Error message in makeTxDbFromGFF()
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Entering edit mode
jjmm1101 • 0
@jjmm1101-9887
Last seen 8.1 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
iranges genomicfeatures • 1.2k views
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Entering edit mode

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.

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