similar to: R CMD check problems

Hi, I have a linear mixed-effects model object and want to extract the 95% confidence intervals for the fixed and random effects, respectively. I found the function intervals() for confidence intervals for the fixed effects but no corresponding function for the random effects. Does it exist or do I have to calculate the confidence intervals for the random effects myself? Greetings, joerg

Hi, concerning my earlier mail, maybe someone has noted from the variable names that I try to analyse mircoarrary experiments. Does anybody know of a R-implementation of the two-step mixed-model normalization procedure proposed by Wolfinger et al. (2001) J. Comput. Biol. 8:625-637? That would be great, best, joerg

Hi, does anybody know of a nice test to detect trend turning points in time series? Possibly with reference? Thanks, joerg

Hi, trying to do a robudt regression of a two-way linear model, I keep getting the following error: > lqs(obs ~ y + s -1,method="lms", contrasts=list(s=("contr.sum"))) Error: lqs failed: all the samples were singular Robust regression with M-estimators works (also regular least square fits, of course): rlm.formula(formula = obs ~ y + s - 1, method = "M",

Hi, I have the following linear mixed model: y(g,i,j,k,l)=u + L(g) + T(i) + D(j) + S(k) + (TS)(i,k) + error(g,i,j,k,l) where S(k) and the combined effect (TS)(i,k) are random effects whereas the rest are fixed effects. How do I specifiy the random part of the model formula in lme(), especially concerning the combined effect (TS)? Moreover, when I run the model as a fixed effect model I get

Hi, I have two non-normal distributions and use interquartile ranges as a dispersion measure. Now I am looking for a test, which tests whether the interquartile ranges from the two distributions are significantly different. Any idea? Thanks, joerg [[alternative HTML version deleted]]

I tried two times to get some help for this from the help list but to no avail. I hope, it's OK to post this here (once...). if not, please ignore (the rest of) this mail: for one of my private packages R CMD CHECK {package} givves me annoying warnings due to 'missing links' in the manpages for functions from another private package mentioned in the manpages. specifically, I have two

hi, I have two private packages, the first (`pkc') depending on the second one (`roiutils'). The source code and DESCRIPTION files describes the dependency as it should be ('Imports', `require'), at least I think so. now, running R CMD CHECK pkc yields the following output in which I have inserted my questions (lines starting with -->): * checking for working latex ...

I'm having a very hard time making R CMD check produce a clean check on examples because of the timings inserted into examples by R CMD check. I am getting a difference on every example output caused by timing information being inserted by 'R CMD check'. The current 'Writing R Extensions' manual[1] states on p. 14: If directory tests has a subdirectory Examples

Dear R-devel, One of our R-Forge developers pointed out that it is not possible to build packages under Windows using the R-Forge repository structure: a package resides in ./pkg - not in a directory with the same name as the package name. Under Linux 'R CMD build pkg' or 'R CMD check pkg' work pretty well (I think Kurt Hornik fixed that in R 2.5.1 or so) whereas under

Dear R devel I am experiencing a problem using R CMD check. I tried to specify the argument outdir, but get every time the error message: Warning: unknown option ‘--outdir==RCHECK’ This happens both on R 2.15.2 Linux, as well as R 3.0.1 Windows, with latest Rtools. Is it just that I am not passing the argument the right way, or is there an issue with R CMD check? I tried to write the argument

Hi, there, I used R CMD check to build my "ATGGS" package under window XP system. My R version is 2.7.2. But I encounter some problems. The log file is like: ********************************************************************************** installing R.css in C:/ATGGS.Rcheck ---------- Making package ATGGS ------------ adding build stamp to DESCRIPTION installing R files

Hi, there, I used R CMD check to build my "ATGGS" package under window XP system. My R version is 2.7.2. But I encounter some problems. The log file is like: ********************************************************************************** installing R.css in C:/ATGGS.Rcheck ---------- Making package ATGGS ------------ adding build stamp to DESCRIPTION installing R files

Hi, I believe this is kind of a long standing bug though. In R-3.0.1, but this also happened in previous versions, the long version '--outdir' is not recognised: For `R CMD check --outdir=mydir pkg_0.1.tar.gz` we get: Warning: unknown option ‘--outdir=mydir’ But with `R CMD check -o mydir pkg_0.1.tar.gz` we get: * using log directory ‘/home/renaud/Documents/projects/mydir/pkg.Rcheck’

I am not sure if this is already known. I checked BUGS and found some references to similar behavior when R_HOME is set? Here is what I get: (1) Fresh build of 1.4.1 under Linux/RH-7.2. All tests pass. > R CMD check ctest * checking for working latex ... OK * using log directory `/home/andyj/stat/R-1.4.1/library/ctest.Rcheck' Installing *source* package `ctest'

Dear r-devel members, I tried to build R packages on a PC running Windows XP but experience problems. However, it is ok when there is no inst directory in a package. Any help would be appreciated. The following is an example, C:\work>R CMD check VR_7.2-19.tar.gz * checking for working latex ... OK * using log directory 'C:/work/VR.Rcheck' * using R version 2.1.1, 2005-06-20 *

Hi, All: What might cause "R CMD check" to report, "could not find function" for a function that has long been in the 'fda' package? Both Jim Ramsay in Ottawa, Canada, and I in San Jose, CA, get this same error. I replicated it with a fresh, anonymous checkout from R-Forge (svn checkout svn://svn.r-forge.r-project.org/svnroot/fda). With this, I did

Hi, I have a couple of new errors in our package when I check it on R 2.13-rc (r55310). The first one that's mystifying me is * checking R code for possible problems ... NOTE Error : object normalizePath is not exported by 'namespace:utils' Error : object normalizePath is not exported by 'namespace:utils' Firstly, it's strange to see NOTE and Error being used

For 'R CMD check', it appears that option '--outdir' is not recognized and generates warning "unknown option '--outdir'". R CMD check --help says: Usage: R CMD check [options] pkgs [...] Options: [...] -o, --outdir=DIR directory used for logfiles, R output, etc. (default is 'pkg.Rcheck' in current directory,

I am trying to re-organizing my Makefile for testing my R packages and I am having trouble finding a structure I like. The problem seems to be that "R CMD check", which does wonderful things, does not allow dependency information to flow through very gracefully. That is, since everything is copied into the pkg.Rcheck directory, it is difficult to make any changes to source files without