Error in Gviz (actually, rtracklayer) | IdeogramTrack
1
0
Entering edit mode
yujin ▴ 10
@25075190
Last seen 7 months ago
South Korea

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
rtracklayer Gviz • 838 views
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0
Entering edit mode

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

> iTrack <- IdeogramTrack(genome = "hg19", chromosome = "chr2", name = "")
> iTrack
Ideogram track '' for chromosome 2 of the hg19 genome

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.

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1
Entering edit mode
@herve-pages-1542
Last seen 12 hours ago
Seattle, WA, United States

You seem to be using Bioconductor 3.12 which is old and unsupported.

Unfortunately, because of a recent change on the UCSC servers, the version of rtracklayer that is included in BioC 3.12 (rtracklayer 1.50 series) doesn't work properly anymore. Only way to fix this is to upgrade your installation to the lastest BioC release (BioC 3.18, released last week) where rtracklayer was fixed. Note that BioC 3.18 requires R 4.3.

Best,

H.

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0
Entering edit mode

Thank you for your reply :)

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