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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