Moonriver1988
commented
7 months ago I just found this https://github.com/lawremi/rtracklayer/issues/113
Open Moonriver1988 opened 7 months ago
Moonriver1988
commented
7 months ago I just found this https://github.com/lawremi/rtracklayer/issues/113
Hello,
I got the following error when using makeTxDbFromUCSC with hg19, could you help me with this? Thank you! hg19.refseq.db <- makeTxDbFromUCSC(genome="hg19", table="refGene") Error in names(trackIds) <- sub("^ ", "", nms) : attempt to set an attribute on NULL
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Matrix products: default
locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: America/New_York tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] GenomicFeatures_1.54.3 AnnotationDbi_1.64.1 ggpubr_0.6.0
[4] pheatmap_1.0.12 reshape2_1.4.4 lubridate_1.9.3
[7] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.3
[10] purrr_1.0.2 readr_2.1.4 tidyr_1.3.0
[13] tibble_3.2.1 tidyverse_2.0.0 ggplot2_3.5.0
[16] GenomicInteractions_1.36.0 InteractionSet_1.30.0 SummarizedExperiment_1.32.0 [19] Biobase_2.62.0 MatrixGenerics_1.14.0 matrixStats_1.0.0
[22] GenomicRanges_1.54.0 GenomeInfoDb_1.38.6 IRanges_2.36.0
[25] S4Vectors_0.40.0 BiocGenerics_0.48.1
loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.8
[4] magrittr_2.0.3 rmarkdown_2.25 BiocIO_1.12.0
[7] zlibbioc_1.48.0 vctrs_0.6.4 memoise_2.0.1
[10] Rsamtools_2.18.0 RCurl_1.98-1.12 base64enc_0.1-3
[13] rstatix_0.7.2 htmltools_0.5.7 S4Arrays_1.2.0
[16] progress_1.2.3 curl_5.2.0 broom_1.0.5
[19] SparseArray_1.1.12 Formula_1.2-5 htmlwidgets_1.6.4
[22] plyr_1.8.9 Gviz_1.46.1 cachem_1.0.8
[25] GenomicAlignments_1.38.0 igraph_1.6.0 lifecycle_1.0.4
[28] pkgconfig_2.0.3 Matrix_1.6-1.1 R6_2.5.1
[31] fastmap_1.1.1 GenomeInfoDbData_1.2.11 digest_0.6.33
[34] colorspace_2.1-0 Hmisc_5.1-1 RSQLite_2.3.4
[37] filelock_1.0.3 timechange_0.2.0 fansi_1.0.5
[40] httr_1.4.7 abind_1.4-5 compiler_4.3.1
[43] bit64_4.0.5 withr_3.0.0 htmlTable_2.4.2
[46] backports_1.4.1 BiocParallel_1.36.0 carData_3.0-5
[49] DBI_1.2.2 ggsignif_0.6.4 biomaRt_2.58.2
[52] rappdirs_0.3.3 DelayedArray_0.28.0 rjson_0.2.21
[55] tools_4.3.1 foreign_0.8-86 nnet_7.3-19
[58] glue_1.6.2 restfulr_0.0.15 grid_4.3.1
[61] checkmate_2.3.1 cluster_2.1.6 generics_0.1.3
[64] gtable_0.3.4 BSgenome_1.70.2 tzdb_0.4.0
[67] ensembldb_2.26.0 data.table_1.14.10 hms_1.1.3
[70] car_3.1-2 xml2_1.3.6 utf8_1.2.4
[73] XVector_0.42.0 pillar_1.9.0 BiocFileCache_2.10.1
[76] lattice_0.21-9 rtracklayer_1.62.0 bit_4.0.5
[79] deldir_2.0-2 biovizBase_1.50.0 tidyselect_1.2.0
[82] Biostrings_2.70.0 knitr_1.45 gridExtra_2.3
[85] ProtGenerics_1.34.0 xfun_0.40 stringi_1.8.3
[88] lazyeval_0.2.2 yaml_2.3.7 evaluate_0.23
[91] codetools_0.2-19 RMariaDB_1.3.1 interp_1.1-5
[94] cli_3.6.1 rpart_4.1.23 munsell_0.5.0
[97] dichromat_2.0-0.1 Rcpp_1.0.11 dbplyr_2.4.0
[100] png_0.1-8 XML_3.99-0.14 parallel_4.3.1
[103] blob_1.2.4 prettyunits_1.2.0 latticeExtra_0.6-30
[106] jpeg_0.1-10 AnnotationFilter_1.26.0 bitops_1.0-7
[109] VariantAnnotation_1.48.1 scales_1.3.0 crayon_1.5.2
[112] rlang_1.1.1 KEGGREST_1.42.0