similar to: R CMD check/build --binary fail with data/RCS map

Hi! I appologize for crossposting, but this might be of broader interest. In case you are interested in fusing RUnit with R CMD check under unix alike OS, here is one way of doing/hacking this. My aim was to perform unit tests: (1) during R CMD check (2) at any other time Say you have a package PKG in a map PKG. I use the following structure PKG |- R |- ... |- inst | |- doc | `-

Duncan, you are a king! Thanks a lot for this cookie. It really helped me. Thanks for the code as well as detailed explanation at the end. >Hi Gregor. > >Here is a function that will collect all of the nodes in the >XML document whose names are in the vector elementNames > >getElements = >function(elementNames) >{ > els = list() > > startElement = function(node,

Hello! I am working on a package where Enhances field seems to be a plausible option. When I add package, say coda, to this field, I get the following warning with recent R-devel: ---- * checking for working latex ... OK * using log directory '/home/ggorjan/programs/R/devel/test.Rcheck' * using R version 2.5.0 Under development (unstable) (2006-12-06 r40129) * checking for file

Hello! I am building a package, which includes also one Fortran subroutine, which works fine if I compile it as a shared library and load it into R via dyn.load(). However, when I launch R CMD check it doesn't stop with checking examples. It's just doing and doing ... I pasted the whole output from R CMD check. Does anyone have any suggestions? I'm still using R 2.0.1.

I unintentionally missed to cc to r-devel. -------- Original Message -------- Subject: Re: [Rd] levels for list and data.frame Date: Tue, 21 Mar 2006 20:50:21 +0100 From: Gregor Gorjanc <gregor.gorjanc at gmail.com> Reply-To: gregor.gorjanc at gmail.com To: Martin Maechler <maechler at stat.math.ethz.ch> References: <441F2C49.8080703 at gmail.com> <17439.50351.172900.987055

Hello! I have just discovered a possible bug or lack of my knowledge. The last option is not so uncommon and I decided to ask here before flooding the bugs repository. Say I have a package test with vignette. Moving package directory to some other name, say test2, fails R CMD check with $ R CMD check test2 * checking for working latex ... OK * using log directory

James, thanks for the response. I understand now my puzzle. tmp <- data.frame(y1=1:4, f1=factor(c("A", "B", "C", "D"))) tmp$y2 <- NA tmp[1:2, "y2"] <- 2 Does the job. I see that I should add a full column. In my case adding full column of NAs and then adding values, solves my problems. Thanks to all. james.holtman at convergys.com

Hello to everyone! I have built CRAN task view for genetics. For now I have not submit it to CRAN yet and it can be accessible from: http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.html http://www.bfro.uni-lj.si/MR/ggorjan/software/R/Genetics.ctv I have not submitted it to CRAN, since I would like first some opinion about it. Genetics is really so broad field that I belive one person

Hello! Is it possible to set na.rm=TRUE in a global way? I'am constantly forgeting on this when performing analyses. I agree that one should be carefull with this when developing some code, but not necesarilly so in data analysis. Lep pozdrav / With regards, Gregor Gorjanc ---------------------------------------------------------------------- University of Ljubljana PhD student

On 12 October 2006 at 13:02, Gregor Gorjanc wrote: | Hello! | | I encounter the following problem when I try to load package foreign | | library(foreign) | Error in dyn.load(x, as.logical(local), as.logical(now)) : | unable to load shared library '/usr/lib/R/library/foreign/libs/foreign.so': | /usr/lib/R/library/foreign/libs/foreign.so: undefined symbol: | Rf_allocString | Error:

And a last post from Paul Gilbert. Thanks to all! This disscusion was really beneficial for me! -----Original Message----- From: Paul Gilbert [mailto:pgilbert at bank-banque-canada.ca] Sent: sre 2005-06-08 21:01 To: Gorjanc Gregor Subject: Re: [R] Random seed problem in MCMC coupling of chains Gorjanc Gregor wrote: > Thanks to Paul and Gabor for additional tips/examples. Actually, I find

Jun hi again! Sorry for bothering. Although I had no problem with building Windows package under Linux, I noticed that man pages are not processed as they should or maybe I have a problem with my setup. My package is called 'GeneticsPed'. Instead of HTML or text files I just got a GeneticsPed.Rd.gz in man directory of a package (this is within GeneticsPed_0.1.zip file!). The file

Hello! I would like to use constrain to sum coeficients of a factor to 0 instead of classical corner contraint i.e. I would like to fit a model like lm(y ~ 1 + effectA + effectB) and say get parameters intercept effectA_1 effectA_2 effectB_1 effectB_2 effectB_3 where effectA_1 represents deviation of level A_1 from intercept and sum(effectA_1, effectA_2) = 0 and the same for factor B. Is

Hello! Can someone provide me an estimate or relevant source of information on how long is command winepath available or from wich version of wine? I would need this as I work on some R[1] package R2WinBUGS[2] that calls a Windows program WinBUGS[3] and that program needs windows paths. Currently winepath or parsing of .wine/config is used and I wonder if I can remove fiddling with .wine/.config.

Hello R-users! I have tried to use Sweave within LyX* and found two ways to accomplish this. I have attached LyX source file for both ways. *<http://www.lyx.org> Lep pozdrav / With regards, Gregor Gorjanc ---------------------------------------------------------------------- University of Ljubljana Biotechnical Faculty URI: http://www.bfro.uni-lj.si/MR/ggorjan Zootechnical

Hello! I am writing some functions and I repeatedly acces internal factor codes. I figured out that internal codes are 1:n where 1 represents 1st level, 2 2nd level etc. This is not documented and I wonder if this is on purpose and subject to change or would be a good idea to add this to documentation for factor? I can prepair a pacth if this is accepted. -- Lep pozdrav / With regards,

Hello! Data.frames have new rownames funcionality, however in use of colnames<- in R-devel "changes" this. Here is the example: > df1 <- data.frame(letters[1:5]) > attributes(df1) $names [1] "letters.1.5." $row.names [1] 1 2 3 4 5 $class [1] "data.frame" > colnames(df1) <- "bla" > attributes(df1) $names [1] "bla"

Hello! I am trying to get specific fields from an XML document and I am totally puzzled. I hope someone can help me. # URL URL<-"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=11877539,11822933,11871444&retmode=xml&rettype=citation" # download a XML file tmp <- xmlTreeParse(URL, isURL = TRUE) tmp <- xmlRoot(tmp) Now I want to extract only

Hello! Looking on how people use optim to get MLE I also noticed that one can use returned Hessian to get corresponding standard errors i.e. something like result <- optim(<< snip >>, hessian=T) result$par # point estimates vc <- solve(result$hessian) # var-cov matrix se <- sqrt(diag(vc)) # standard errors What is actually Hessian representing here?

Hello! I think that link to page of Duncan Murdoch (bellow) should be given http://www.murdoch-sutherland.com/Rtools/ at http://developer.r-project.org/. It's easy to launch Google and find mentioned page, but it took me quite some time to do this, because I was sure, that it is noted somewhere on {www,CRAN}.r-project.org. Maybe I didn't read carefully ... Lep pozdrav / With