Entering edit mode
When I run this code (below)
iTrack <- IdeogramTrack(genome = "hg19", chromosome = "chr2", name = "")
then I get the error
Error: failed to load external entity "http://genome.ucsc.edu/FAQ/FAQreleases"
Did someone else encounter this error as well?
Thanks a lot.
Here is my sessionInfo() (below)
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 8
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] DMRcatedata_2.8.2 bladderbatch_1.28.0
[3] pamr_1.56.1 survival_3.2-13
[5] sva_3.38.0 BiocParallel_1.24.1
[7] mgcv_1.9-0 ENmix_1.37.04
[9] doParallel_1.0.17 ggvenn_0.1.10
[11] Rmisc_1.5 plyr_1.8.8
[13] lattice_0.20-45 fastman_0.1.0
[15] sp_2.0-0 lubridate_1.9.2
[17] forcats_1.0.0 purrr_1.0.2
[19] tibble_3.2.1 tidyverse_2.0.0
[21] annotate_1.68.0 XML_3.99-0.14
[23] ChAMP_2.20.1 RPMM_1.25
[25] cluster_2.1.4 DT_0.29
[27] Illumina450ProbeVariants.db_1.26.0 ChAMPdata_2.30.0
[29] chipenrich_2.14.0 annotatr_1.16.0
[31] Repitools_1.36.0 rtracklayer_1.50.0
[33] ensembldb_2.14.1 AnnotationFilter_1.14.0
[35] RCurl_1.98-1.12 ggpubr_0.4.0
[37] devtools_2.4.5 usethis_2.2.2
[39] ggpmisc_0.5.3 ggpp_0.5.3
[41] hrbrthemes_0.8.0 FlowSorted.Blood.EPIC_1.8.0
[43] ExperimentHub_1.16.1 nlme_3.1-155
[45] quadprog_1.5-8 genefilter_1.72.1
[47] maxprobes_0.0.2 DMRcate_2.4.1
[49] Gviz_1.34.1 minfiData_0.36.0
[51] IlluminaHumanMethylation450kmanifest_0.4.0 missMethyl_1.24.0
[53] RColorBrewer_1.1-3 IlluminaHumanMethylationEPICmanifest_0.3.0
[55] limma_3.46.0 knitr_1.43
[57] readr_2.1.4 R.utils_2.12.2
[59] R.oo_1.24.0 R.methodsS3_1.8.1
[61] Homo.sapiens_1.3.1 org.Hs.eg.db_3.12.0
[63] GO.db_3.12.1 OrganismDbi_1.32.0
[65] CAGEr_1.32.1 MultiAssayExperiment_1.16.0
[67] clusterProfiler_3.18.1 ChIPseeker_1.26.2
[69] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicState_0.99.9
[71] AnnotationHub_2.22.1 BiocFileCache_1.14.0
[73] dbplyr_2.3.3 GenomicFeatures_1.42.3
[75] AnnotationDbi_1.52.0 IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[77] biomaRt_2.46.3 nortest_1.0-4
[79] tidyr_1.3.0 dplyr_1.1.3
[81] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0 patchwork_1.1.2
[83] argparse_2.1.3 scales_1.2.1
[85] stringr_1.5.0 data.table_1.14.2
[87] qqman_0.1.8 TeachingDemos_2.12
[89] ggrepel_0.9.3 ggplot2_3.4.2
[91] minfi_1.36.0 bumphunter_1.32.0
[93] locfit_1.5-9.4 iterators_1.0.14
[95] foreach_1.5.2 Biostrings_2.58.0
[97] XVector_0.30.0 SummarizedExperiment_1.20.0
[99] Biobase_2.50.0 MatrixGenerics_1.2.1
[101] matrixStats_1.0.0 GenomicRanges_1.42.0
[103] GenomeInfoDb_1.26.7 IRanges_2.24.1
[105] S4Vectors_0.28.1 BiocGenerics_0.36.1
loaded via a namespace (and not attached):
[1] Ringo_1.54.0 graphlayouts_0.8.0 vctrs_0.6.3 fastICA_1.2-3
[5] beanplot_1.3.1 DSS_2.38.0 blob_1.2.4 RBGL_1.66.0
[9] later_1.3.1 DBI_1.1.3 rappdirs_0.3.3 jpeg_0.1-9
[13] zlibbioc_1.36.0 MatrixModels_0.5-0 htmlwidgets_1.6.2 mvtnorm_1.1-3
[17] illuminaio_0.32.0 tidygraph_1.2.0 Rcpp_1.0.11 KernSmooth_2.23-20
[21] promises_1.2.1 methylumi_2.36.0 DelayedArray_0.16.3 vegan_2.6-4
[25] pkgload_1.3.2.1 graph_1.68.0 Hmisc_4.8-0 geneLenDataBase_1.26.0
[29] fs_1.6.3 fastmatch_1.1-3 digest_0.6.33 png_0.1-7
[33] polspline_1.1.19 nor1mix_1.3-0 scatterpie_0.1.7 cowplot_1.1.1
[37] DOSE_3.16.0 nleqslv_3.3.2 ggraph_2.0.5 pkgconfig_2.0.3
[41] DelayedMatrixStats_1.12.3 chipenrich.data_2.14.0 xfun_0.40 zoo_1.8-12
[45] tidyselect_1.2.0 reshape2_1.4.4 DNAcopy_1.64.0 operator.tools_1.6.3
[49] viridisLite_0.4.2 marray_1.68.0 pkgbuild_1.3.1 rlang_1.1.1
[53] glue_1.6.2 gdtools_0.2.4 lambda.r_1.2.4 ggsignif_0.6.3
[57] labeling_0.4.2 SparseM_1.81 httpuv_1.6.9 preprocessCore_1.52.1
[61] Rttf2pt1_1.3.10 TH.data_1.1-0 isva_1.9 DO.db_2.9
[65] bsseq_1.26.0 jsonlite_1.7.3 ROC_1.66.0 bit_4.0.5
[69] mime_0.12 systemfonts_1.0.4 gridExtra_2.3 gplots_3.1.3
[73] Rsamtools_2.6.0 stringi_1.7.12 processx_3.8.2 wateRmelon_1.34.0
[77] yulab.utils_0.0.4 bitops_1.0-7 cli_3.6.1 rhdf5filters_1.2.1
[81] RSQLite_2.3.1 timechange_0.2.0 rstudioapi_0.15.0 org.Mm.eg.db_3.12.0
[85] GenomicAlignments_1.26.0 qvalue_2.22.0 VariantAnnotation_1.36.0 miniUI_0.1.1.1
[89] urlchecker_1.0.1 readxl_1.4.3 sessioninfo_1.2.2 lifecycle_1.0.3
[93] cellranger_1.1.0 munsell_0.5.0 caTools_1.18.2 codetools_0.2-18
[97] htmlTable_2.4.0 xtable_1.8-4 formatR_1.14 BiocManager_1.30.22
[101] abind_1.4-5 farver_2.1.1 askpass_1.2.0 biovizBase_1.38.0
[105] GEOquery_2.58.0 shinythemes_1.2.0 futile.options_1.0.1 profvis_0.3.7
[109] dichromat_2.0-0 dendextend_1.15.2 extrafontdb_1.0 Matrix_1.4-0
[113] ellipsis_0.3.2 prettyunits_1.1.1 goseq_1.42.0 VennDiagram_1.7.1
[117] mclust_5.4.9 igraph_1.2.11 multtest_2.46.0 fgsea_1.16.0
[121] remotes_2.4.2.1 htmltools_0.5.6 org.Rn.eg.db_3.12.0 yaml_2.3.7
[125] plotly_4.10.0 utf8_1.2.3 interactiveDisplayBase_1.28.0 foreign_0.8-82
[129] withr_2.5.0 bit64_4.0.5 BiasedUrn_1.07 rngtools_1.5.2
[133] doRNG_1.8.2 affyio_1.60.0 multcomp_1.4-25 ProtGenerics_1.22.0
[137] combinat_0.0-8 GOSemSim_2.16.1 globaltest_5.44.0 memoise_2.0.1
[141] evaluate_0.21 VGAM_1.1-6 geneplotter_1.68.0 tzdb_0.2.0
[145] permute_0.9-7 extrafont_0.17 callr_3.7.3 ps_1.6.0
[149] ChIPpeakAnno_3.24.2 curl_5.0.2 fansi_1.0.4 edgeR_3.32.1
[153] polynom_1.4-0 checkmate_2.0.0 regioneR_1.22.0 cachem_1.0.8
[157] truncnorm_1.0-8 impute_1.64.0 rstatix_0.7.0 lumi_2.42.0
[161] clue_0.3-60 tools_4.0.5 sandwich_3.0-1 magrittr_2.0.3
[165] Rsolnp_1.16 car_3.0-12 xml2_1.3.5 httr_1.4.7
[169] rmarkdown_2.24 boot_1.3-28 R6_2.5.1 Rhdf5lib_1.12.1
[173] nnet_7.3-17 KEGGREST_1.30.1 progress_1.2.2 stringdist_0.9.8
[177] gtools_3.9.4 statmod_1.4.36 BiocVersion_3.12.0 HDF5Array_1.18.1
[181] rhdf5_2.34.0 splines_4.0.5 carData_3.0-5 ggfun_0.0.5
[185] colorspace_2.1-0 generics_0.1.3 base64enc_0.1-3 vsn_3.58.0
[189] pillar_1.9.0 tweenr_1.0.2 affy_1.68.0 calibrate_1.7.7
[193] rvcheck_0.2.1 GenomeInfoDbData_1.2.4 futile.logger_1.4.3 gtable_0.3.3
[197] gsmoothr_0.1.7 latticeExtra_0.6-29 shadowtext_0.1.1 fastmap_1.1.1
[201] quantreg_5.95 broom_0.7.12 openssl_2.1.0 som_0.3-5.1
[205] BSgenome_1.58.0 backports_1.4.1 plotrix_3.8-2 base64_2.0.1
[209] org.Dr.eg.db_3.12.0 rms_6.5-0 kpmt_0.1.0 enrichplot_1.10.2
[213] hms_1.1.3 ggforce_0.3.3 scrime_1.3.5 formula.tools_1.7.1
[217] shiny_1.7.5 polyclip_1.10-0 siggenes_1.64.0 lazyeval_0.2.2
[221] dynamicTreeCut_1.63-1 JADE_2.0-4 Formula_1.2-4 crayon_1.5.0
[225] MASS_7.3-60 downloader_0.4 org.Dm.eg.db_3.12.0 sparseMatrixStats_1.2.1
[229] viridis_0.6.2 reshape_0.8.8 rpart_4.1.16 compiler_4.0.5
Have you tried again; maybe it was a temporary issue? Do you have a strong internet connection when running? I just tried with R4.3 and the latest version of Gviz 1.47.0 and it seemed to work without any ERROR
I don't have a version of R 4.0 to test readily but if it is possible to update the versions of R and Gviz/tracklayer that would be good to do.