similar to: JGR problem with installPackages()?

Dear r-helpers, After updating to R version 2.2.1, 2005-12-20, powerpc-apple- darwin7.9.0 (from binary), JGR wouldn't launch. I then deleted everything I could find related to JGR, and reinstalled it from the latest binary. Both R and JGR are installed in /Applications/ \~LocalApps/mathStat/. Advice on how to identify the source of the problem? My machine: Machine Name:

Dear R-helpers, In JGR: jpeg() Error in X11(paste("jpeg::", quality, ":", filename, sep = ""), width, : unable to start device JPEG In addition: Warning message: unable to open connection to X11 display '' > sessionInfo() Version 2.3.1 (2006-06-01) powerpc-apple-darwin8.6.0 attached base packages: [1] "grid" "datasets"

Dear r-helpers, I wonder if you can figure out why the following is working: ******************************************************************** > sessionInfo() Version 2.3.1 (2006-06-01) powerpc-apple-darwin8.6.0 attached base packages: [1] "tcltk" "methods" "stats" "graphics" "grDevices" "utils"

Dear R-helpers, In JGR, how to I get the help() to update when I install a new package? > sessionInfo() Version 2.3.1 (2006-06-01) powerpc-apple-darwin8.6.0 attached base packages: [1] "datasets" "methods" "stats" "graphics" "grDevices" "utils" "base" other attached packages: lattice MASS

Dear r-helpers, Could you please help me solve the following problem: When I run require(AlgDesign) trt <- LETTERS[1:5] blk <- 10 trtblk <- 3 BIB <- optBlock(~., withinData = trt, blocksizes = rep(trtblk, blk)) In response to the last command, R complains: Error in optBlock(~., withinData = trt, blocksizes = rep(trtblk, blk)) : object ".Random.seed" not found The

> (fm1 <- lmer2(Reaction ~ Days + (Days|Subject), sleepstudy)) Error in as.double(start) : Calloc could not allocate (888475968 of 4) memory ************************* > sessionInfo() R version 2.4.1 (2006-12-18) powerpc-apple-darwin8.8.0 locale: C attached base packages: [1] "grid" "datasets" "stats" "graphics" "grDevices"

Dear r-helpers, When I do an xYplot and display the result in a JavaGD() window, the font is sans-serif (presumably Helvetica). When I send the figure to a pdf, I get a serif font (presumably times). How do I insure that the font in the pdf is indeed the default sans serif? > sessionInfo() R version 2.4.1 (2006-12-18) i386-apple-darwin8.8.1 locale: C attached base packages: [1]

library(glmmADMB) #Example for glmm.admb data(epil2) glmm.admb(y~Base*trt+Age +Visit,random=~Visit,group="subject",data=epil2,family="nbinom") Gives: Error in glmm.admb(y ~ Base * trt + Age + Visit, random = ~Visit, group = "subject", : The function maximizer failed ****************** R version 2.4.1 RC (2006-12-14 r40181) powerpc-apple-darwin8.8.0 locale: C

Dear r-helpers, I'm running Version 2.3.0 (2006-04-24) under OS X 10.4.6. (1) When I start R from the terminal, it has no complaints. (2) When I start R.app using R for Mac OS X Aqua GUI version 1.15 (3106) I get (I have increased the quote level of what is different from the output of the terminal): ... Loading required package: grDevices Loading required package: mvtnorm >

Dear R-helpers, I don't see a difference between the following two plots of effect objects, which I understand should be different. What am I missing? require(doBy) require(effects) data(budworm) m1 <- glm(ndead/20 ~ sex + log(dose), data=budworm, weight=ntotal, family=binomial) m1.eff <- all.effects(m1) plot(m1.eff, rescale.axis = FALSE, selection = 2, main = 'rescale =

Dear R-helpers, When I try > anova(txtE2.lme, txtE2.lme1) Model df AIC BIC logLik Test L.Ratio p-value txtE2.lme 1 10 8590 8638 -4285 txtE2.lme1 2 7 8591 8624 -4288 1 vs 2 6.79 0.0789 > latex(anova(txtE2.lme, txtE2.lme1)) Error: object "n.group" not found I don't even see n.group as one of the arguments of latex() I checked to see >

Dear R-helpers, Can anyone tell me how to fix this: > library(Rgraphviz) Loading required package: graph Loading required package: Ruuid Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/ Resources/library/Rgraphviz/libs/ppc/Rgraphviz.so': dlopen(/Library/Frameworks/R.framework/Resources/library/Rgraphviz/

R version 2.7.0 Under development (unstable) (2008-03-04 r44677) i386-apple-darwin8.10.1 locale: C attached base packages: [1] grid grDevices datasets graphics stats utils methods base other attached packages: [1] lattice_0.17-6 MASS_7.2-41 JGR_1.5-18 iplots_1.1-2 JavaGD_0.5-1 rJava_0.5-1 The following opens a JavaGD window and freezes JGR: super.sym <-

Dear r-helpers, Can anyone suggest a remedy to the following failure of Rgraphviz to load? > library(Rgraphviz) Loading required package: graph Loading required package: Ruuid Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/Library/Frameworks/R.framework/ Resources/library/Rgraphviz/libs/ppc/Rgraphviz.so':

require(gplots) data(rtPCR) overplot( RQ ~ Conc..ug.ml. | Test.Substance, data=rtPCR, subset=Detector=="ProbeType 7" & Conc..ug.ml. > 0, same.scale=TRUE, log="xy", f=3/4, main="Detector=ProbeType 7", xlab="Concentration (ug/ml)", ylab="Relative Gene Quantification" ) # Error in lowess.default(mf[[-response]], mf[[response]], f = f,

Issue with sos package I am now using R 2.14 and the sos package did work with 2.13 > library(sos) Loading required package: brew Attaching package: 'sos' The following object(s) are masked from 'package:JGR': installPackages The following object(s) are masked from 'package:utils': > library("sos"); findFn("random forest") found 253

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: ******************installing****************** > source("http://bioconductor.org/biocLite.R") > biocLite("weaver") Running getBioC version 0.1.8 with R version

Dear R-helpers, I would like the bands in an xYplot() to be gray without dark edges. I've tried playing around with col.bands, but that seems not to affect the edges, although changin col.fill does change the fill as I would expect. I would appreciate pointers. _____________________________ Professor Michael Kubovy University of Virginia Department of Psychology USPS: P.O.Box

Dear developers I am unable to (properly) load JGR on Debian testing. The JGR window will pop out and R will start up, but it will not perform any of the JGR specific library() calls (rJava, JavaGD, etc.) and will stuck at 100% CPU while the prompt will be non-responsive. The hack that helped previously in such cases, accessing Help > About [1], works no more. All R packages are installed via

Hi, I have all CRAN packages installed on my Linux. Now I have problems with JGR. When I make a plot and close a device, the device dont work anymore, I nedd to use before javaGD() and after plot(). When I try do close JGR and save a session, It return a erro and dont close. Look: Exception in thread "Thread-2" java.lang.IllegalArgumentException: Value too long: