Dear Paolo, I experienced same problem. A simple test is 'example(hopach)'. From a fresh R session, it works fine. If you load Matrix library, it will failed. So, looks like some incompatibilities (rcond or xtabs or ...?). Regards, Samuel Paolo Innocenti wrote: > 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 _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=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;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=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 >