Dear Vincent and list, hopefully I managed to provide a non-working example. It looks like the lme4 (the lme4-required package Matrix in particular) causes some incompatibilities: library(lme4) 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) produces this on my computer: > library(Matrix) Loading required package: lattice Attaching package: 'Matrix' The following object(s) are masked from package:stats : xtabs The following object(s) are masked from package:base : rcond > require(hopach) Loading required package: hopach Loading required package: cluster Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > 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) > 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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hopach_2.4.0 Biobase_2.4.1 cluster_1.11.13 Matrix_0.999375-24 [5] lattice_0.17-22 loaded via a namespace (and not attached): [1] grid_2.9.0 tools_2.9.0 While the same code - without calling lme4 - works smoothly. Can anyone suggest a workaround? Best, paolo Vincent Carey wrote: > 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 at="" ebc.uu.se="" <mailto:paolo.innocenti="" at="" 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 > <http: 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 > Norbyv?gen 18D > 75236 Uppsala, Sweden > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Vincent Carey, PhD > Biostatistics, Channing Lab > 617 525 2265 -- Paolo Innocenti Department of Animal Ecology, EBC Uppsala University Norbyv?gen 18D 75236 Uppsala, Sweden