Hi Burak, Thanks for reporting this. A fix is in the way. I'll announce here when it's ready. Cheers, H. burak kutlu wrote: > Hi > I am trying to use matchPDict() and below's the error I get. > This happens with my objects as well, but I am showing the vignette example. > thanks in advance > -burak > > # I've made sure that ce2dict0 was corectly created >> ce2dict0cw15 <- DNAStringSet(ce2dict0, end=15) >> runAnalysis2(ce2dict0cw15, outfile="ce2dict0cw15_ana2.txt") > > Target: strand + of ce2 chromosomes chrI, chrII, chrIII, chrIV, chrV, chrX, chrM >>>> Finding all hits in strand + of chromosome chrI ... > Error in initialize(value, ...) : > invalid names for slots of class "ByName_MIndex": length > > >> sessionInfo() > R version 2.8.1 (2008-12-22) > 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] grDevices datasets splines graphics stats utils tools > [8] methods base > > other attached packages: > [1] BSgenome.Celegans.UCSC.ce2_1.3.11 BSgenome_1.10.3 > [3] Biostrings_2.10.16 IRanges_1.0.12 > [5] simpleaffy_2.18.0 gcrma_2.14.1 > [7] matchprobes_1.14.1 genefilter_1.22.0 > [9] survival_2.34-1 affy_1.20.0 > [11] Biobase_2.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.2 > [4] DBI_0.2-4 grid_2.8.1 lattice_0.17-17 > [7] Matrix_0.999375-17 preprocessCore_1.4.0 RSQLite_0.7-1 > > _______________________________________________ > Bioconductor mailing list > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319

Hi Burak, This problem is now fixed in release (Biostrings 2.10.21 and BSgenome 1.10.5) and devel (Biostrings 2.11.40 and BSgenome 1.11.13). The updated packages will be available in the next 12 hours for release and are already available for devel. See http://bioconductor.org/docs/install/ for how to update your installation. Cheers, H. burak kutlu wrote: > Hi > I am trying to use matchPDict() and below's the error I get. > This happens with my objects as well, but I am showing the vignette example. > thanks in advance > -burak > > # I've made sure that ce2dict0 was corectly created >> ce2dict0cw15 <- DNAStringSet(ce2dict0, end=15) >> runAnalysis2(ce2dict0cw15, outfile="ce2dict0cw15_ana2.txt") > > Target: strand + of ce2 chromosomes chrI, chrII, chrIII, chrIV, chrV, chrX, chrM >>>> Finding all hits in strand + of chromosome chrI ... > Error in initialize(value, ...) : > invalid names for slots of class "ByName_MIndex": length > > >> sessionInfo() > R version 2.8.1 (2008-12-22) > 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] grDevices datasets splines graphics stats utils tools > [8] methods base > > other attached packages: > [1] BSgenome.Celegans.UCSC.ce2_1.3.11 BSgenome_1.10.3 > [3] Biostrings_2.10.16 IRanges_1.0.12 > [5] simpleaffy_2.18.0 gcrma_2.14.1 > [7] matchprobes_1.14.1 genefilter_1.22.0 > [9] survival_2.34-1 affy_1.20.0 > [11] Biobase_2.2.1 > > loaded via a namespace (and not attached): > [1] affyio_1.10.1 annotate_1.20.1 AnnotationDbi_1.4.2 > [4] DBI_0.2-4 grid_2.8.1 lattice_0.17-17 > [7] Matrix_0.999375-17 preprocessCore_1.4.0 RSQLite_0.7-1 > > _______________________________________________ > Bioconductor mailing list > 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 -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319