[BioC] methyAnalysis error

Wed Nov 13 16:29:05 CET 2013

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 at 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 at udc.es
>>
>>
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