Re: [Rd] S4: inheritance of validity methods?

Vitalie S. wrote: > On Tue, 18 Aug 2009 15:42:48 +0200, Martin Morgan > wrote: > >> "Vitalie S." writes: >> >>> Dear Developers, >>> >>> In current implementation of validity method, objects are first >>> coerced to superclass

Re: [Rd] package dependencies specification

Hi Christos -- Christos Hatzis wrote: > > Hello, > > After running R CMD check on my package I received the following error on > package dependencies: > > * using log directory 'C:/z-zBackup/Nuvera Bio on > Iatros01/Development/RPackages/nvNormalize/nvNormalize.Rcheck' > * using R version 2.9.

Re: [Rd] Clarifications please.

return 0; > > } > > Regards > > Abhijit Bera > > > On Wed, Aug 26, 2009 at 12:37 PM, Abhijit Bera <mailto:abhib...@gmail.com>> wrote: > > Hi Martin > > Thanks. I think I got the hang of it. I will try it out and post any >

Re: [Rd] Unexpected behaviour initializing S4 class

ing of named arguments taking precedence of positional matching of unnamed arguments. > I assume this is due to the naming similarity of k and kl, probably > confusing the matching algorithm: if another first argument for > b.initialize is used (not starting with k), everything is fine. > &g

Re: [Rd] Suggestion: Allow packages to add additional information to sessionInfo()

of pages) rather than the summary intended. Yes these are bugs, and I guess 'package x is producing complete garbage for sessionInfo, likely because your package is out of date. Please update your package and provide sessionInfo again' might well serve to address the user's original problem, but it would have been better to spot the outdated package by looking at the version number produced by sessionInfo(). Martin Morgan > Best, > Fritz > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] enabling core dumps

pleyd...@supagro.inra.fr wrote: > "Writing R Extensions" says > > {quotes} > If you have a crash which gives a core dump you can use something like > > gdb /path/to/R/bin/exec/R core.12345 > > to examine the core dump. If core dumps are disabled... > {unquotes} > > sadly it doesn't go on t

Re: [Rd] enabling core dumps

pleyd...@supagro.inra.fr wrote: >> not really answering your question, but I find it more useful to >> >> R -d gdb >> >> or >> >> R -d gdb -f test.R >> >> where test.R reproduces the bug in some minimal code. A variant is >> >> R -d valgrind -f test.R >> >> if the memory problem is not easy to s

Re: [Rd] importing/loading package without a namespace

Hi Christos -- Christos Hatzis wrote: > I am developing a package that imports some functions from another package. > The imported package (qcc) does not have a namespace and this is causing > problems with loading of my package, which has a namespace. Is there a > workaround to allow loading the

Re: [Rd] S3 objects in S4 slots

as the feel of a workaround, but setOldClass(class(a)[1:2]); setIs("Corpus", "list") helps here, first registering c('vCorpus', 'Corpus') as an S3 hierarchy and then defining the relationship between the root of the hierarchy and (the S4 class) 'list'. Mar

[Rd] DYLIB_EXT vs. SHLIB_EXT?

The graph Bioconductor package wants to compile its C code to a shared library that is named differently from the package, to avoid conflict with graph.dll and friends from graphviz. So recently we tried after: $(SHLIB) mv $(SHLIB) BioC_graph$(DYLIB_EXT) and useDynLib(BioC_graph) in the

Re: [Rd] How do I access class slots from C?

stall("setWeights"),portSpec,portWeights)); PROTECT(portSpec=R_tryEval(e,R_GlobalEnv,NULL)); PROTECT(e=lang2(install("print"),portSpec)); R_tryEval(e,R_GlobalEnv,NULL); UNPROTECT(3); Rf_endEmbeddedR(0); return 0; } Regards Abhijit Bera [[alternative HTML version deleted]] ___

Re: [Rd] Dependency 'sma' is not available

.ch/mailman/listinfo/r-devel -- Martin Morgan 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 __ R-devel@r-project.org maili

Re: [Rd] mysteriously persistent generic definition

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 > > __ > R-devel@r

Re: [Rd] group generics

probably v <- callNextMethod(e1, e2) Martin > print(v) > new("B", v, xb=e1...@xb) > } > ) > > > Results: >> t1 <- new("B", new("A", xa=4), xb=2) >> t1 > An object of class “B” > Slot "xb": > [1] 2 > >

Re: [Rd] group generics

Hi Ross -- Ross Boylan wrote: > > > Martin Morgan wrote: >> Hi Ross -- > >> Ross Boylan writes: > >>> I have classes A and B, where B contains A. In the implementation of >>> the group generic for B I would like to use the corresponding group

[Rd] how to catch useDynLib errors? Rgraphviz

success using library.dynam in .onLoad? Thanks in advacne Martin -- Martin Morgan 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

Re: [Rd] recursive data-structures in R - An S4 "node" Class

Call to a C-level manipulation on the pointer's content. You have some responsibility to make sure that the object is managed appropriately (e.g., with a finalizer that frees memory when the ExternalPtr is no longer referenced in R). You also need to protect or prepare your user for the action-a

Re: [Rd] S4 setClass / initialize misunderstanding

call to new("Bar", <...>)) and get the expected 'initialize' behavior. Placing 'file' after '...' means that 'file' doesn't capture unnamed arguments, which are supposed to be prototypes for classes that .Object extends. Martin > > Thanks, jim > >

[Rd] org-mode (was Re: Feature Request: Multiline Comments)

> } > > #+end_src > > and so on . > > Thanks > Saptarshi > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview

Re: [Rd] Problem with S3 to S4 transition

) is defined as suggested above, the new generic is generated when the package is installed (not loaded, so the message creating a new generic is only presented at installation) and placed in the package environment (e.g., ls(name="package:pkgA")) and not .GlobalEnv. Explicitly calling

Re: [Rd] DESCRIPTION: Imports: assertion of version?

of the code importing the >> other package, and hence we cannot know which DESCRIPTION file to >> check against? > > I'm not aware of any use case in which the current lack of checking is a > "feature". I would be interested in a patch (with testing) for this.

Re: [Rd] Some more help on S4 mechanism

th the NAMESPACE where I can add > "import(P1)". Finally when, as a user, I load both by library() (first > P1 then P2), I receive a message about function .onLoad being loaded twice. > > How can I avoid this. your export pattern includes .onLoad; arrange for .onLoad not to be expor

Re: [Rd] full copy on assignment?

imitive replacement doesn't >> copy it. > ... > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairvie

Re: [Rd] S4 method defined but not used

tools_2.11.0 > > ### end R code > > R was compiled from the sources. All packages are up-to-date (as of the 21 > May 2010). My system is a Ubuntu 10.04 (32 bits), with kernel > 2.6.31-20-generic. I could not reproduce the problem using R 2.11.0 on > Windows Vista, or

Re: [Rd] "[" operator and indexing ambiguity

gt; warning("using index [int], cannot distinguish from > [int,,ANY], use [int,1:dim(x)[2],ANY] otherwise") > tmp = [EMAIL PROTECTED], drop = FALSE] > } > else { > tmp = [EMAIL P

[Rd] non-interactive R_tryEval does not return

[1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] non-interactive R_tryEval does not return

Yes, I know this, but R then acts as though it were interactive! Thanks for the suggestion though. Martin Thomas Friedrichsmeier <[EMAIL PROTECTED]> writes: > On Wednesday 21 February 2007 23:09, Martin Morgan wrote: >> > ./tryEval --slave < tmp.R >> >> Error i

Re: [Rd] non-interactive R_tryEval does not return

hoose to do differently in response to interactive()). Thanks to both for the help, Martin > On Wed, 21 Feb 2007, Martin Morgan wrote: > >> ...at least I think that is what happens, at least on some >> configurations. Here's a repeatable example: >> >> cd R_HOME

Re: [Rd] Problem using callNextMethod() in S4

> msg <- validMsg(msg, paste(sQuote("mydir"), "is not a system > directory")); > }#if > print(paste("base:mydir = ",[EMAIL PROTECTED])) > if (is.null(msg)) TRUE else msg; >} > )#setValidity > > setMethod("initialize", "derivedClass", >function(.Object, ...) { > print("---initialize:derivedClass---") > #.Object <- callNextMethod(); > if ([EMAIL PROTECTED] == "") { > [EMAIL PROTECTED] = "MyTitle"; > }#if > print(paste("derived:mytitle = ",[EMAIL PROTECTED])) > .Object <- callNextMethod(); > .Object; >} > )#initialize > > setValidity("derivedClass", >function(object) { > print("---setValidity:derivedClass---") > msg <- NULL; > strg <- [EMAIL PROTECTED]; > if (!(is(strg, "character") && nchar(strg) > 0)) { > msg <- validMsg(msg, paste(sQuote("mytitle"), "is missing")); > }#if > print(paste("derived:mytitle = ",[EMAIL PROTECTED])) > if (is.null(msg)) TRUE else msg; >} > )#setValidity > > > Here is the new output with the same error: > > > library(methods) > > source("testS4.R") > > tmp<-new("derivedClass") > [1] "---initialize:derivedClass---" > [1] "derived:mytitle = MyTitle" > [1] "---initialize:baseClass---" > [1] "base:strg = " > [1] "base:mydir = /Volumes/CoreData/CRAN/Workspaces/tests" > > > > tmp<-new("derivedClass",myname="testname",mydir="",mytitle="testitle") > [1] "---initialize:derivedClass---" > [1] "derived:mytitle = MyTitle" > [1] "---initialize:baseClass---" > [1] "base:strg = " > [1] "base:mydir = /Volumes/CoreData/CRAN/Workspaces/tests" > [1] "---setValidity:baseClass---" > [1] "base:myname = testname" > [1] "base:mydir = " > Error in validObject(.Object) : invalid class "derivedClass" object: > 'mydir' is not a system directory > > I do not understand why "mydir" is not recognized correctly? > > Thank you > Christian > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Invalidating inaccessible SEXP?

down a bug (it sometimes doesn't occur), or to know that a patch fixes the problem. Thanks, Martin -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/ma

[Rd] Incomplete valgrind instrumentation level documentation

c, logical, integer vectors and R_alloc memory level 2 marks free memory (DATAPTR, STRING_PTR) and the protection stack as inaccessible level 3 marks SEXP as inaccessible -- Martin Morgan Bioconductor / Computational Biology http://biocon

[Rd] Shared lib locations (was Re: [R] problem with RCurl install on Unix0

[EMAIL PROTECTED] > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UKFax: +44 1865 272595 > > __ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Bug in str or issue with class management in my package?

wiss,b=100)) > str(bte) > > yields the error message > > Errorr in FUN(c("lmg.lower", "lmg.upper", "lmg.rank.lower", > "lmg.rank.upper", : > no slot named "pmvd.lower" for this object of class > "relim

Re: [Rd] Problem with S4 inheritance: unexpected re-initialization?

ject)) >> .Object <- callNextMethod(.Object, filename=filename, >> filedir=filedir, ...) >> [EMAIL PROTECTED] <- filename >> [EMAIL PROTECTED] <- filedir >> .Object >> } >> ) >> >> That's for the style. Now let's talk about the semantic. Here is the >> definition of >> your BaseClass class: >> >> setClass("BaseClass", >> representation( >> "VIRTUAL", >> filename="character", >> filedir="character" >> ), >> prototype( >> filename = character(), >> filedir = as.character(getwd()) >> ) >> ) >> >> (Note that this definition is what _I_ get after I cleaned it and indented >> it which >> is something that _you_ are expected to do.) >> >> o Initializing the 'filename' slot to character() is useless since this is >> the default. >> o Wrapping getwd() inside as.character() is useless since getwd() returns a >> character vector. >> o BUT MOST IMPORTANTLY THAN ANYTHING ELSE: given the fact that you've >> provided a prototype >> for class BaseClass, your initialize method is useless since it does >> _nothing_ more >> than what the default initialize method does! If you want to define your >> own "initialize" >> method for the only purpose of printing messages, then you could do it in >> a much simpler >> way: >> >> setMethod("initialize", "BaseClass", >> function(.Object, ...) >> { >> cat("--initialize:BaseClass--\n") >> cat("BaseClass:init:class(.Object) = ", class(.Object), "\n", >> sep="") >> callNextMethod() >> } >> ) >> >> But as I said initially, the file system related stuff is useless to >> illustrate the >> S4 issue you want to show us so why didn't you just provide: >> >> setClass("BaseClass", >> representation("VIRTUAL", slot1="character"), >> prototype(slot1="aaa") >> ) >> >> setMethod("initialize", "BaseClass", >> function(.Object, ...) >> { >> cat("--initialize:BaseClass--\n") >> cat("BaseClass:init:class(.Object) = ", class(.Object), "\n", >> sep="") >> callNextMethod() >> } >> ) >> >> See? I ended up by replacing 25 lines of your hard-to-read/confusing code by >> 12 >> lines of clean code containing only the STRICTLY NECESSARY stuff for an S4 >> discussion. >> That's what you should have done instead of sending us 150 lines of code. >> >> Sorrowly people will not try to read your code unless it's obvious that >> _you_ did your >> best to provide the cleanest/simplest possible code that illustrates the >> issue you want >> to discuss. >> >> Also maybe you could try to read a little bit more about S4 and >> initialization mechanisms. >> >> Cheers, >> H. >> >> > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] R CMD build fails with try(stop()) in vignette

LC_IDENTIFICATION=C attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "base" -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org ___

Re: [Rd] setClass inside a function

Hi Iago -- Here's my attempt at an answer. "Iago Mosqueira (Cefas)" <[EMAIL PROTECTED]> writes: > Hello, > > I would like to create a function that gets passed a class name and > then calls setClass, and a few other functions, inside. I have done > this in the past with setmethod, creating acces

Re: [Rd] setClass inside a function

e complcated substitutions; eval(substitute({ setGeneric(NAME, function(object, ...) { standardGeneric(NAME) }) }, list(NAME=name))) >> >setMethod(name, signature(object='missing'), >> &g

[Rd] Inherited S4 .Data prototype not assigned

aPart(pri)) dataPartDone <- TRUE } } > sessionInfo() R version 2.6.0 Under development (unstable) (2007-05-03 r41426) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETA

[Rd] Help understanding LAPACK symbol resolution

g symbols to libraries will occur in a way consistent with the last two points (as opposed to the implementation details) across platforms, compilers, and static vs. shared libraries? Thanks for any reassurance or corrective guidance. Martin -- Martin Morgan Bioconductor / Computational Biolog

Re: [Rd] Help understanding LAPACK symbol resolution

Prof. Ripley, Thank you for the very helpful guidance and pointer to fastICA. Martin Prof Brian Ripley <[EMAIL PROTECTED]> writes: > On Sun, 13 May 2007, Martin Morgan wrote: > >> R developers, >> >> I am trying to understand how symbols are resolved, so that I c

Re: [Rd] list element names in S4 class extending list

t;> setClass("c1", contains="list") > [1] "c1" >> l1 = list(a=1, b=2) >> o1 = new("c1", l1) >> names(o1) # pleasant surprise > [1] "a" "b" >> setClass("c2", contains="c1") > [1] "c2" >> o2 = new("c2", l1) >> names(o2) # sad > NULL >> sessionInfo() > R version 2.6.0 Under development (unstable) (2007-05-11 r41535) > powerpc-apple-darwin8.9.0 > > locale: > C > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" > [7] "base" > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] [Bioc-devel] promptClass

tached. > > If showMethods or a wrapper for it could be convinced to output a link > to a help file, then it might actually be a good way to go... > > + seth > > -- > Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center > http://bioconductor.org > &g

[Rd] segfault during cbind

3 (gdb) p i $7 = 22839 (gdb) p idx $8 = 22840 Both rm and lapply are needed to trigger the fault; an R level gc() before the final line 'cures' the fault (and the valgind complaint). The data file is available (with free registration) at https://www.affymetrix.com/support/file_download

Re: [Rd] segfault during cbind

To amend, the traceback is only > Traceback: > 1: cbind(probe, gb) > aborting ... Oops. Martin Martin Morgan <[EMAIL PROTECTED]> writes: > The following code results in a seg fault. > >> sessionInfo() > R version 2.6.0 Under development (unstable) (2007-06-21 r

Re: [Rd] segfault during cbind

break; > > around 1258 in bind.c. Can you test that please? > > > On Thu, 21 Jun 2007, Martin Morgan wrote: > >> The following code results in a seg fault. >> >>> sessionInfo() >> R version 2.6.0 Under development (unstable) (2007-06-21 r42013)

Re: [Rd] How to get the names of the classes exported by a specific package.

")" however I can not find a similar > process to get the S4 classes. Are there functions to access this > information ? > > Best and thanks > > EJ > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] suggesting \alias* for Rd files (in particular for S4 method documentation)

t the best way of going around documentation and > code/documentation mismatches. > > Best regards, > Oleg > > -- > Dr. Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-464466 > > __ > R-devel@r-project.org mailing

[Rd] locales and readLines

conventions of the files they read, and to know how R deals with encodings. Are there other / better solutions? Any chance for some (additional) 'smarts' when reading files? Martin -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org _

Re: [Rd] locales and readLines

s.html says, > >It is hopefully obvious from the preceding discussion that a sequence of >octets can be interpreted in a multitude of ways when processed as >character data. By looking at the octet sequence only, you cannot even >know whether each octet presents one

Re: [Rd] RUnit testing with R CMD check and more

testing, etc., > but could provide more feedback (sure some of it will be bogous) on > testing on various configurations. > > With regards, Gregor > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-d

[Rd] Sweave vignettes and bitmap on windows

(C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under the terms of the GNU General Public License version 2. For more information about these matters see http://www.gnu.org/licenses/

Re: [Rd] packages MANOR, qvalue, and tkWidgets fail install on Fedora 7 with latest R-beta build

; Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel

[Rd] Locale problems with too-fancy quotes in Windows CMD.exe

e('x') [1] "æxÆ" C:\R>R --version R version 2.6.0 beta (2007-09-20 r42920) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Windows is XP 2002 SP2 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org _

Re: [Rd] Locale problems with too-fancy quotes in Windows CMD.exe

rong' data got into R. Doing c:\> chcp 1252 Active code page: 1252 Allows smart quotes to display correctly. Thanks, Martin Prof Brian Ripley <[EMAIL PROTECTED]> writes: > On Thu, 20 Sep 2007, Martin Morgan wrote: > >> 'Fancy' quotes are displayed incorre

[Rd] 'load' does not properly add 'show' methods for classes extending 'list'

ge: DBI Loading required package: RSQLite An object of class "GeneSetCollection" [[1]] setName: NA geneIds: X (total: 1) geneIdType: Null collectionType: Null details: use 'details(object)' Actually, the behavior is more complicate than appears; in a new R session after l

Re: [Rd] R-Server remotecontrolled via browser-GUI

constructive critics and what you think > about the effort for configuring mod_R/RAPACHE, cairo and the > db-package for r. > > thanks a lot in advance for your help! > > cheers, > > josuah r. > > ______ > R-deve

Re: [Rd] CHAR () and Rmpi

; Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UKFax: +44 1865 272595 > > _

Re: [Rd] R 2.6.0 S4 data breakage, R _data_class(), class<-, etc.

ta_class() needs to be documented and exposed as part of the >> public API (and included in the Rinternals.h include), >> and the recommended way of making an S4 object in C? I found >> classgets() + SET_S4_OBJECT() seem to work, but I'd like an >> authoritative answer... >> >> 5) I am

Re: [Rd] R 2.6.0 S4 data breakage, R _data_class(), class<-, etc.

[EMAIL PROTECTED] (Bjørn-Helge Mevik) writes: > Martin Morgan wrote: > >> But both 'new' and 'as' appear to produce invalid (in a different >> sense, I guess) objects: >> >>> setClass("snp", contains="raw", >> +

[Rd] data.frame row.names=NULL with named vector

A minor issue with data.frame is a change introduced leading to R 2.5.0, where row.names=NULL (i.e., do not name rows) is not honored with a named vector > x <- letters[1:3] > names(x) <- x > data.frame(x, row.names=NULL) x a a b b c c and a slightly more subtle example > data.frame(y=1:3, x,

[Rd] Windows fixed/etc/Makeconf SHELL incorrect?

R CMD config. R version 2.7.0 Under development (unstable) (2007-10-19 r43218) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Martin -- Martin Morgan Bioconductor / Computational Biology __ R-devel@r-project.org mailing

Re: [Rd] Windows fixed/etc/Makeconf SHELL incorrect?

medies the situation. Thanks, Martin Duncan Murdoch <[EMAIL PROTECTED]> writes: > Martin Morgan wrote: >> R developers, >> >> On windows, it seems like R_HOME/etc/Makeconf has >> >> SHELL = /bin/sh >> >> instead of the location of Rtools'

Re: [Rd] Windows fixed/etc/Makeconf SHELL incorrect?

n things up. Thanks for your time. Martin Duncan Murdoch <[EMAIL PROTECTED]> writes: > Martin Morgan wrote: >> D:\mtmorgan\src\R-devel>bin\R CMD config CC >> make: /bin/sh: Command not found >> make: ** [print] Error 127 >> make: /bin/sh: Command not found >&g

Re: [Rd] another S4 question ...

> of arguments like "digits", etc. > > Is it impossible, or a horrible idea, to override the > generic definition? (The "arm" package has defined a > new generic, "display", which does a similar thing but > has an intermediate level of detail

Re: [Rd] S4 class extending data.frame?

t; >> hoping for enlightenment (it would be lovely to be >> shown how to make this work, but a definitive statement >> that it is impossible would be useful too). >> >> cheers >> Ben Bolker >> >> -BEGIN PGP SIGNATURE- >> Version: GnuPG v

Re: [Rd] Problem with initialize of S4 classes

ject) <- unlist(mad) >.Object <- callNextMethod(.Object, ...) >.Object > } > setMethod("initialize", "PreFilter", initialize.PreFilter) > > setValidity("PreFilter", >function(object) { > print("--setValidity:

[Rd] Finding windows DLLs

The XML package relies on libxml2.dll (e.g., bundled with the CRAN binary) installed in library/XML/libs. Unfortunately, c:/WINDOWS/system32/libxml2.dll will be found and loaded before this. Is there any programatic solution? Thanks, Martin -- Martin Morgan Computational Biology / Fred

Re: [Rd] Finding windows DLLs

There is a way to change this: > > http://msdn2.microsoft.com/en-us/library/ms686203(VS.85).aspx > > but it would preclude Windows 2000. > > Perhaps Martin can explain how libxml2.dll got into c:/WINDOWS/system32/? > My suggestion is that we rename the DLL when copied into >

Re: [Rd] Finding windows DLLs

t is not). > > > On Mon, 7 Jan 2008, Prof Brian Ripley wrote: > >> On Mon, 7 Jan 2008, Duncan Murdoch wrote: >> >>> On 1/7/2008 2:51 PM, Martin Morgan wrote: >>>> The XML package relies on libxml2.dll (e.g., bundled with the CRAN >>>>

Re: [Rd] Package Building and Name Space

ne it's pretty hard to be sure, but I'd >> assume you have the expression MyPackage::MyFunction somewhere in your >> package, but MyPackage doesn't have a namespace. In that case, you have >> to make sure it is attached

[Rd] NAMESPACEs and S4 classes

as defined in tmpA? Thanks, Martin > sessionInfo() R version 2.7.0 Under development (unstable) (2008-02-09 r44397) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.U

Re: [Rd] NAMESPACEs and S4 classes

tly.  I > think the fix is easy & will try to add it to r-devel fairly soon. > - There are limitations to using duplicated class names, because not all > computations will carry the appropriate package information to say which > "myClass" we mean.  So if one can avoid dup

Re: [Rd] DNAcopy package output data

isregard and delete > this email if you are not the intended recipient. > > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel

Re: [Rd] Problems initializing an extended S4 class

type for A that I know won't break my > initialize method, but that seems inelegant and hard to maintain. Is > there a better way to code this so that I can reliably instantiate B > using a valid A object? Hopefully I've just got something wrong in the > formals for my initi

[Rd] write.table with row.names=FALSE unnecessarily slow?

lt;- seq_len(nrow(x)) +d <- list(if (makeRownames==TRUE) row.names(x) else NULL, + if (makeColnames==TRUE) names(x) else NULL) p <- ncol(x) } nocols <- p==0 improves performance at least in proportion to nrow(x): > system.time({ + write.

Re: [Rd] write.table with row.names=FALSE unnecessarily slow?

I neglected to include my test case, > df <- data.frame(x=1:(10^7)) Martin Martin Morgan <[EMAIL PROTECTED]> writes: > write.table with large data frames takes quite a long time > >> system.time({ > + write.table(df, '/tmp/dftest.txt', row.names=

Re: [Rd] "[<-" plus drop-type extra argument

_ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > > ** > The contents of this email are for the named addressee

[Rd] X11 image problem in R-2.8.0 Under development / R-2.7

abilities() jpeg pngtcltk X11 aqua http/ftp sockets libxml TRUE TRUE TRUE TRUEFALSE TRUE TRUE TRUE fifo clediticonv NLS profmemcairo TRUE TRUE TRUE TRUE TRUE TRUE Martin -- Martin Morgan Computa

Re: [Rd] X11 image problem in R-2.8.0 Under development / R-2.7

-- if so, it was an X11 timing issue and we > needed to re-read the X11 window size at a later time. Please try > r45102 or later. > > On Fri, 4 Apr 2008, Prof Brian Ripley wrote: > >> On Thu, 3 Apr 2008, Martin Morgan wrote: >> >>> I apologize if this is to

Re: [Rd] X11 image problem in R-2.8.0 Under development / R-2.7

Prof Brian Ripley <[EMAIL PROTECTED]> writes: > On Sat, 5 Apr 2008, Martin Morgan wrote: > >> Yes, thank you, this fixes the problem for me. >> >> As a follow-up, and again with my ignorance of where processing is >> actually occuring, it seems like the X11

Re: [Rd] X11 image problem in R-2.8.0 Under development / R-2.7

s type argument, consequences of display type for different aspects of performance, and use of alpha (vectorized, so I can, e.g., make failed tiles have alpha=1; previously I had found that setting a scalar alpha<1 did indeed help with point overlap, but the interesting points (failures) were

Re: [Rd] HOW TO AVOID LOOPS

ngs are quite variable; perhaps they're about equal?) Martin "carlos martinez" <[EMAIL PROTECTED]> writes: > Appreciate the ingenious and effective suggestions and feedback from: > > Dan Davison > Vincent Goulet > Martin Morgan > Hadley Wickham > >

Re: [Rd] Doing the right amount of copy for large data frames.

gt; > > ### Usage: > nn <- 10 > ## dd1 below could possibly be created by read.table or scan and data.frame > dd1 <- data.frame(xx = rnorm(nn), yy = rnorm(nn)) > dd2 <- new('DataFrame', data = dd1) > rm(dd1) > ## Now work with dd2 > > > Thanks a lot, > Gopi Gosw

[Rd] 2.7.0 RC (2008-04-19 r45391) package.skeleton LazyLoad incorrect

package.skeleton inserts a lowercase second l in LazyLoad, so that the package is not, in fact, lazy loaded. Martin -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206

[Rd] doc buglet / bug: row / col as.factor requires dimnames

of factor(.Internal(col(dim(x))), labels=colnames(x, do.NULL=FALSE, prefix="")) > sessionInfo() R version 2.8.0 Under development (unstable) (2008-05-13 r45682) x86_64-unknown-linux-gnu Martin -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100

Re: [Rd] seeing an S4 method, not using it

-04-22) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_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 attached bas

Re: [Rd] Multiple Intersections

k subsets' implies all elements of n? Martin > My question is two-fold: > > 1. If such a function already exists, what is it called? > 2. If such a function does not exists, it is worthwhile to encode it (i.e. > can I send my code to someone?). > > Cheers, > --tony > &

[Rd] NAMESPACE & methods guidance, please

gs the user does to their environment) but in other ways it seems to undo any benefit of method dispatch and requires the tmpA author to fully discover (and monitor -- what if AnnotationDbi splits 'ls' into a AnnotationBase pkg?) the class hierarchy. The specific example of KEGG.db and A

[Rd] R CMD CHECK WARNING inappropriate for S4 method?

aking GSEABase Depend: graph rather than Import: graph does not help. Any guidance welcome. Thanks, Martin -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnol

Re: [Rd] slot(obj, "nosuch") documentation question

2008-06-04 r45830) >> >> -- >> SIGSIG -- signature too long (core dumped) >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> >

Re: [Rd] R CMD CHECK WARNING inappropriate for S4 method?

ot;P1") > > objects(parent.env(n1), all=TRUE, pattern="union") > [1] ".__M__union:base" ".__T__union:base" "union" > > > One final catch: In this version, you do need to ensure that the > user's call to union() sees the

Re: [Rd] Rmpi segfault after install on Ubuntu Hardy Heron

I use R-help? As | I read the posting guide, I'm not sure. | 2. Has anyone considered an R-SIG-HPC list? Anyone besides me interested? I'd join. Dirk -- Three out of two people have difficulties with fractions. __ R-devel@r-project.or

Re: [Rd] Snow or alternative MPI packages on Windows

nvestment. Its contents are based on information > obtained from sources believed to be reliable but HSBC makes no > representation and accepts no responsibility or liability as to its > completeness or accuracy. > > __ > R-devel@r-project.org mailing list > https

Re: [Rd] problems with plotting of graphNEL (PR#11993)

he dark, have you tried to update your packages to their most recent version, e.g., following the instructions at http://bioconductor.org/download ? Martin > Thanks very much! > Christian > > ______ > R-devel@r-project.org mailing list

Re: [Rd] Outdated dependencies and install.packages()

A small addendum is that if the outdated dependency is in the LinkingTo: field, the error can be more cryptic. Installation then fails with compilation errors rather than the hint that the dependency is out of date. Martin Morgan Peter Dalgaard <[EMAIL PROTECTED]> writes: > This loo

Re: [Rd] S4 coercion

TSdeleteSQL(serIDs = serIDs, con = con, ...) > 2: TSdelete("vec", con) > 1: TSdelete("vec", con) > > str(con) > Formal class 'TSPostgreSQLConnection' [package "TSPostgreSQL"] with 4 slots > ..@ Id : int [1:2] 21795 1 > ..@ dbname

Re: [Rd] Using R from Java

nks in advance for any suggestion. > > Regards, > -Marzio > > -- > http://marzio.sala.googlepages.com > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.

Re: [Rd] Extract method for a new class

OTECTED]) }) because the initialize call will [provided any initialize methods defined on contained classes don't interfer] minimize copying. You'll also likely want methods for $ and [[, and assignment methods [<- etc.) Hope that helps, Martin > Thank

[Rd] more efficient small subsets from moderate vectors?

packages: [1] stats graphics grDevices utils datasets methods base -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

Re: [Rd] NAMESPACE/DESCRIPTION and imports

r MI 48109-0646 > 734-936-8662 > ** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > > __ > R-devel@r-pro

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