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lawremi / ggbio

Grid and ggplot2 based visualization for biological data
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could not find function ".unsafe.update.GRanges" #43

Open alexpenson opened 11 years ago

alexpenson commented 11 years ago

Many ggbio commands give me the above which I understand is due to the latest version of GenomicRanges, for example:

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene wh <- GRanges("chr16", IRanges(30064491, 30081734)) p1 <- autoplot(txdb, which = wh, names.expr = "gene_id") Aggregating TranscriptDb... Parsing exons... Error in .local(object, ...) : could not find function ".unsafe.update.GRanges" In addition: Warning messages: 1: 'isActiveSeq' is deprecated. Use 'seqlevels' instead.

How can I get a version of R & Bioconductor in which ggbio is known to work?

Thanks Alex

sessionInfo() R version 3.0.1 (2013-05-16) 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 stats graphics grDevices utils datasets [7] methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2 [2] GenomicFeatures_1.13.47 [3] AnnotationDbi_1.23.27 [4] Biobase_2.21.7 [5] BiocInstaller_1.10.3 [6] ggbio_1.8.8 [7] ggplot2_0.9.3.1 [8] GenomicRanges_1.13.51 [9] XVector_0.1.4 [10] IRanges_1.19.38 [11] BiocGenerics_0.7.5

loaded via a namespace (and not attached): [1] biomaRt_2.17.3 Biostrings_2.29.19 [3] biovizBase_1.9.4 bitops_1.0-6 [5] BSgenome_1.29.1 cluster_1.14.4 [7] colorspace_1.2-3 DBI_0.2-7 [9] dichromat_2.0-0 digest_0.6.3 [11] grid_3.0.1 gridExtra_0.9.1 [13] gtable_0.1.2 Hmisc_3.12-2 [15] labeling_0.2 lattice_0.20-23 [17] MASS_7.3-29 munsell_0.4.2 [19] plyr_1.8 proto_0.3-10 [21] RColorBrewer_1.0-5 RCurl_1.95-4.1 [23] reshape2_1.2.2 rpart_4.1-3 [25] Rsamtools_1.13.48 RSQLite_0.11.4 [27] rtracklayer_1.21.12 scales_0.2.3 [29] stats4_3.0.1 stringr_0.6.2 [31] tools_3.0.1 VariantAnnotation_1.7.54 [33] XML_3.95-0.2 zlibbioc_1.7.0

lawremi commented 11 years ago

You need to grab the devel ggbio; you're currently on devel GenomicRanges but release ggbio.

On Tue, Oct 8, 2013 at 11:25 AM, Alex Penson notifications@github.comwrote:

Many ggbio commands give me the above which I understand is due to the latest version of GenomicRanges, for example:

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene wh <- GRanges("chr16", IRanges(30064491, 30081734)) p1 <- autoplot(txdb, which = wh, names.expr = "gene_id") Aggregating TranscriptDb... Parsing exons... Error in .local(object, ...) : could not find function ".unsafe.update.GRanges" In addition: Warning messages: 1: 'isActiveSeq' is deprecated. Use 'seqlevels' instead.

How can I get a version of R & Bioconductor in which ggbio is known to work?

Thanks Alex

sessionInfo() R version 3.0.1 (2013-05-16) 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 stats graphics grDevices utils datasets [7] methods base

other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.9.2 [2] GenomicFeatures_1.13.47 [3] AnnotationDbi_1.23.27 [4] Biobase_2.21.7 [5] BiocInstaller_1.10.3 [6] ggbio_1.8.8 [7] ggplot2_0.9.3.1 [8] GenomicRanges_1.13.51 [9] XVector_0.1.4 [10] IRanges_1.19.38 [11] BiocGenerics_0.7.5

loaded via a namespace (and not attached): [1] biomaRt_2.17.3 Biostrings_2.29.19 [3] biovizBase_1.9.4 bitops_1.0-6 [5] BSgenome_1.29.1 cluster_1.14.4 [7] colorspace_1.2-3 DBI_0.2-7 [9] dichromat_2.0-0 digest_0.6.3 [11] grid_3.0.1 gridExtra_0.9.1 [13] gtable_0.1.2 Hmisc_3.12-2 [15] labeling_0.2 lattice_0.20-23 [17] MASS_7.3-29 munsell_0.4.2 [19] plyr_1.8 proto_0.3-10 [21] RColorBrewer_1.0-5 RCurl_1.95-4.1 [23] reshape2_1.2.2 rpart_4.1-3 [25] Rsamtools_1.13.48 RSQLite_0.11.4 [27] rtracklayer_1.21.12 scales_0.2.3 [29] stats4_3.0.1 stringr_0.6.2 [31] tools_3.0.1 VariantAnnotation_1.7.54 [33] XML_3.95-0.2 zlibbioc_1.7.0

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