org/help/discussions/p

Re: [Rd] cat with backspace and newline characters

2013-11-05 Thread Renaud Gaujoux
e was an error though, but only asked if this was normal behaviour, and apparently many standard Linux terminals get it wrong. This looks a bit sad for a very terminal-driven OS. Renaud [[alternative HTML version deleted]] __ R-devel@r-project.org

Re: [Rd] cat with backspace and newline characters

2013-11-05 Thread Renaud Gaujoux
Maybe it's a Linux problem: > cat("abc\b") ab> cat("abc\b\n") abc > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8LC_MESS

Re: [Rd] cat with backspace and newline characters

2013-11-01 Thread Renaud Gaujoux
: > cat("abc\b\b\b") > c Here, I end up with the cursor being on the 'c', i.e. if I type something it erase the 'c'. It is strange that the 'c' appears _after_ the console prompt, isn't it? Renaud On 1 November 2013 13:41, Sean O'Riorda

[Rd] cat with backspace and newline characters

2013-11-01 Thread Renaud Gaujoux
Hi, when mixing newline and backspace characters I get the following output (see below). In the second call, the backspace character is simply not applied. Is this normal behaviour? Thank you. > cat("abc\b") ab> cat("abc\b\n") abc > [[alternative HTML version deleted]] _

[Rd] [Windows] Behaviour of shell on error

2013-10-07 Thread Renaud Gaujoux
t be run. " Thank you. Bests, Renaud ## Example ### # no error as expected shell('notacommand') shell('notacommand', intern=TRUE) # error as expected shell('notacommand', mustWork = TRUE) # I am expecting to get an error here as well, but none is thrown shell(&#

Re: [Rd] R CMD check: unknown option ?--outdir==RCHECK?

2013-05-21 Thread Renaud Gaujoux
Oh... I read too quickly your previous post, which actually gives me some hope on explaining why some R-forge checks might be broken. Great thanks! :) On 21 May 2013 15:54, Duncan Murdoch wrote: > On 21/05/2013 8:13 AM, Renaud Gaujoux wrote: > >> Hi, >> >> I believ

Re: [Rd] R CMD check: unknown option ?--outdir==RCHECK?

2013-05-21 Thread Renaud Gaujoux
k -o mydir pkg_0.1.tar.gz` we get: * using log directory ‘/home/renaud/Documents/projects/mydir/pkg.Rcheck’ ... which works perfectly fine, and puts pkg.Rcheck in 'mydir'. Renaud [[alternative HTML version deleted]] __ R-devel@r-project.or

Re: [Rd] Namespace/inheritance problem in S4 methods for a union class

2013-05-08 Thread Renaud Gaujoux
he same to deal with union of unions. Renaud On 8 May 2013 19:02, John Chambers wrote: > No need for generic functions and methods. Just looking at the hierarchy > of the classes shows the problem. > > With Martin's simplified version: > > > library(PkgA) > >

[Rd] Namespace/inheritance problem in S4 methods for a union class

2013-05-07 Thread Renaud Gaujoux
Hi, I started this post on bioc-devel but this seems to be more general: https://stat.ethz.ch/pipermail/bioc-devel/2013-May/004311.html See reproducible example from Martin below. Thank you. Renaud -- Forwarded message -- From: Martin Morgan Date: 7 May 2013 19:55 Subject

Re: [Rd] lsfit: Error in formatting error message

2013-04-29 Thread Renaud Gaujoux
Ah yes, nice, I had noticed the swapped words in other situations, it will definitely help me to tell users about sample size issues... :) Bests, Renaud On 29 April 2013 12:15, Uwe Ligges wrote: > On 25.04.2013 13:29, Renaud Gaujoux wrote: > >> Hi, >> >> in R-3.0 I

[Rd] lsfit: Error in formatting error message

2013-04-25 Thread Renaud Gaujoux
"), ", ", ngettext(ncx, "but only %d variable", "but only %d variables"), nry, ncx) 2: stop(sprintf(ngettext(nry, "%d response", "%d responses"), ", ", ngettext(ncx, "but only %d variable", "but only %d variab

Re: [Rd] Empty package skeleton

2013-04-14 Thread Renaud Gaujoux
... and my suggestion for an easy way to skip defined variables comes from the case of fresh non-vanilla sessions that willingly inherit user-defined variables from .Rprofile. 2013/4/14 Dirk Eddelbuettel > > On 14 April 2013 at 14:10, Renaud Gaujoux wrote: > | Hi, > | > | I kno

[Rd] Empty package skeleton

2013-04-14 Thread Renaud Gaujoux
utomatically allow/handle a call like "package.skeleton('pkg', character())". Conclusion, nothing urgent, which could be done in 1min spare time, but could save 1min to many friendly future package developers :) Thank you. Bests, Renaud ### Example on R-3.0.0.0 >

[Rd] loadNamespace tries to load an optional dependency from a required dependency

2013-04-07 Thread Renaud Gaujoux
extra functionality provided by package C, at lazy-load time, which means it must be loaded via .onLoad (right?). In this case, clearly, one would have package C as Depends, which then would not give rise to the issue I have here. Thank you. Bests, Renaud [[alternative HTML version de

Re: [Rd] source, sys.source and error line numbers

2013-03-26 Thread Renaud Gaujoux
TRUE or the error location won't be known. > > I'll fix the difference you noticed after 3.0.0 is released; I think it is > not serious enough to slip in at this point. > > Duncan Murdoch > > > >> Hadley >> >> On Tue, Mar 19, 2013 at 4:03 AM, R

Re: [Rd] removing union class

2013-03-19 Thread Renaud Gaujoux
All good then. Thanks. Renaud 2013/3/19 Martin Maechler > >>>>> "RG" == Renaud Gaujoux > >>>>> on Sun, 17 Mar 2013 10:38:44 +0200 writes: > > RG> Late report is better than never isn't it? :) > >>

[Rd] source, sys.source and error line numbers

2013-03-19 Thread Renaud Gaujoux
number) and sys.source (has no line number). Thank you, Renaud # code codefile <- tempfile() write("# some comment # some good lines a <- 1 # a bad line stop('an error') # another good line b <- 2 ", file=codefile) # with source() the line number

Re: [Rd] removing union class

2013-03-17 Thread Renaud Gaujoux
> and > >> crashes with no hint on the original error. > > I guess a quick fix for devtools, would be to wrap the cleanup procedure into a try or tryCatch (Hadley?). Thanks, Renaud [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] removing union class

2013-03-13 Thread Renaud Gaujoux
packages: [1] stats graphics grDevices utils datasets methods base Is this normal? Am I doing something wrong? Hadley, this is problematic for devtools, because load_all tries to cleanup S4 classes when an error occurs when loading a development package and crashes with no hint

Re: [Rd] Keeping up to date with R-devel

2013-02-27 Thread Renaud
t it? When compiling from source, R and R-devel coexist happily if one specifies an installation prefix other than the default. What other conflict could happen? Renaud 2013/2/27 Dirk Eddelbuettel > > On 27 February 2013 at 12:08, Renaud wrote: > | is checking out R SVN trunk the

[Rd] Keeping up to date with R-devel

2013-02-27 Thread Renaud
Hi, is checking out R SVN trunk the recommended way to keep up to date with R-devel and check packages with the latest version? My objective is to be able to have both R and R-devel versions installed/working and up to date. R-devel binaries would be available as symlinks in my home directory so

Re: [Rd] Call function only when running via R CMD check?

2012-12-18 Thread Renaud
a definite identification of R CMD check and other special calls (e.g. in \Sexpr in Rd files). Bests, Renaud 2012/12/18 Spencer Graves > Have you considered the CRAN function in "fda"? Spencer > > > > On 12/18/2012 4:00 AM, Henrik Bengtsson wrote: > >> Hi Ren

Re: [Rd] Call function only when running via R CMD check?

2012-12-17 Thread Renaud Gaujoux
Hi Henrik (and list), I am interested in a similar feature, and would be happy to see the suggestions you got off-line :) Have you come up with a robust solution, which would work in a variety of situations (in examples, tests, \Sexpr calls, etc..)? Thank you. Bests, Renaud -- Renaud

Re: [Rd] Extracting srcref for S4 methods

2012-07-05 Thread Renaud Gaujoux
tandardGeneric('myfun')) setMethod('myfun', 'numeric', function(x, ...){ 'myfun,numeric' }) ") source(f, keep.source=TRUE) # there are srcref data for functions str(f) # no srcref data str(attr(myfun, 'srcref')) str(attr(selectMethod(myfun, 'numer

[Rd] Extracting srcref for S4 methods

2012-07-05 Thread Renaud Gaujoux
Hi, on R version 2.15.1 (2012-06-22) (Platform: i686-pc-linux-gnu (32-bit)) sourced functions have srcref attached as an attribute. Are such data also available for S4 generics and methods? How? (See sample code below) Thank you. Bests, Renaud f <- textConnection( " f <

[Rd] [Suggestion] Installation of CRAN packages that depend on Bioconductor packages

2012-06-28 Thread Renaud Gaujoux
e hence completely transparent, which would simplify the installation of such packages, as the user would not need to know that a repository other than CRAN is required. Resolution could make use of the function chooseBioCMirror to ask the user to select her preferred mirror, as it is done for the CRA

Re: [Rd] "Incompatible methods" for overloaded operator

2012-06-21 Thread Renaud Gaujoux
de of primitive function or are these pure C functions, which need to be searched for in R source code? Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Multiple sub-architecture: linking issue

2012-06-12 Thread Renaud Gaujoux
Dirk, who thinks this should have been on r-sig-debian all along Moved to r-sig-debian as suggested: https://stat.ethz.ch/pipermail/r-sig-debian/2012-June/001885.html __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-d

Re: [Rd] Multiple sub-architecture: linking issue

2012-06-11 Thread Renaud Gaujoux
On 11/06/2012 03:43, Simon Urbanek wrote: > On Jun 10, 2012, at 9:24 PM, Dirk Eddelbuettel wrote: > >> On 8 June 2012 at 12:27, Renaud Gaujoux wrote: >> | PS: Dirk do you want me to post this on the Rcpp list for record? >> >> Yes, that generally is where Rcpp quest

Re: [Rd] Multiple sub-architecture: linking issue

2012-06-08 Thread Renaud Gaujoux
: $ sudo apt-get install ia32-libs-dev lib32readline6-dev lib32ncurses5-dev lib32icu-dev gcc-multilib gfortran-multilib [sudo] password for renaud: Reading package lists... Done Building dependency tree Reading state information... Done Package ia32-libs-dev is not available, but is referred to by

[Rd] Multiple sub-architecture: linking issue

2012-06-08 Thread Renaud Gaujoux
Hi again, following my previous post on RCurl, I cannot install Rcpp either: g++ -m32 -I/home/renaud/bin/R/2.15/lib64/R/include -I/home/renaud/bin/R/2.15/lib64/R/include/i386 -DNDEBUG -I../inst/include/ -I/usr/local/include-fpic -g -O2 -c r_cast.cpp -o r_cast.o g++ -m32 -shared -L/usr

[Rd] Multiple sub-architecture: problem installing RCurl

2012-06-08 Thread Renaud Gaujoux
tatus config.status: creating src/Makevars ** libs *** arch - i386 gcc -std=gnu99 -m32 -I/home/renaud/bin/R/2.15/lib64/R/include -I/home/renaud/bin/R/2.15/lib64/R/include/i386 -DNDEBUG -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_C

Re: [Rd] url, readLines, source behind a proxy

2012-05-10 Thread Renaud Gaujoux
Thanks Henrik for the work around. It worked perfectly and save me lots of check time. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa On 24/04/2012 17:57, Henrik Bengtsson wrote: Looking at the source code (src/library/tools/R/check.R and src/library

Re: [Rd] url, readLines, source behind a proxy

2012-04-24 Thread Renaud Gaujoux
On 23/04/2012 17:39, Prof Brian Ripley wrote: On 18/04/2012 16:04, Joshua Ulrich wrote: Hi Renaud, On Wed, Apr 18, 2012 at 12:22 AM, Renaud Gaujoux wrote: Hi Henrik, Could anybody behind a proxy check if the issue can be reproduced? My proxy is in fact provided by cntml, which acts as

Re: [Rd] url, readLines, source behind a proxy

2012-04-17 Thread Renaud Gaujoux
actual university proxy, not natively supported by my system (Ubuntu). Anybody in this case? Thanks. Renaud On Tue, 17 Apr 2012, Henrik Bengtsson wrote: > On Tue, Apr 17, 2012 at 1:01 AM, Renaud Gaujoux > wrote: > > Hi, > > > > when I run R CMD check with flag --as-cr

[Rd] url, readLines, source behind a proxy

2012-04-17 Thread Renaud Gaujoux
ed to work behind a proxy (correct?). Does anybody else have this problem? I was wondering if there is a way around, as I would like to be able to use --as-cran for my checks. Thank you. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town So

[Rd] Default subset and concatenation operators for namedList

2012-01-24 Thread Renaud Gaujoux
uld at least deal with the slot `names` and not convert the object to a standard list, which is troublesome. Is there a reason why these operators are not pre-defined in namedList? Thank you. Renaud ## setClass('A', contains='namedList') a <- new(&

Re: [Rd] R package BibTex entries: looking for a more general solution

2011-12-19 Thread Renaud Gaujoux
a fix for this now. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa On 19/12/2011 15:56, Michael Friendly wrote: On 12/19/2011 2:02 AM, Renaud Gaujoux wrote: Hi, I actually adapted and integrated this feature into Achim's -- nice -- function (p

Re: [Rd] R package BibTex entries: looking for a more general solution

2011-12-18 Thread Renaud Gaujoux
n) citation. Romain, I think I will submit a patch for this. Hope this helps. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Identify \Sexpr call?

2011-11-05 Thread Renaud Gaujoux
More or less in the same vein as Henrik's post, is it possible to detect that a function is being called in an \Sexpr when generating an Rd file? Thank you -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa __ R-de

Re: [Rd] R CMD check and error in an \Sexpr in an Rd file

2011-11-04 Thread Renaud Gaujoux
his is the result of tools:::Rd_expr_PR(1234):", tools:::Rd_expr_PR(1234), sep="")} \rdVerb{paste("This is the result of tools:::Rd_expr_PR(1234):", tools:::Rd_expr_PR(1234), sep="\n")} But backslashes must be escaped twice: \rdVerb{"\begin{section

Re: [Rd] R CMD check and error in an \Sexpr in an Rd file

2011-11-03 Thread Renaud Gaujoux
On 03/11/2011 16:33, Georgi Boshnakov wrote: Dear Renalud,, Would a 'results=tex' (html, text) be possible? or 'results=source' that could be combined with \if{format}{text}? This may well be a clean approach. After my previous email, I looked again at the definition of thr \AsIs macro. Its

Re: [Rd] R CMD check and error in an \Sexpr in an Rd file

2011-11-03 Thread Renaud Gaujoux
On 03/11/2011 16:28, Duncan Murdoch wrote: On 03/11/2011 10:21 AM, Renaud Gaujoux wrote: Thank you Georgi. With the fix \long the output is indeed consistent with the documentation. I think my use of cat() worked by luck as its output should not have been rendered. Would a 'result

Re: [Rd] R CMD check and error in an \Sexpr in an Rd file

2011-11-03 Thread Renaud Gaujoux
ith \if{format}{text}? This would allow to generate custom Latex, or HTML code, but it might also be is hazardous... Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa On 03/11/2011 15:50, Georgi Boshnakov wrote: Dear Duncan and Renauld, The error caused by t

Re: [Rd] R CMD check and error in an \Sexpr in an Rd file

2011-11-03 Thread Renaud Gaujoux
Although I use Latex quite a lot, I am not literate in Latex macro languages (e.g. the definition of AsIs). Is there (I am sure there is) a reason why a plain verbatim environment is not used in this case? On 03/11/2011 14:19, Duncan Murdoch wrote: On 11-11-03 7:58 AM, Renaud Gaujoux wrote

Re: [Rd] R CMD check and error in an \Sexpr in an Rd file

2011-11-03 Thread Renaud Gaujoux
ybe this is not what 'results=verbatim' is supposed to do nor to be used for? Renaud Another test Rd file. % \name{Sexpr} \alias{Sexpr} \title{Error and verbatim in Sexpr} \description{ Testing Sexpr in Rd files %\Sexpr[results=verbatim, stage=render]{stop("er

Re: [Rd] R CMD check and error in an \Sexpr in an Rd file

2011-11-01 Thread Renaud Gaujoux
g in R CMD check: * checking examples ... ERROR Error in paste(before, x, after, sep = "") : object 'exfile' not found Execution halted The two first issues can be reproduced with a call to R CMD Rd2pdf on the Rd code below. Thank you. Renaud. %%% \name{Sexpr} \alias{Sexpr

Re: [Rd] R CMD check and error in an \Sexpr in an Rd file

2011-10-31 Thread Renaud Gaujoux
Thank you very much Duncan, Uwe and Peter. Sorry if I missed the announcement, I follow more r-devel than r-help, which I find a bit hard to quickly read. Will try now on the 2.14.0. Renaud On 31/10/2011 14:28, Prof Brian Ripley wrote: On Mon, 31 Oct 2011, Renaud Gaujoux wrote: I do not

Re: [Rd] R CMD check and error in an \Sexpr in an Rd file

2011-10-31 Thread Renaud Gaujoux
I do not see it on main CRAN home page. Do you mean http://cran.r-project.org/src/base-prerelease/R-latest.tar.gz ? On 31/10/2011 14:19, Uwe Ligges wrote: On 31.10.2011 13:13, Renaud Gaujoux wrote: Thank you Duncan. I tried with: * using R version 2.14.0 RC (2011-10-24 r57417) * using

Re: [Rd] R CMD check and error in an \Sexpr in an Rd file

2011-10-31 Thread Renaud Gaujoux
R-rc_2011-10-27_r57452.tar.gz. Renaud On 28/10/2011 17:25, Duncan Murdoch wrote: On 28/10/2011 10:53 AM, Duncan Murdoch wrote: On 28/10/2011 10:49 AM, Renaud Gaujoux wrote: > Hi, > > another Rd related issue I encountered is that if an error occurs in an > \Sexpr in an Rd f

[Rd] R CMD check and error in an \Sexpr in an Rd file

2011-10-28 Thread Renaud Gaujoux
ecking step. Not sure why it does not break before. Thank you. Renaud PS: I am on R version 2.13.2 (2011-09-30) - x86_64-pc-linux-gnu (64-bit) -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa __ R-devel@r-project.org

[Rd] Output multiline verbatim in Rd files with \Sexpr in PDF manual

2011-10-28 Thread Renaud Gaujoux
) but these are always somehow escaped when generating the Latex file. Is there a way to go around these issues? Maybe I am not using the correct way. Thank you. Renaud -- Renaud Gaujoux Computational Biology - University of Cape Town South Africa __

Re: [Rd] Error message library()

2011-10-28 Thread Renaud Gaujoux
t Deepayan did not tell anybody about it ;) ) The help page ?completion in the utils package explains how to enable it: utils::rc.settings(ipck=TRUE) It simply worked on my Ubuntu box -- and directly went in my .Rprofile :) Hope this helps. Renaud -- Renaud Gaujoux Computational Biology - Universi

Re: [Rd] getNativeSymbolInfo("user_unif_rand") returns different results on windows and linux

2011-08-23 Thread Renaud Gaujoux
lts are different (see below: the first returns the complete information, the second has a NULL element package). I noticed other issues which makes very difficult to predict which DLL will actually be resolved (e.g. when one plays with loading/unloading packages that provides the hook), but I gu

[Rd] getNativeSymbolInfo("user_unif_rand") returns different results on windows and linux

2011-08-23 Thread Renaud Gaujoux
called on the same symbol (see test code below. Each sequence needs to be run on on a fresh R session). Things works perfectly under Linux. Thank you for any explanation on the matter. Renaud ## SEQUENCE 1 ## library(rstream) getNativeSymbolInfo('user_unif_rand&#

[Rd] getNativeSymbolInfo("user_unif_rand") returns different results on windows and linux

2011-08-17 Thread Renaud Gaujoux
P and Vista) however the symbol information does not change (same pointer address) and the package data is NULL. See results for both systems below. I tested this with R 2.12.1, 2.13.0 and 2.13.1 on Windows. Is this a normal behaviour for dll loaded on Windows? Thank you. Renaud #

Re: [Rd] R cmd check and multicore foreach loop

2011-08-17 Thread Renaud Gaujoux
ovide optional separate logging as doMPI does? (I guess this might be better posted to R-hpc) Thank you. Renaud On 17/08/2011 14:56, Brian G. Peterson wrote: On Wed, 2011-08-17 at 04:50 -0700, Tim Triche, Jr. wrote: I'll see if I can put together a self-contained example. Primarily, the ti

Re: [Rd] R cmd check and multicore foreach loop

2011-08-17 Thread Renaud Gaujoux
operation wedges. I'm told > that doSMP really only works well with Revolution R, but per above, I > will try to put together a working self-contained example to show how. > > > On Wed, Aug 17, 2011 at 4:39 AM, Renaud Gaujoux <mailto:ren...@cbio.uct.ac.za>> wrote: >

Re: [Rd] R cmd check and multicore foreach loop

2011-08-17 Thread Renaud Gaujoux
crete examples of the issues you talked with other developers? Thank you. Renaud On 17/08/2011 12:45, Tim Triche, Jr. wrote: > yes -- doMC (and doSMP) are kind of bogus and I just use > multicore::mclapply() to good effect these days. I checked around > with other people doing similar

[Rd] R cmd check and multicore foreach loop

2011-08-17 Thread Renaud Gaujoux
encountered a similar issue? Thank you. Renaud ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mai...{{dropped:5}} __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] [R-sig-hpc] doMC - compiler - concatenate an expression vector into a single expression?

2011-06-29 Thread Renaud Gaujoux
Thank you very much Steve. Your suggestion works perfectly -- at least with doSEQ, doMC and doMPI. Bests, Renaud On 28/06/2011 15:35, Stephen Weston wrote: I think that the result of the concatenation should be a call object, rather than an expression object. How about something along the

[Rd] doMC - compiler - concatenate an expression vector into a single expression?

2011-06-28 Thread Renaud Gaujoux
Locals(e, cntxt)) genCode(e, cntxt) } My guess is that the function findLocals or genCode can not handle a 2-length expression vector. Maybe somebody who knows the internals of these functions could explain better this behaviour? How can I concatenate two expressions into a single one? Th

Re: [Rd] Class not found when search in .onLoad

2011-06-27 Thread Renaud Gaujoux
All is clear now. Thank you for this clarification. Cheers, Renaud On 27/06/2011 15:38, Simon Urbanek wrote: On Jun 27, 2011, at 8:43 AM, Renaud Gaujoux wrote: On 27/06/2011 14:27, Simon Urbanek wrote: On Jun 27, 2011, at 3:17 AM, Renaud Gaujoux wrote: On 24/06/2011 22:04, John Chambers

Re: [Rd] Class not found when search in .onLoad

2011-06-27 Thread Renaud Gaujoux
On 27/06/2011 14:27, Simon Urbanek wrote: On Jun 27, 2011, at 3:17 AM, Renaud Gaujoux wrote: On 24/06/2011 22:04, John Chambers wrote: Strictly speaking, that is not meaningful. A class (like any R object) is uniquely referenced by a name *and an environment*. The name of a package can be

Re: [Rd] Class not found when search in .onLoad

2011-06-27 Thread Renaud Gaujoux
nks (result of getClass). However, this does not explain why .onLoad does not find the class while .onAttach finds it, does it? Is .onLoad evaluated outside the namespace environment, while .onAttach is evaluated within the namespace? Thank you. Renaud ### UNIVERSITY OF CAPE TOWN Th

Re: [Rd] Class not found when search in .onLoad

2011-06-24 Thread Renaud Gaujoux
ading. - why things seemed to work ok in R-2.12.1 at the installation loading check, but do not work when loading the package from an R session? Could you please briefly give some explanations or pointers? Thank you. Bests, Renaud On 23/06/2011 18:44, John Chambers wrote: The workaround is to use

[Rd] Class not found when search in .onLoad

2011-06-23 Thread Renaud Gaujoux
lized. All this should be done in .onLoad, but I cannot do it due to this behaviour of `extends`. Can someone provide some explanations or work around. Thank you, Renaud # script.R setClass('A', representation(data='numeric')) setClass(&#

[Rd] Why does slot<- duplicate its argument?

2011-06-17 Thread Renaud Gaujoux
Hi, is there a reason why `slot<-` should duplicate its argument? I am under R 2.12.1. Thank you, Renaud For example: setClass('A', representation(data='matrix')) a <- new('A') x <- matrix(1,2,3) tracemem(x) slot(a, 'data') <- x ### UNIV

[Rd] Extending type list: names and inherited methods issue

2011-03-04 Thread Renaud Gaujoux
the list methods [, $, etc...). Thank you. Bests, Renaud # define S4 class that inherits from list setClass('A', contains='list') # nothing to say when one creates an object with an unnamed list x <- new('A', list(1,2,3)) x # set the names: seems ok but they are

Re: [Rd] Missing argument vs. empty argument

2011-01-25 Thread Renaud Gaujoux
My purpose is indeed to write a '[' method. I will go for the `[.data.frame` solution then. Thank you. On 25/01/2011 12:53, Prof Brian Ripley wrote: On Tue, 25 Jan 2011, Renaud Gaujoux wrote: Hi, is there an easy, robust, and/or recommended way to distinguish a missing argume

[Rd] Missing argument vs. empty argument

2011-01-25 Thread Renaud Gaujoux
function(i, j, k){ print( empty.arg(j) ) print(nargs()) } would result in: foo(i) # FALSE, 1 foo(i, ) # TRUE, 2 foo(i, j) # FALSE, 2 foo(i, k=2) # FALSE, 2 foo(i, k=2, ) # TRUE, 3 Thank you for any help or pointer. Bests, Renaud ### UNIVERSITY OF CAPE TOWN This e-mail is subjec

[Rd] library: loading of required packages and argument 'lib.loc'

2010-10-05 Thread Renaud Gaujoux
ce if library() could do it locally (e.g. pass the argument), without changing the global settings. Thanks, Renaud ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclai

Re: [Rd] Encoding problem in Rd file

2010-10-03 Thread Renaud Lancelot
/10/3 Renaud Lancelot : > I see C:/R\R-2.11.1\share\texmf\Rd.sty which is my current R > installation. By the way, there is no error during the compilation > with > >  R CMD Rd2dvi --no-clean dja.Rd > > So, it looks that the problem is located elsewhere... > > Thank you

Re: [Rd] Encoding problem in Rd file

2010-10-03 Thread Renaud Lancelot
I see C:/R\R-2.11.1\share\texmf\Rd.sty which is my current R installation. By the way, there is no error during the compilation with R CMD Rd2dvi --no-clean dja.Rd So, it looks that the problem is located elsewhere... Thank you for your help. All the best, Renaud 2010/10/3 Duncan Murdoch

Re: [Rd] Encoding problem in Rd file

2010-10-03 Thread Renaud Lancelot
? Renaud 2010/10/3 Duncan Murdoch : > On 03/10/2010 12:23 PM, Renaud Lancelot wrote: >> >> Dear all, >> >> I have a problem with an Rd file containing French accentuated >> characters. I have uploaded the file at >> http://filex.cirad.fr/get?k=cjW7lImMaNC6Ci

[Rd] Encoding problem in Rd file

2010-10-03 Thread Renaud Lancelot
datasets methods [8] base other attached packages: [1] fortunes_1.4-0 -- Renaud Lancelot EDEN Project, coordinator http://www.eden-fp6project.net/ UMR CIRAD-INRA "Contrôle des maladies animales exotiques et émergentes" Joint research unit "Control of emerging and exotic animal d

Re: [Rd] Non identical numerical results from R code vs C/C++ code?

2010-09-10 Thread Renaud Gaujoux
0.0 to see if it makes a difference. What do you mean by "You also need to be careful about conversion from integer to real, to do double conversion." ? Where are the trap in this type of conversion? Thanks. Renaud On 10/09/2010 16:07, Paul Gilbert wrote: With fortran I have always m

Re: [Rd] Non identical numerical results from R code vs C/C++ code?

2010-09-10 Thread Renaud Gaujoux
Ok. I quickly tried using LDOUBLE wherever I could, but it did not changed the results. I might try harder... I agree with you Barry, and I will re-double re-check my code. Thank you both for your help. Bests, Renaud On 10/09/2010 13:24, Barry Rowlingson wrote: On Fri, Sep 10, 2010 at 11:46

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