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jjmm1101
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@jjmm1101-9887
Last seen 9.0 years ago
When I run makeTxDbFromGFF, I got the error message ... Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'min_overlap_score' not found.
I don't know how to solve this issue. any suggestion is welcome.
Below is detail:
> gtffile <- file.path("../resource", "illumina_igenomes_mus_musculus_ucsc_mm9.gtf") > (txdb <- makeTxDbFromGFF(gtffile, format="gtf")) Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... Error in get(name, envir = asNamespace(pkg), inherits = FALSE) : object 'min_overlap_score' not found > sessionInfo() R version 3.2.2 (2015-08-14) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux Server release 6.3 (Santiago) locale: [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915 [5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915 [7] LC_PAPER=en_US.iso885915 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicFeatures_1.22.12 AnnotationDbi_1.32.3 [3] Rsamtools_1.22.0 Biostrings_2.38.3 [5] XVector_0.10.0 HTSFilter_1.10.0 [7] mixOmics_5.2.0 ggplot2_2.0.0 [9] lattice_0.20-33 MASS_7.3-44 [11] RColorBrewer_1.1-2 DESeq2_1.10.1 [13] RcppArmadillo_0.6.100.0.0 Rcpp_0.12.3 [15] SummarizedExperiment_1.0.1 Biobase_2.30.0 [17] GenomicRanges_1.22.1 GenomeInfoDb_1.6.3 [19] IRanges_2.4.6 S4Vectors_0.8.11 [21] BiocGenerics_0.16.1 BiocInstaller_1.20.1 loaded via a namespace (and not attached): [1] locfit_1.5-9.1 corpcor_1.6.8 plyr_1.8.3 [4] futile.options_1.0.0 acepack_1.3-3.3 RSQLite_1.0.0 [7] DESeq_1.22.0 ellipse_0.3-8 zlibbioc_1.16.0 [10] annotate_1.48.0 rpart_4.1-10 proto_0.3-10 [13] splines_3.2.2 BiocParallel_1.4.3 geneplotter_1.48.0 [16] foreign_0.8-66 igraph_1.0.1 RCurl_1.95-4.7 [19] biomaRt_2.26.1 munsell_0.4.3 rtracklayer_1.30.2 [22] nnet_7.3-11 gridExtra_2.0.0 edgeR_3.12.0 [25] Hmisc_3.17-0 XML_3.98-1.3 GenomicAlignments_1.6.3 [28] bitops_1.0-6 grid_3.2.2 xtable_1.8-2 [31] gtable_0.1.2 DBI_0.3.1 magrittr_1.5 [34] scales_0.3.0 genefilter_1.52.0 limma_3.26.7 [37] latticeExtra_0.6-26 futile.logger_1.4.1 Formula_1.2-1 [40] lambda.r_1.1.7 tools_3.2.2 survival_2.38-3 [43] colorspace_1.2-6 cluster_2.0.3
This sounds like a version mis-match; does
BiocInstaller::biocValid()
report any problems? Also, try running the code in a new R session, so that the relevant dependencies are more apparent.