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ivanek / Gviz

This is the Gviz development repository. Gviz plots data and annotation information along genomic coordinates.
https://bioconductor.org/packages/Gviz/
Artistic License 2.0
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UcscTrack: track issue #87

Open jennyujin22 opened 1 year ago

jennyujin22 commented 1 year ago

Dear Gviz team:

Hello, this is Yujin Kim.

Thanks for the great tool.

when I run the code rTrack <- UcscTrack(genome="hg19", chromosome=chrom, track = "NCBI RefSeq", from=minbase, to=maxbase, trackType="GeneRegionTrack", rstarts="exonStarts", rends="exonEnds", gene="name", symbol="name2", transcript="name", strand="strand", fill="darkblue",stacking="squish", name="RefSeq", showId=TRUE, geneSymbol=TRUE)

I got the error

'Error in normArgTrack(track, trackids) : Unknown track: refSeqComposite In addition, a warning message: In.local(x,...) : 'track' parameter is deprecated; now you go by the 'table' instead Use ucscTables (genome, track) to retrieve the list of tables for a track'

But when I look up the UCSC table browser, I could find 'NCBI RefSeq' https://genome.ucsc.edu/cgi-bin/hgTables?command=start

image

my session info

`> sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.1 LTS

Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

time zone: Asia/Seoul tzcode source: system (glibc)

attached base packages: [1] grid parallel stats4 stats graphics grDevices utils datasets methods
[10] base

other attached packages: [1] DMRcatedata_2.20.0
[2] ggrepel_0.9.4
[3] ggplot2_3.4.4
[4] tibble_3.2.1
[5] dplyr_1.1.3
[6] FlowSorted.Blood.EPIC_2.6.0
[7] ExperimentHub_2.10.0
[8] AnnotationHub_3.10.0
[9] BiocFileCache_2.10.1
[10] dbplyr_2.4.0
[11] stringr_1.5.0
[12] Gviz_1.46.0
[13] minfiData_0.48.0
[14] IlluminaHumanMethylation450kmanifest_0.4.0
[15] missMethyl_1.36.0
[16] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.1 [17] RColorBrewer_1.1-3
[18] IlluminaHumanMethylationEPICmanifest_0.3.0
[19] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0 [20] minfi_1.48.0
[21] bumphunter_1.44.0
[22] locfit_1.5-9.8
[23] Biostrings_2.70.1
[24] XVector_0.42.0
[25] limma_3.58.0
[26] knitr_1.45
[27] ENmix_1.38.01
[28] SummarizedExperiment_1.32.0
[29] MatrixGenerics_1.14.0
[30] matrixStats_1.0.0
[31] doParallel_1.0.17
[32] iterators_1.0.14
[33] foreach_1.5.2
[34] mCSEA_1.22.0
[35] Homo.sapiens_1.3.1
[36] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[37] org.Hs.eg.db_3.18.0
[38] GO.db_3.18.0
[39] OrganismDbi_1.44.0
[40] GenomicFeatures_1.54.0
[41] GenomicRanges_1.54.0
[42] GenomeInfoDb_1.38.0
[43] AnnotationDbi_1.64.0
[44] IRanges_2.36.0
[45] S4Vectors_0.40.1
[46] Biobase_2.62.0
[47] BiocGenerics_0.48.0
[48] mCSEAdata_1.22.0
[49] DMRcate_2.16.0

loaded via a namespace (and not attached): [1] DSS_2.49.0 ProtGenerics_1.34.0 bitops_1.0-7
[4] httr_1.4.7 dynamicTreeCut_1.63-1 tools_4.3.1
[7] doRNG_1.8.6 backports_1.4.1 utf8_1.2.4
[10] R6_2.5.1 HDF5Array_1.30.0 lazyeval_0.2.2
[13] maxprobes_0.0.2 rhdf5filters_1.14.0 permute_0.9-7
[16] withr_2.5.2 prettyunits_1.2.0 gridExtra_2.3
[19] base64_2.0.1 preprocessCore_1.64.0 cli_3.6.1
[22] labeling_0.4.3 readr_2.1.4 genefilter_1.84.0
[25] askpass_1.2.0 Rsamtools_2.18.0 foreign_0.8-85
[28] siggenes_1.76.0 illuminaio_0.44.0 R.utils_2.12.2
[31] dichromat_2.0-0.1 scrime_1.3.5 BSgenome_1.70.0
[34] readxl_1.4.3 impute_1.76.0 rstudioapi_0.15.0
[37] RSQLite_2.3.2 generics_0.1.3 BiocIO_1.12.0
[40] gtools_3.9.4 Matrix_1.6-1.1 interp_1.1-4
[43] fansi_1.0.5 abind_1.4-5 R.methodsS3_1.8.2
[46] lifecycle_1.0.3 yaml_2.3.7 edgeR_4.0.0
[49] gplots_3.1.3 rhdf5_2.46.0 SparseArray_1.2.0
[52] blob_1.2.4 promises_1.2.1 crayon_1.5.2
[55] lattice_0.22-5 annotate_1.80.0 KEGGREST_1.42.0
[58] pillar_1.9.0 beanplot_1.3.1 rjson_0.2.21
[61] codetools_0.2-19 glue_1.6.2 data.table_1.14.8
[64] vctrs_0.6.4 png_0.1-8 cellranger_1.1.0
[67] gtable_0.3.4 cachem_1.0.8 xfun_0.40
[70] S4Arrays_1.2.0 mime_0.12 survival_3.5-7
[73] statmod_1.5.0 interactiveDisplayBase_1.40.0 ellipsis_0.3.2
[76] nlme_3.1-163 bit64_4.0.5 bsseq_1.38.0
[79] progress_1.2.2 filelock_1.0.2 nor1mix_1.3-0
[82] irlba_2.3.5.1 KernSmooth_2.23-22 rpart_4.1.21
[85] colorspace_2.1-0 DBI_1.1.3 Hmisc_5.1-1
[88] nnet_7.3-19 tidyselect_1.2.0 bit_4.0.5
[91] compiler_4.3.1 curl_5.1.0 graph_1.80.0
[94] htmlTable_2.4.2 xml2_1.3.5 RPMM_1.25
[97] DelayedArray_0.28.0 rtracklayer_1.62.0 caTools_1.18.2
[100] checkmate_2.3.0 scales_1.2.1 quadprog_1.5-8
[103] RBGL_1.78.0 rappdirs_0.3.3 digest_0.6.33
[106] rmarkdown_2.25 GEOquery_2.70.0 htmltools_0.5.6.1
[109] pkgconfig_2.0.3 jpeg_0.1-10 base64enc_0.1-3
[112] sparseMatrixStats_1.14.0 fastmap_1.1.1 ensembldb_2.26.0
[115] rlang_1.1.1 htmlwidgets_1.6.2 shiny_1.7.5.1
[118] DelayedMatrixStats_1.24.0 farver_2.1.1 BiocParallel_1.36.0
[121] mclust_6.0.0 R.oo_1.25.0 VariantAnnotation_1.48.0
[124] RCurl_1.98-1.12 magrittr_2.0.3 Formula_1.2-5
[127] GenomeInfoDbData_1.2.11 Rhdf5lib_1.24.0 munsell_0.5.0
[130] Rcpp_1.0.11 stringi_1.7.12 zlibbioc_1.48.0
[133] MASS_7.3-60 plyr_1.8.9 deldir_1.0-9
[136] splines_4.3.1 multtest_2.58.0 hms_1.1.3
[139] rngtools_1.5.2 geneplotter_1.80.0 biomaRt_2.58.0
[142] BiocVersion_3.18.0 XML_3.99-0.14 evaluate_0.22
[145] latticeExtra_0.6-30 biovizBase_1.50.0 BiocManager_1.30.22
[148] tzdb_0.4.0 httpuv_1.6.12 tidyr_1.3.0
[151] openssl_2.1.1 purrr_1.0.2 reshape_0.8.9
[154] xtable_1.8-4 restfulr_0.0.15 AnnotationFilter_1.26.0
[157] later_1.3.1 memoise_2.0.1 GenomicAlignments_1.38.0
[160] cluster_2.1.4 `

Could you please help me?

If you could do something for me, I'd really appreciate it.

Many thanks,

Yujin Kim.

danielsu0523 commented 1 year ago

Meet the similar problem. Should I set the parameter of 'track' and 'table' simultaneously in UcscTrack function to retrieve the right data tables? Many thanks.

Fefile commented 1 year ago

Same problem here. Is there a solution to make the function work properly?

eld211 commented 8 months ago

having the same problem I have doubled checked all the UCSC table/track names and still getting an error. The code worked fine 6 months ago

Fefile commented 8 months ago

There was an update and it's been corrected on the devel version I think.

GRealesM commented 5 months ago

I'm still having the same issue, even after updating to the dev version. This is what my code looks like:

ucsct <- UcscTrack(genome = "hg38", chromosome = paste0("chr", pp$CHR38), track = "GENCODE V44", table="knownGene", from = from, to = to, trackType = "GeneRegionTrack", fill = "#8282d2", name = "UCSC Genes") This is the error I get: Warning messages: 1: In .local(x, ...) : 'track' parameter is deprecated now you go by the 'table' instead Use ucscTables(genome, track) to retrieve the list of tables for a track 2: In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) : Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x557cc911d8d0): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!

And my sessionInfo():

R version 4.3.3 (2024-02-29) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: Rocky Linux 8.9 (Green Obsidian)

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblaso-r0.3.15.so; LAPACK version 3.9.0

locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C

time zone: GB tzcode source: system (glibc)

attached base packages: [1] grid stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] Gviz_1.47.1 GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1 magrittr_2.0.3
[8] data.table_1.15.4

loaded via a namespace (and not attached): [1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8 GenomicFeatures_1.54.4 rmarkdown_2.27
[6] BiocIO_1.12.0 zlibbioc_1.48.2 vctrs_0.6.5 memoise_2.0.1 Rsamtools_2.18.0
[11] RCurl_1.98-1.14 base64enc_0.1-3 htmltools_0.5.8.1 S4Arrays_1.2.1 progress_1.2.3
[16] curl_5.2.1 SparseArray_1.2.4 Formula_1.2-5 htmlwidgets_1.6.4 desc_1.4.3
[21] cachem_1.1.0 GenomicAlignments_1.38.2 lifecycle_1.0.4 pkgconfig_2.0.3 Matrix_1.6-5
[26] R6_2.5.1 fastmap_1.2.0 GenomeInfoDbData_1.2.11 MatrixGenerics_1.14.0 digest_0.6.35
[31] colorspace_2.1-0 AnnotationDbi_1.64.1 ps_1.7.6 Hmisc_5.1-2 RSQLite_2.3.6
[36] filelock_1.0.3 fansi_1.0.6 httr_1.4.7 abind_1.4-5 compiler_4.3.3
[41] remotes_2.5.0 bit64_4.0.5 htmlTable_2.4.2 backports_1.4.1 BiocParallel_1.36.0
[46] DBI_1.2.2 pkgbuild_1.4.4 R.utils_2.12.3 biomaRt_2.58.2 rappdirs_0.3.3
[51] DelayedArray_0.28.0 rjson_0.2.21 tools_4.3.3 foreign_0.8-86 nnet_7.3-19
[56] R.oo_1.26.0 glue_1.7.0 restfulr_0.0.15 callr_3.7.6 checkmate_2.3.1
[61] cluster_2.1.6 generics_0.1.3 gtable_0.3.5 BSgenome_1.70.2 R.methodsS3_1.8.2
[66] ensembldb_2.26.0 hms_1.1.3 xml2_1.3.6 utf8_1.2.4 XVector_0.42.0
[71] pillar_1.9.0 stringr_1.5.1 dplyr_1.1.4 BiocFileCache_2.10.2 lattice_0.22-6
[76] rtracklayer_1.62.0 bit_4.0.5 deldir_2.0-4 biovizBase_1.50.0 tidyselect_1.2.1
[81] Biostrings_2.70.3 knitr_1.46 gridExtra_2.3 ProtGenerics_1.34.0 SummarizedExperiment_1.32.0 [86] xfun_0.44 Biobase_2.62.0 matrixStats_1.3.0 stringi_1.8.4 lazyeval_0.2.2
[91] yaml_2.3.8 evaluate_0.23 codetools_0.2-20 interp_1.1-6 tibble_3.2.1
[96] cli_3.6.2 rpart_4.1.23 munsell_0.5.1 processx_3.8.4 dichromat_2.0-0.1
[101] Rcpp_1.0.12 dbplyr_2.5.0 png_0.1-8 XML_3.99-0.16.1 parallel_4.3.3
[106] ggplot2_3.5.1 blob_1.2.4 prettyunits_1.2.0 latticeExtra_0.6-30 jpeg_0.1-10
[111] AnnotationFilter_1.26.0 bitops_1.0-7 VariantAnnotation_1.48.1 scales_1.3.0 crayon_1.5.2
[116] rlang_1.1.3 KEGGREST_1.42.0

Thanks!