Brian Ripley got me looking at the .Rprofile off list, and indeed, the problem originates from some subtle behavior of one package which I am still trying to understand.  It doesn't appear to be a general problem, so let's consider this fixed (and it's probably not unique to Mac).  If I find otherwise, I'll report back.

Thanks to all.  Bryan

On Nov 11, 2011, at 11:05 PM, Hadley Wickham wrote:

> Try R --vanilla to see if it's a profile problem. 
> Hadley
> 
> On Friday, November 11, 2011, Bryan Hanson <hanson@depauw.edu> wrote:
> > [a variation of this was posted on r-help the other day with no answers]
> >
> > I've done something to my installation and can't find the cause.  This started up a few days ago, it could be related to the problem that Simon was working on in the past 48, but I increasingly think not.
> >
> > My current install is totally fresh this morning off of r.research.att.com and the problem persists.  Here's a couple of examples:
> >
> > Example 1:
> >> ?sd
> > Error in help("sd", package = NULL) :
> >  could not find function "%is.not.a%"
> >
> > Example 2 (from r-help posting):
> >
> > I have 3 packages that I authored and they build and check just fine locally.  However, when I try to install the local source packages (from the .tar.gz), I get the following message:
> >
> > Error in `+.POSIXt`(as.POSIXct(origin, tz = tz, ...), x) :
> >  could not find function "%is.a%"
> > In addition: Warning message:
> > In install.packages(file.choose(), .libPaths()[1], NULL, type = "source") :
> >  installation of package ‘/Users/bryanhanson/Documents/Research/MetabolomicsProjects/ChemometricsStuff/BAHpackages/FuncMap_1.0-1.tar.gz’ had non-zero exit status
> >
> > Now this is pretty surprising to me; I don't use this function or any having to do with times or time series.  I get the same message no matter which of the 3 packages I try to install locally.  Further, if I go looking for whatever this function is, the following occurs, and no browser window opens:
> >
> >> findFn("is.a")
> > found 3 matches
> > Error in stopifnot(x %is.a% "POSIXct") : could not find function "%is.a%"
> >
> > Which is the same error as one gets just asking for help (Example 1), so I think that error is superceding any display of help pages.
> >
> > And a google search of the error message doesn't produce anything recent.
> >
> > Does anyone recognize this problem/error?  I've thrown out and re-installed several times and it persists.  I feel like it might be in a hidden file (I have not yet tried to remove all existing .Rhistory files).  I also had a development version of ggplot2 installed a few days ago, in an attempt to fix a different problem.  My current sessionInfo() is below.
> >
> > Thanks for any suggestions about where to look.  Bryan
> > ***********
> > Bryan Hanson
> > Professor of Chemistry & Biochemistry
> > DePauw University
> >
> >> sessionInfo()
> > R version 2.14.0 Patched (2011-11-09 r57624)
> > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> >
> > locale:
> > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
> >
> > attached base packages:
> > [1] graphics  utils     datasets  grid      grDevices stats     methods   base
> >
> > other attached packages:
> >  [1] HiveR_0.2-1      FuncMap_1.0-1    ChemoSpec_1.48-4 ggExtra_0.5.1    gridExtra_0.8.5
> >  [6] GGally_0.3.1     stringr_0.5      ggplot2_0.8.9    proto_0.3-9.2    reshape_0.8.4
> > [11] plyr_1.6         sos_1.3-1        brew_1.0-6       xtable_1.6-0     rgl_0.92.798
> >
> > loaded via a namespace (and not attached):
> >  [1] amap_0.8-7         bipartite_1.17     chemometrics_1.3.7 class_7.3-3
> >  [5] e1071_1.6          igraph_0.5.5-3     lattice_0.20-0     MASS_7.3-16
> >  [9] mclust_3.4.10      mvbutils_2.5.101   mvoutlier_1.9.4    mvtnorm_0.9-9991
> > [13] nnet_7.3-1         pcaPP_1.9-44       pls_2.2-0          R.oo_1.8.3
> > [17] R.utils_1.9.3      RColorBrewer_1.0-5 RFOC_2.0-02        robustbase_0.7-8
> > [21] rpart_3.1-50       seriation_1.0-6    sna_2.2-0          som_0.3-5
> > [25] splines_2.14.0     survival_2.36-10   tnet_3.0.5         tools_2.14.0
> > [29] TSP_1.0-5          vegan_2.0-1
> >
> > _______________________________________________
> > R-SIG-Mac mailing list
> > R-SIG-Mac@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mac
> >
> 
> -- 
> Assistant Professor / Dobelman Family Junior Chair
> Department of Statistics / Rice University
> http://had.co.nz/


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