[Bioc-devel] Error msg in "makeTxDbFromGFF" using GenomicFeatures package

[Martin Morgan]

The appropriate place for the this question is the support site; no need 
to cross-post https://support.bioconductor.org/p/79460/

Martin

On 03/09/2016 11:22 PM, huizhu.gmail wrote:
> Dear all,
>
>    When I run "makeTxDbFromGFF", I got the error message ... Error in
> get(name, envir = asNamespace(pkg), inherits = FALSE) :  object
> 'min_overlap_score' not found.
>
>   Could you help me to solve this problem? Any suggestion is greatly
> appreciated.
>
> Thank you very much!
>
> Hui
>
> 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
>
>
>
>
>
>
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>
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