Thanks! Martin The bugs are due to the changes of other depended packages. I have submitted the bug fix to the released version. Hope this will solve problems. Pan On Wed, Nov 13, 2013 at 7:29 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 11/12/2013 11:11 PM, Pan Du wrote: > >> Hi Juan >> >> You need to try the latest developing version of methyAnalysis package. >> For >> some unknown reason, the Bioc reports some checking error of the vignette. >> So the latest developing version is not available through biocLite. It >> will >> send the package to you in another email. Thanks for reporting the >> problem! >> > > Hi Pan -- update your installation and you'll be able to see the error; no > sense distributing packages that don't work!. I introduced a change / bug > in Biobase and will fix this today; the package should be available via > biocLite tomorrow. > > Martin > > >> Pan >> >> >> On Tue, Nov 12, 2013 at 1:11 PM, jfertaj <jfernandezt@udc.es> wrote: >> >> Dear list and Pan, >>> >>> I’m still having some problems with the methyAnalysis package, after >>> update some functions thanks to Pan I’m still experiencing some problems >>> with certain functions, for example I am not able to plot the heatmap >>> with >>> >>> heatmapByChromosome(methyGenoSet, gene='55342', >>>> >>> genomicFeature='TxDb.Hsapiens.UCSC.hg19.knownGene', >>> includeGeneBody=TRUE) >>> Error in .local(range, ...) : could not find function "restoreSeqlevels" >>> Error: could not find function "restoreSeqlevels" >>> >>> or annotate the DMR regions with >>> >>> >DMRInfo.ann <- annotateDMRInfo(allDMRInfo, >>> 'TxDb.Hsapiens.UCSC.hg19.knownGene') >>> There were 50 or more warnings (use warnings() to see the first 50) >>> Error in IRanges::as.matrix(nearest(grange[naInd], tr, select = "all")) >>> : >>> error in evaluating the argument 'x' in selecting a method for >>> function >>> 'as.matrix': Error in mergeNamedAtomicVectors(genome(x), genome(y), >>> what = >>> c("sequence", : >>> sequences chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, >>> chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, >>> chr21, chr22, chrX, chrY have incompatible genomes: >>> - in 'x': , , , , , , , , , , , , , , , , , , , , , , , >>> - in 'y': hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, >>> hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, hg19, >>> hg19, hg19 >>> >>> Here is my sessionInfo() >>> >>> R version 3.0.2 (2013-09-25) >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> locale: >>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 >>> >>> attached base packages: >>> [1] parallel grid stats graphics grDevices utils datasets >>> methods base >>> >>> other attached packages: >>> [1] IlluminaHumanMethylation450k.db_2.0.7 >>> FDb.InfiniumMethylation.hg19_2.0.10 BSgenome.Hsapiens.UCSC.hg19_1.3.19 >>> BSgenome_1.28.0 >>> [5] Biostrings_2.28.0 GenomicFeatures_1.12.3 >>> plyr_1.8 pheatmap_0.7.7 >>> >>> [9] genefilter_1.42.0 multtest_2.18.0 >>> annotate_1.38.0 GOstats_2.26.0 >>> >>> [13] graph_1.38.3 Category_2.26.0 >>> IlluminaHumanMethylation27k.db_1.4.7 limma_3.16.6 >>> >>> [17] lumi_2.14.0 methylumi_2.8.0 >>> matrixStats_0.8.5 ggplot2_0.9.3.1 >>> >>> [21] reshape2_1.2.2 scales_0.2.3 >>> methyAnalysis_1.4.0 org.Hs.eg.db_2.9.0 >>> >>> [25] RSQLite_0.11.4 DBI_0.2-7 >>> AnnotationDbi_1.22.6 Biobase_2.20.1 >>> >>> [29] GenomicRanges_1.12.4 IRanges_1.20.2 >>> BiocGenerics_0.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affy_1.38.1 affyio_1.28.0 AnnotationForge_1.2.2 >>> base64_1.1 beanplot_1.1 BiocInstaller_1.10.3 >>> biomaRt_2.16.0 >>> [8] biovizBase_1.8.1 bitops_1.0-6 bumphunter_1.2.0 >>> cluster_1.14.4 codetools_0.2-8 colorspace_1.2-2 >>> dichromat_2.0-0 >>> [15] digest_0.6.3 doRNG_1.5.5 foreach_1.4.1 >>> genoset_1.14.0 GO.db_2.9.0 GSEABase_1.22.0 >>> gtable_0.1.2 >>> [22] Gviz_1.6.0 Hmisc_3.12-2 illuminaio_0.4.0 >>> iterators_1.0.6 itertools_0.1-1 KernSmooth_2.23-10 >>> labeling_0.2 >>> [29] lattice_0.20-23 latticeExtra_0.6-26 locfit_1.5-9.1 >>> MASS_7.3-29 Matrix_1.0-14 mclust_4.2 >>> mgcv_1.7-26 >>> [36] minfi_1.8.3 munsell_0.4.2 nleqslv_2.0 >>> nlme_3.1-111 nor1mix_1.1-4 pkgmaker_0.17.4 >>> preprocessCore_1.22.0 >>> [43] proto_0.3-10 R.methodsS3_1.4.4 RBGL_1.36.2 >>> RColorBrewer_1.0-5 RCurl_1.95-4.1 registry_0.2 >>> reshape_0.8.4 >>> [50] rngtools_1.2.3 rpart_4.1-3 Rsamtools_1.12.3 >>> rtracklayer_1.20.4 siggenes_1.36.0 splines_3.0.2 >>> stats4_3.0.2 >>> [57] stringr_0.6.2 survival_2.37-4 tools_3.0.2 >>> XML_3.95-0.2 xtable_1.7-1 XVector_0.2.0 >>> zlibbioc_1.6.0 >>> >>> Thanks >>> >>> Juan >>> --- >>> Juan Fernandez Tajes, phD >>> Grupo Xenomar – Área de Genética >>> Facultad de Ciencias – A Zapateira >>> Universidad de A Coruña >>> Spain >>> Tlf - +34 981 16700 >>> Email: Jfernandezt@udc.es >>> >>> >>> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > [[alternative HTML version deleted]]