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

huizhu.gmail huizhu05 at gmail.com
Thu Mar 10 05:19:26 CET 2016

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

Thank you very much!


Below is detail: 

> gtffile <- file.path("/.../resource",

> (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)



[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



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.  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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