alas, i cannot replicate this with the devel version

> sessionInfo()
R version 2.10.0 Under development (unstable) (2009-04-06 r48294)
i386-apple-darwin9.6.0

locale:
C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] hopach_2.5.0    Biobase_2.3.10  cluster_1.11.12

loaded via a namespace (and not attached):
[1] tools_2.10.0

in which your example runs to completion.

On Wed, May 20, 2009 at 6:30 AM, Paolo Innocenti
<paolo.innocenti@ebc.uu.se>wrote:

> Hi all,
>
> I'm experiencing this problem with hopach package. The following code runs
> just fine in a fresh session, but gives an error (see below) in my working
> directory:
>
> > require(hopach)
> > data(golub)
> > vars <- apply(golub, 1, var)
> > subset <- vars > quantile(vars, (nrow(golub) - 200)/nrow(golub))
> > golub.subset <- golub[subset, ]
> > gnames.subset <- golub.gnames[subset, ]
> > gene.dist <- distancematrix(golub.subset, "cosangle")
> > gene.hobj <- hopach(golub.subset, dmat = gene.dist)
> Error in dmat[ord, ] :
>  element 1 is empty;
>   the part of the args list of 'is.logical' being evaluated was:
>   (j)
> > traceback()
> 4: dmat[ord, ]
> 3: dmat[ord, ]
> 2: orderelements(cuttree, data, rel = ord, d, dmat)
> 1: hopach(golub.subset, dmat = gene.dist)
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
>
> locale:
>
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
>
> other attached packages:
> [1] hopach_2.4.0    Biobase_2.4.1   cluster_1.11.13 RSQLite_0.7-1
> [5] DBI_0.2-4
>
> loaded via a namespace (and not attached):
>  [1] affy_1.22.0           affyio_1.12.0         AnnotationDbi_1.6.0
>  [4] drosophila2.db_2.2.11 grid_2.9.0            lattice_0.17-22
>  [7] lme4_0.999375-28      Matrix_0.999375-26    MCMCglmm_1.09
> [10] preprocessCore_1.6.0  tools_2.9.0
>
>
> The "real" code I am running, that gives the same error message, is the
> following:
>
> > hopach.eset.antag <- eset[which(featureNames(eset) %in% rtop.int$ID),]
> > antag.dist.matrix <- distancematrix(exprs(hopach.eset.antag), "cosangle")
> > hopach.clusters.antag <- hopach(hopach.eset.antag,
> dmat=antag.dist.matrix)
> Error in dmat[ord, ] :
>  element 1 is empty;
>   the part of the args list of 'is.logical' being evaluated was:
>   (j)
>
> I haven't found the same error reported in the ML.
> Cheers,
> paolo
>
>
>
> --
> Paolo Innocenti
> Department of Animal Ecology, EBC
> Uppsala University
> Norbyvägen 18D
> 75236 Uppsala, Sweden
>
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-- 
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265

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