Re: [R] Nodes edges with similarity matrix

. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Nodes edges with similarity matrix

package which provides many powerful graph algorithms. All of these packages are available via Bioconductor (no bio required) and can be installed as: source(http://bioconductor.org/biocLite.R;) biocLite(c(RBGL, Rgraphviz)) + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer

Re: [R] Nodes edges with similarity matrix

Along with the example I gave using graphAM, you might also want to look at the help page for the distGraph class which may be more directly what you want: library(graph) class ? distGraph __ R-help@stat.math.ethz.ch mailing list

Re: [R] Suspected memory leak with R v.2.5.x and large matrices with dimnames set

a concern that there is a leak that needs fixing? It is worth noting that the internal handling of character vectors has changed in R-devel and so IMO testing there would make sense before persuing this further, I suspect your results will be different. + seth -- Seth Falcon | Computational

Re: [R] A clean way to initialize class slot of type numeric vector

be really appreciated. Thank you. How about: setClass(foo, representation(members=numeric), prototype(members=numeric(0))) That is, use a zero-length vector to signify a vector that isn't there. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research

Re: [R] tcltk error on Linux

-- there will be a considerable performance hit so only load them when you need them. Presumably, that's why they are there in the first place. The warning messages are a problem and suggest some needed improvements to the methods packages. These are being worked on. + seth -- Seth Falcon

Re: [R] Need Help: Installing/Using xtable package

. The addition of the namespace is really a good. Yes, it will cause some hicups for folks who were calling the methods directory (tsk tsk). But the addition fixes breakage that was occuring due to internal xtable helper functions being masked. + seth -- Seth Falcon | Computational Biology | Fred

Re: [R] S4 methods: unable to find an inherited method

is not an S4 class, there will be tricks required). Or you need to pass in an xcmsRaw object. Cheers, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user

Re: [R] Problems with expresso

packages are up to date: ## *new* R session, no saved data loaded source(http://bioconductor.org/biocLite.R;) biocLite(Biobase) library(Biobase) update.packges(repos=biocReposList()) + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http

Re: [R] Catch errors

) { print(caught an error) 1 }) tag + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-help@stat.math.ethz.ch mailing list

Re: [R] initalizing and checking validity of S4 classes

finished with initialize). This is a good point. It suggests that, at least, one must initialize all non-inherited slots to valid values _before_ calling the next method. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

Re: [R] R and HTTP get 'has file changed'

) something(x$value())) I've used this in the pkgDepTools package to retrieve package download sizes. Cheers, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch

Re: [R] installing Rgraphviz under fedora 5

will need to use graphviz 2.12. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] locked environment and inheritance

your are trying to achieve overall. Perhaps there are other approaches... Also, at this point, the discussion is more appropriate for R-devel. Perhaps you can move the conversation there? Best, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http

Re: [R] locked environment and inheritance

). Using: setClass(myS4class, representation(otherS4class, mydata = numeric), where = topenv()) have you tried just omitting the where argument? Classes will get defined in the package environment and I think that's what you want. + seth -- Seth Falcon | Computational Biology | Fred

Re: [R] Affycoretools

PROTECTED] writes: I am having problem installing the affycoretools package. When I do it through biocLite, I get error messages saying the package XML cannot be installed and that I need a more recent version of libxml2. And did you resolve this by instaling a more recent libxml2? + seth -- Seth

Re: [R] summing up colum values for unique IDs when multiple ID's exist in data frame

(lapply(idIdx, function(x) sum(df[[cn]][x])), use.names=FALSE) }) attributes(ans) - list(names=colNms, row.names=names(idIdx), class=data.frame) ans } -- Seth Falcon | Computational Biology | Fred

Re: [R] S4 object slot of type 'call'

explicit tests like: if (class(obj) == NullCall) ... else ... For example, you could define a show metho that printed 'NULL' or something. It is also possible to define a class union and use that as the slot type. I don't like this solution, but YMMV. + seth -- Seth Falcon | Computational

Re: [R] accessing unexported functions

might also be interested in assignInNamespace -- perhaps you can add you function to the package's name space and then call it using :::. Be warned, this is the wrong way to solve a long-term problem. Bad things will happen and nobody will feel sorry for you. + seth -- Seth Falcon | Computational

Re: [R] questions on package of KEGG

way for KEGG in R? Many Thanks!! Hua I think you should ask this question on the bioconductor list. http://www.bioconductor.org/docs/postingGuide.html + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

Re: [R] names of objects in .rda

of objects. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] Unit Testing Frameworks: summary and brief discussion

suppose it can be useful to make sure that any formatting of inputs is being done properly. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https

Re: [R] unable to find inherited method for function edges, for signature ugsh, missing

means and about why this function causes problems. Can anyone help. Thanks in advance. Does your package have a name space? What does your package's DESCRIPTION file look like? Do any of the examples call library() or require()? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson

Re: [R] apply problem

. But the return value will be a list, not a data.frame. I think for loops get a bad wrap. There are times when they are appropriate and even optimal in R programming. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

Re: [R] Method dispatch for print() in package its

alone. Not sure if that helps you. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] Subsetting list of vectors with list of (boolean) vectors?

Johannes Graumann [EMAIL PROTECTED] writes: Dear Rologists, I'm stuck with this. How would you do this efficiently: aPGI [[1]] [1] 864 5576 aPGItest [[1]] [1] TRUE FALSE result - [magic box involving subset) result - aPGI[aPGItest[[1]]] result [[1]] [1] 864 + seth -- Seth

Re: [R] how to reverse a list

+ seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ 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

Re: [R] RMySQL *was* working...

, dbDriver() threw an error: dbDriver(MySQL) Error in function (classes, fdef, mtable) : unable to find an inherited method for function dbDriver, for signature function Do you mean dbDriver(MySQL)? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http

Re: [R] getting ess/emacs to link with a remote instance of R

running R remotely. YMMV. * You may find that sending commands to the remote session without echoing is much faster. So you might try C-u C-c C-r to send a region. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

Re: [R] Over-writing functions from other packages? What is a good strategy??

that import might be preferred over Depends for packages that have namespaces. Finally, if you were depending on graph and not Rgraphviz, then you could rename graph::edges when you import it in your NAMESPACE file: importFrom(graph, someOtherName=edges) + seth -- Seth Falcon | Computational

Re: [R] Fast lookup in ragged array

and collisions are resolved using chaining. To reduce collisions and have a more efficient hashtable, you want to have more slots in the vector than items since the hash function is rarely perfect for your data. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http

Re: [R] Fast lookup in ragged array

of branches you will search. Using an environment implies you will need unique character names for each subgraph. Do you have that? If not, you could concatenate node names. For a 200 node graph, that should be ok. Hope that helps some. + seth -- Seth Falcon | Computational Biology | Fred

Re: [R] Fast lookup in ragged array

that the underlying hashtable will need to be resized and this has a performance impact. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

Re: [R] Sweave question: prevent expansion of unevaluated reused code chunk

Kevin R. Coombes [EMAIL PROTECTED] writes: [2] You are also correct that there is no advantage if I just call them chunk1 and chunk2. But if I call them something more interesting, like perform.quantile.normalization or truncate.and.log.transform, then I can use this structure to explain the

Re: [R] Sweave question: prevent expansion of unevaluated reused code chunk

and chunk2 won't have appeared in labels earlier in the rendered document? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

Re: [R] RMySQL on win32

about it as well. All I really need to do at this point is send select and join queries to the local server--perhaps I should just install RSQLite from CRAN? Well, if you don't need MySQL, then SQLite and RSQLite will get you going. If you do need MySQL, you can try RODBC. + seth -- Seth Falcon

Re: [R] Download packages problem.

will get any useful help. Please have a look at the posting guide and send an update. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

Re: [R] Error loading a dependency in a package: missing namespace?

having to do with namespaces. The thing is that package outliers does not have a NAMESPACE file. Could this be an issue? Yes, you cannot do import(pkg) in the NAMESPACE file if pkg doesn't itself have a NAMESPACE file. So try just removing that from your NAMESPACE file. + seth -- Seth Falcon

Re: [R] from function to its name?

Ido M. Tamir [EMAIL PROTECTED] writes: I wanted to pass a vector of functions as an argument to a function to do some calculations and put the results in a list where each list entry has the name of the function. I thought I could either pass a vector of function names as character, then

Re: [R] object is not subsettable

(hasChr)) + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ 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

Re: [R] help with RMySQL

Ravi S. Shankar [EMAIL PROTECTED] writes: Hi R users, I am using RMySQL to connect to a database in MySQL. I have 3 questions. 1)When I give the following command dbListTables(con) I get the output stack imbalance in .Call, 142 then 143 stack imbalance in -, 140 then

Re: [R] Problems with 'delay'/'delayedAssign' when installing data package

Hi Wolfram, Wolfram Fischer [EMAIL PROTECTED] writes: I downloaded: http://www.bioconductor.org/data/metaData/hgu95av2_1.7.0.tar.gz described as: Package: hgu95av2 Title: A data package containing annotation data for hgu95av2 Version: 1.7.0 Created: Wed Jan 12

Re: [R] RES: RdbiPgSQL in R 2.4.1

Eduardo Dutra de Armas [EMAIL PROTECTED] writes: Hi Seth I'm running R on WinXP. On the first time I've installed Rdbi and RdbiPgSQL from zip files not downloaded from Bioconductor. No problems during installation. Now I tried to install from biocLite and a message was showed for RdbiPgSQL.

Re: [R] RdbiPgSQL in R 2.4.1

Hi Eduardo, It would probably be best to send question regarding Bioconductor packages to the bioconductor email list. Eduardo Dutra de Armas [EMAIL PROTECTED] writes: Hi R-users I recently downloaded RdbiPgSQL 1.8.0 and Rdbi 1.8.0 from Bioconductor to be installed under R 2.4.1. When

Re: [R] R for bioinformatics

Benoit Ballester [EMAIL PROTECTED] writes: Hi, I was wondering if someone could tell me more about this book, (if it's a good or bad one). I can't find it, as it seems that O'Reilly doesn't publish any more. I've never seen a copy so I can't comment about its quality (has anyone seen a

Re: [R] help with regexpr in gsub

Kimpel, Mark William [EMAIL PROTECTED] writes: I have a very long vector of character strings of the format GO:0008104.ISS and need to strip off the dot and anything that follows it. There are always 10 characters before the dot. The actual characters and the number of them after the dot is

Re: [R] RSQLite NA on input

Hi Richard, It would help if you provided a bit more on how you are going about the import (along with your version of R and RSQLite). R Gott [EMAIL PROTECTED] writes: I haev some .csv data files with missing values - eg below

Re: [R] listing all functions in R

Earl F. Glynn [EMAIL PROTECTED] writes: Prof Brian Ripley [EMAIL PROTECTED] wrote in message news:[EMAIL PROTECTED] Here is a reasonable shot: findfuns - function(x) { if(require(x, character.only=TRUE)) { env - paste(package, x, sep=:) nm - ls(env, all=TRUE)

[R] [R-pkgs] RSQLite 0.4-18 sent to CRAN

files. This resolves performance issues and line ending quandries on Windows. * Fix for a bug in dbWriteTable when used to import text files; files lacking a trailing end of line marker can now be used. Questions? Send them to the r-sig-db mailing list. Best Wishes, + seth -- Seth

Re: [R] SQLite: When reading a table, a \r is padded onto the last column. Why?

Prof Brian Ripley [EMAIL PROTECTED] writes: [I am not sure who is actually maintaining RSQLite, so am Cc: both the stated maintainer and the person who prepared the package for distribution. The posting guide asked you to contact the maintainer: what response did _you_ get?] For the record, I

Re: [R] package dependency tree

: [144] Seth Falcon. Modeling package dependencies using graphs. R News, 6(5):8-12, December 2006. + seth __ 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

Re: [R] biocondutor installation problem

I'm pretty sure your subject should be: Help configure R to use web proxy on RHEL4. You don't have a Bioconductor specific problem (yet). Kesavan Asaithambi [EMAIL PROTECTED] writes: source(http://www.bioconductor.org/biocLite.R;) Error in file(file, r, encoding = encoding) :

[R] BioC Advanced Course Jan 10th-12th (Space Still Available)

Hello all, There is still space available for the upcoming BioC Advanced Course being held in Seattle January 10th-12th. For details and registration, please visit: https://secure.bioconductor.org/biocadv/ Best Wishes, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer

Re: [R] RSQLite +textConnection()

Alexander Nervedi [EMAIL PROTECTED] writes: Hi Seth, Thank you for taking the trouble to look. I have created some code that simulates the problem. SOme additional observations are: a) After giving the error Error in textConnection(readLines(f, n = 2)) : all connections are in use I cannot

[R] ANN: BioC Advanced Course, Jan 10-12 in Seattle

://secure.bioconductor.org/biocadv/ + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] RSQLite basic

Hi Alexander, Alexander Nervedi [EMAIL PROTECTED] writes: However, this gives all kinds of errors when I run it on a linux box and I am not sure what the error message is telling me. I thought I'd crave your indulgence and ask for advice. m - dbDriver(SQLite, max.con = 25) con -

Re: [R] RSQLite +textConnection()

Alexander Nervedi [EMAIL PROTECTED] writes: Hi ! I am trying to read in 1000 really small text files. When on adams, R bails out after reading 125 files with the error message Error in textConnection(readLines(f, n = 2)) : all connections are in use Please try updating your

Re: [R] RSQLite +textConnection()

Alexander Nervedi [EMAIL PROTECTED] writes: They are uptodate. When I run it on windows the i can load upto 200 files, while on Linux it stops after loading 125. Could you provide as much of a reproducible example as possible (along with sessionInfo())? I will try and have a look. + seth

Re: [R] Rgraphviz -404 Page not found

j.joshua thomas [EMAIL PROTECTED] writes: Again i have problem in locating the package for clique-graphs I tried with BioConductor under Browse for packages, it doesn't work atall. Kindly guid me I think you already got an answer on the Bioconductor list: RBGL is likely the package you are

Re: [R] SNA packages/network package

Bagatti Davide wrote: Hello everyone, I am an italian student who is working with packages SNA (social network analysis) and network. I ask you if there is a simple way to write a R-script using these packages to extract from an adjacency matrix the following things: -number of cliques

Re: [R] Forming SQL Query at run-time

Rahul Thathoo [EMAIL PROTECTED] writes: Hi. I am trying to get data from mysql database using a couple of queries. I do one query to find out the indexes. Then i need to use these indexes in another query, but i keep getting errors. Here is something: numb - dbSendQuery(con2, select

Re: [R] Install RMySQL with R 2.4.0

Joe W. Byers [EMAIL PROTECTED] writes: Seth Falcon wrote: Joe W. Byers [EMAIL PROTECTED] writes: I am having trouble as well with the new version of R 2.4. I downloaded the gz file from the cran website, followed the instructions in the README.win file and installed RMySQL. I have

Re: [R] Install RMySQL with R 2.4.0

Joe W. Byers [EMAIL PROTECTED] writes: I am having trouble as well with the new version of R 2.4. I downloaded the gz file from the cran website, followed the instructions in the README.win file and installed RMySQL. I have mysql installed under c:\mysql not the program files directory

Re: [R] accesing MySQL through JDBC

Your EPEC ICT Team - Ricardo Rodríguez [EMAIL PROTECTED] writes: Please, does R support JDBC access to MySQL databases? Could you point me in the right direction to find some documents about this issue? Have you found the RMySQL package? It allows you to talk to MySQL databases from R. + seth

Re: [R] 'weaver' package problem

Hi Michael, Michael Kubovy [EMAIL PROTECTED] writes: Hi Seth, The possibility of caching computations would be a great boon when one is iteratively refining a paper; so I'm most grateful for your work on this. Unfortunately I have a problem to report: **testing

[R] [R-pkgs] DBI, RMySQL, RSQLite updated

(no feature changes). Best Wishes, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org ___ R-packages mailing list R-packages@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r

Re: [R] Block comments in R?

Uwe Ligges [EMAIL PROTECTED] writes: Use an editor that comments out a whole block which is what I do all the time, e.g. use Tinn-R, Emacs or WinEdt, to mention just a few of them. This, of course, works. The if(FALSE) approach does not because it requires the comment to be syntactically

Re: [R] New project: littler for GNU R

Jeffrey Horner [EMAIL PROTECTED] writes: Seth Falcon wrote: Wow, looks neat. OS X users will be unhappy with your naming choice as the default filesystem there is not case-sensitive :-( IOW, r and R do the same thing. I would expect it to otherwise work on OS X so a change of some sort

Re: [R] New project: littler for GNU R

Wow, looks neat. OS X users will be unhappy with your naming choice as the default filesystem there is not case-sensitive :-( IOW, r and R do the same thing. I would expect it to otherwise work on OS X so a change of some sort might be worthwhile. + seth

[R] ANN: R/BioC Intro Course Oct 9th-11th in Seattle

Hello all, We will be holding an R/BioC intro course in Seattle. The dates are October 9th-11th. For more information, please visit: https://secure.bioconductor.org/biocintro/ Best Wishes, + seth PS: At the moment we are using a self-signed SSL certificate (this is just as

Re: [R] AffyChip Background Analysis

Gunther Höning [EMAIL PROTECTED] writes: Dear list, I want to analyse some HG133Plus2.0 Affymetrix chips. The first thing I intent to do, is just to perform a background correction (mas, rma, gcrma,...) with the cel files. Then I want to take a look at the files. How can I do this ? You

Re: [R] Bioconductor installation errors

Ge, Weigong* [EMAIL PROTECTED] writes: Hello, I follow the Bioconductor instruction (http://www.bioconductor.org/download http://www.bioconductor.org/download ) to install Biocoductor, there have some errors: Please post questions about Bioconductor to the bioconductor mailing list:

Re: [R] Rgraphviz - neato layout - edge weights do not have an effect

Hi Franz, This might be better directed to the bioconductor mail list. Franz Quehenberger [EMAIL PROTECTED] writes: Dear all, neato makes layouts according to a physical model in which the length of the edges is determined by springs. The weight of the edge is the strength of the spring.

[R] [R-pkgs] ANN: 'weaver' package, caching for Sweave

Hi all, I've added a new package 'weaver' to the BioC repository: http://www.bioconductor.org/packages/1.9/bioc/html/weaver.html The weaver package provides extensions to the Sweave utilities included in R's base package. The focus of the extensions is on caching computationally expensive

Re: [R] [R-pkgs] ANN: 'weaver' package, caching for Sweave

Hi again, Sorry for the noise, but I need to make a correction: Seth Falcon [EMAIL PROTECTED] writes: To install: source(http://bioconductor.org/biocLite.R;) biocLite(weaver) At present, the above install sequence will _only_ work if you are using a development version of R. If you

Re: [R] Rgraphviz installation Problem

j.joshua thomas [EMAIL PROTECTED] writes: Dear Robert, Thanks for your time. I have downloaded Rgraphviz (windows binary) from www.bioconductor.org and put inside R2.3.0 library then i installed from the local zip its says package 'graph' couldnot be loaded. Am i doing the installation

Re: [R] Running out of memory when using lapply

Hi Kamila, Kamila Naxerova [EMAIL PROTECTED] writes: Hi all! I'm afraid I programmed something totally non-sensical and inefficient, but I can't figure out how to do it better. I have a list of ~ 40 000 characters. I want to take each element at a time, map it to a large data frame with

Re: [R] invisible() - does not return immediately as return() does

Matthias Burger [EMAIL PROTECTED] writes: Hi, I stumbled across the following (unexpected for me) behavior after replacing a return() statement in the middle of a function by invisible(). Example: foo - function() { cat(before\n); return(); cat(after\n)} foo() before NULL foo2 -

Re: [R] RCurl

Rajarshi Guha [EMAIL PROTECTED] writes: Hi, does anybody know where I might the RCurl package - the omegahat.org server seems to be down The Bioconductor project hosts a mirror of a subset of Omegahat packages (RCurl is included). You can find the listing here:

Re: [R] Drosophila Genome 2.0 annaffy annotation

Hi Marco, I'm pretty sure you want to resend your question to the Bioconductor mailing list. AFAICT your question is rather BioC specific and you will likely get a more helpful response there. + seth __ R-help@stat.math.ethz.ch mailing list

Re: [R] cluster analysis of microarray data

Mahdi Osman [EMAIL PROTECTED] writes: Hi list, I am interested in cluster analysis of microarray data. The data was generated using cDNA method and a loop design. I was wondering if any one has a suggestion about which package I can use to analyse such data. There are many packages

Re: [R] Rgraphviz: Setting the edge width

Søren Højsgaard [EMAIL PROTECTED] writes: I create an undirected graph with Rgraphviz (see code below). I would like to make the edges thicker. Can anyone help on this?? Questions on Rgraphviz are best directed to the bioconductor mail list. I think you already discovered that, but for the

Re: [R] Installing bioconductor

Hi Kristine, Kristine Kleivi [EMAIL PROTECTED] writes: I been trying to install bioconducter into R using the script on the bioconductor home page. However, I get this error message: source(http://www.bioconductor.org/biocLite.R;) Error in file(file, r, encoding = encoding) : unable to open

[R] BioC2006 Conference, Aug 3-4 in Seattle

Early registration ends July 1 BioC2006August 3-4 in Seattle, WA, USA http://bioconductor.org/BioC2006/ About BioC2006: This conference highlights developments within and beyond Bioconductor and provides a forum to discuss the use and design of software for analyzing data arising in

Re: [R] apologies if you aready received this ?

[EMAIL PROTECTED] writes: Basically, I wrote a function called wait() wait-function() { cat(press return to continue) unix(read stuff) } Is readline what you want? See help(readline). __ R-help@stat.math.ethz.ch mailing list

Re: [R] Building packages in R - 'private' functions

Antonio, Fabio Di Narzo [EMAIL PROTECTED] writes: 1. If you have time to change internal functions naming, you can rename internal functions by putting a leading '.'. Even without namespace, I have noticed there is no check for corresponding docs for such functions. 2. If you don't want to

Re: [R] vague errors on R CMD check for very minimal S4-style package

Roels, Steven [EMAIL PROTECTED] writes: Hello, I have a very minimal package simplepkg (DESCRIPTION, NAMESPACE, and R) with S4 classes/methods (defines a class foo and a show method for that class - both the class and show method are exported). I can seemingly install the package, then

Re: [R] Install R problem

Pramod Anugu [EMAIL PROTECTED] writes: I have copied R-2.3.0.tar.gx and uncompressed the directory R-2.3.0 is created. ./configure Make Typed R in the directory /root/downloads/R-2.3.0/bin/exec -bash-2.05b# pwd /root/downloads/R-2.3.0/bin/exec -bash-2.05b# R Fatal error: R home

Re: [R] Too many open files

Omar Lakkis [EMAIL PROTECTED] writes: This may be more of an OS question ... I have this call r = get.hist.quote(symbol, start= format(start, %Y-%m-%d), end= format(end, %Y-%m-%d)) which does a url request in a loop and my program runs out of file handlers after few hundred rotations.

Re: [R] Manipulating code?

Johannes Hüsing [EMAIL PROTECTED] writes: Dear expeRts, I am currently struggling with the problem of finding cut points for a set of stimulus variables. I would like to obtain cut points iteratively for each variable by re-applying a dichotomised variable in the model and then recalculate

Re: [R] RMySQL on Mac OS 10.4

Ryan Hafen [EMAIL PROTECTED] writes: dbWriteTable(con, test, rnorm(100)) Error in .class1(object) : no direct or inherited method for function 'dbWriteTable' for this call For more info, I am running OS X 10.4.6, R 2.2.1, I have compiled RMySQL from source version 0.5-7, and I'm

Re: [R] How to a handle an error in a loop

Farrel Buchinsky [EMAIL PROTECTED] writes: No heaven on earth yet. how would I incorporate this kind of functionality into Resultdt-lapply(PGWide[,240:389], tdt) If you want to do more than one thing, you want to create an anonymous function. Here's an example: d - runif(20, min=-2,

Re: [R] accessing a SOAP based web service from R

Rajarshi Guha [EMAIL PROTECTED] writes: Hi, I have a number of web services that run on a server and can be accessed via SOAP as well as by creating a specific URL. Now, for certain services, the argument that I need to send is about 10 to 20 characters and the URL approach works fine.

Re: [R] programming advice?

Charles Annis, P.E. [EMAIL PROTECTED] writes: Dear R-helpers: I am doing some exploratory programming and am considering a routine that has several other routines defined within it, so that I can avoid a large and messy global re-programming to avoid naming conflicts. My question is

Re: [R] suppressing output

Florian Koller [EMAIL PROTECTED] writes: Dear all, I am using the multinom() function from the nnet library within my own code and I want to suppress multinom's output (#weights, iter 10, 20...). My code generates output too, and I don't want it to be mixed with the output messages the

Re: [R] load file RData which store in zip file

Prof Brian Ripley [EMAIL PROTECTED] writes: [As an aside, I wonder whether compress=TRUE should not be the default for binary save/save.image. It adds little time and may save a lot of disc space.] Here's one user who thinks that is a great idea. I often have to remind developers who

[R] Help understanding behavior of apply vs sapply

Hi, I was surprised that apply and sapply don't return the same results in the example below. Can someone tell me what I'm missing? zls - function(x) character(0) m - matrix(0, nrow=2, ncol=2) apply(m, 1, zls) character(0) sapply(m, zls) [[1]] character(0) [[2]] character(0) [[3]]

Re: [R] setting argument defaults in setMethod

Steven Lacey [EMAIL PROTECTED] writes: I want to set a default value in a method of a generic function. This seems as though it should be possible. From R help on setMethod... So, I try this... setGeneric(test,function(x,y){standardGeneric(test)}) setMethod(test,numeric,

Re: [R] installation problem with Biobase

Haleh, This question would be better asked on the Bioconductor mailing list. You haven't told us what version of R you are using. I suspect you have a version mismatch. With R 2.2.x you should be able to do the following to get MergeMaid installed: From the R prompt do:

Re: [R] lapply and list attributes

Hi, michael watson (IAH-C) [EMAIL PROTECTED] writes: I have a list that has attributes: attributes(lis[2]) $names [1] 150096_at I want to use those attributes in a function and then use lapply to apply that function to every element of the list, eg for simplicity's sake: my.fun -

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