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@lucasmacielbiotec-15278
Last seen 6.7 years ago
Hello, I have been trying to make a TxDb from na gtf but always occur this error. I already saw posts about reinstallation of packages but I tried almost everything and I couldn't fix it. Could anyone helpe me, please? txdb = GenomicFeatures::makeTxDbFromGFF("schisto-transcriptome/schisto.gtf",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 c(x, value) : could not find symbol "recursive" in environment of the generic function
Session info:
R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.24.0 edgeR_3.16.5 limma_3.30.13 [4] GenomicAlignments_1.10.0 Rsamtools_1.26.1 Biostrings_2.42.0 [7] XVector_0.14.0 GenomicFeatures_1.26.0 AnnotationDbi_1.36.0 [10] tximportData_1.2.0 DESeq2_1.14.1 SummarizedExperiment_1.4.0 [13] Biobase_2.34.0 GenomicRanges_1.26.1 GenomeInfoDb_1.10.0 [16] IRanges_2.8.0 S4Vectors_0.12.0 BiocGenerics_0.20.0 loaded via a namespace (and not attached): [1] genefilter_1.56.0 locfit_1.5-9.1 splines_3.4.3 lattice_0.20-35 colorspace_1.2-7 [6] rtracklayer_1.34.0 yaml_2.1.13 survival_2.41-3 XML_3.98-1.3 rlang_0.2.0 [11] pillar_1.2.1 foreign_0.8-69 glue_1.2.0 DBI_0.8 BiocParallel_1.8.1 [16] RColorBrewer_1.1-2 bindrcpp_0.2 plyr_1.8.4 bindr_0.1.1 zlibbioc_1.20.0 [21] munsell_0.4.3 gtable_0.2.0 latticeExtra_0.6-28 biomaRt_2.30.0 geneplotter_1.52.0 [26] Rcpp_0.12.16 acepack_1.4.1 xtable_1.8-2 scales_0.5.0 Hmisc_3.17-4 [31] annotate_1.52.1 gridExtra_2.2.1 ggplot2_2.2.1 dplyr_0.7.4 grid_3.4.3 [36] tools_3.4.3 bitops_1.0-6 magrittr_1.5 lazyeval_0.2.1 RCurl_1.95-4.8 [41] tibble_1.4.2 RSQLite_1.0.0 Formula_1.2-1 cluster_2.0.6 pkgconfig_2.0.1 [46] Matrix_1.2-11 data.table_1.10.4-3 assertthat_0.2.0 R6_2.2.2 rpart_4.1-13 [51] nnet_7.3-12 compiler_3.4.3
Sounds like you may have out of date packages. Please run BiocInstaller::biocValid(), update old packages and let us know if the error persists.
Valerie