hpages
commented
8 months ago Works for me:
library(EnsDb.Hsapiens.v75)
library(Signac)
annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75)
seqlevels(annotations)
# [1] "X" "20" "1" "6" "3" "7" "12" "11" "4" "17" "2" "16" "8" "19" "9"
# [16] "13" "14" "5" "22" "10" "Y" "18" "15" "21" "MT"
seqlevelsStyle(annotations)
# [1] "NCBI"
seqlevels(annotations)
# [1] "chrX" "chr20" "chr1" "chr6" "chr3" "chr7" "chr12" "chr11" "chr4"
# [10] "chr17" "chr2" "chr16" "chr8" "chr19" "chr9" "chr13" "chr14" "chr5"
# [19] "chr22" "chr10" "chrY" "chr18" "chr15" "chr21" "chrMT"Looks like a transient network issue to me. Please try again.
Best, H.
sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 23.10
Matrix products: default
BLAS: /home/hpages/R/R-4.3.0/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.3.0/lib/libRlapack.so; LAPACK version 3.11.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/Los_Angeles
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Signac_1.12.0 EnsDb.Hsapiens.v75_2.99.0
[3] ensembldb_2.26.0 AnnotationFilter_1.26.0
[5] GenomicFeatures_1.54.3 AnnotationDbi_1.64.1
[7] Biobase_2.62.0 GenomicRanges_1.54.1
[9] GenomeInfoDb_1.38.6 IRanges_2.36.0
[11] S4Vectors_0.40.2 BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.15.0
[3] magrittr_2.0.3 rmarkdown_2.25
[5] BiocIO_1.12.0 zlibbioc_1.48.0
[7] vctrs_0.6.5 memoise_2.0.1
[9] Rsamtools_2.18.0 RCurl_1.98-1.14
[11] base64enc_0.1-3 RcppRoll_0.3.0
[13] htmltools_0.5.7 S4Arrays_1.2.0
[15] progress_1.2.3 curl_5.2.1
[17] SparseArray_1.2.4 Formula_1.2-5
[19] parallelly_1.37.1 htmlwidgets_1.6.4
[21] cachem_1.0.8 GenomicAlignments_1.38.2
[23] lifecycle_1.0.4 pkgconfig_2.0.3
[25] Matrix_1.6-5 R6_2.5.1
[27] fastmap_1.1.1 GenomeInfoDbData_1.2.11
[29] MatrixGenerics_1.14.0 future_1.33.1
[31] digest_0.6.34 colorspace_2.1-0
[33] patchwork_1.2.0 irlba_2.3.5.1
[35] Hmisc_5.1-1 RSQLite_2.3.5
[37] filelock_1.0.3 progressr_0.14.0
[39] fansi_1.0.6 httr_1.4.7
[41] abind_1.4-5 compiler_4.3.0
[43] bit64_4.0.5 htmlTable_2.4.2
[45] backports_1.4.1 BiocParallel_1.36.0
[47] DBI_1.2.2 biomaRt_2.58.2
[49] rappdirs_0.3.3 DelayedArray_0.28.0
[51] rjson_0.2.21 tools_4.3.0
[53] foreign_0.8-86 future.apply_1.11.1
[55] nnet_7.3-19 glue_1.7.0
[57] restfulr_0.0.15 grid_4.3.0
[59] checkmate_2.3.1 cluster_2.1.6
[61] generics_0.1.3 BSgenome_1.70.2
[63] gtable_0.3.4 tidyr_1.3.1
[65] data.table_1.15.2 hms_1.1.3
[67] sp_2.1-3 xml2_1.3.6
[69] utf8_1.2.4 XVector_0.42.0
[71] pillar_1.9.0 stringr_1.5.1
[73] spam_2.10-0 dplyr_1.1.4
[75] BiocFileCache_2.10.1 lattice_0.22-5
[77] rtracklayer_1.62.0 bit_4.0.5
[79] biovizBase_1.50.0 tidyselect_1.2.0
[81] Biostrings_2.70.2 pbapply_1.7-2
[83] knitr_1.45 gridExtra_2.3
[85] ProtGenerics_1.34.0 SummarizedExperiment_1.32.0
[87] xfun_0.42 matrixStats_1.2.0
[89] stringi_1.8.3 lazyeval_0.2.2
[91] yaml_2.3.8 evaluate_0.23
[93] codetools_0.2-19 tibble_3.2.1
[95] cli_3.6.2 rpart_4.1.23
[97] munsell_0.5.0 dichromat_2.0-0.1
[99] Rcpp_1.0.12 globals_0.16.2
[101] dbplyr_2.4.0 png_0.1-8
[103] XML_3.99-0.16.1 parallel_4.3.0
[105] ggplot2_3.5.0 blob_1.2.4
[107] prettyunits_1.2.0 dotCall64_1.1-1
[109] bitops_1.0-7 listenv_0.9.1
[111] VariantAnnotation_1.48.1 scales_1.3.0
[113] SeuratObject_5.0.1 purrr_1.0.2
[115] crayon_1.5.2 rlang_1.1.3
[117] fastmatch_1.1-4 KEGGREST_1.42.0
Hi! I am facing the error while using the function of seqlevelsStyle , the message is as below.
Error in download.file(url, destfile, quiet = TRUE) : 无法打开URL'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_report.txt'
And the code is as below.
library(EnsDb.Hsapiens.v75) annotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v75) seqlevelsStyle(annotations) <- "UCSC"
Environment is as below.
Matrix products: default
locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8
time zone: Asia/Shanghai tzcode source: internal
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] EnsDb.Hsapiens.v75_2.99.0 future_1.33.1 biovizBase_1.50.0
[4] Metrics_0.1.4 umap_0.2.10.0 Rtsne_0.17
[7] spatstat.geom_3.2-8 spatstat.data_3.0-4 hdf5r_1.3.9
[10] cowplot_1.1.3 ggplot2_3.4.4 EnsDb.Hsapiens.v86_2.99.0
[13] ensembldb_2.26.0 AnnotationFilter_1.26.0 GenomicFeatures_1.54.3
[16] AnnotationDbi_1.64.1 harmony_1.2.0 Rcpp_1.0.12
[19] tidyr_1.3.1 readr_2.1.5 magrittr_2.0.3
[22] Matrix_1.6-5 Signac_1.10.0 patchwork_1.2.0
[25] dplyr_1.1.4 SeuratObject_4.1.4 Seurat_4.4.0
[28] devtools_2.4.5 usethis_2.2.2 celldex_1.12.0
[31] SingleR_2.4.1 SummarizedExperiment_1.32.0 Biobase_2.62.0
[34] GenomicRanges_1.54.1 GenomeInfoDb_1.39.7 IRanges_2.36.0
[37] S4Vectors_0.40.2 BiocGenerics_0.48.1 MatrixGenerics_1.14.0
[40] matrixStats_1.2.0 pheatmap_1.0.12
loaded via a namespace (and not attached): [1] fs_1.6.3 ProtGenerics_1.34.0 spatstat.sparse_3.0-3
[4] bitops_1.0-7 httr_1.4.7 RColorBrewer_1.1-3
[7] backports_1.4.1 profvis_0.3.8 tools_4.3.2
[10] sctransform_0.4.1 utf8_1.2.4 R6_2.5.1
[13] lazyeval_0.2.2 uwot_0.1.16 urlchecker_1.0.1
[16] withr_3.0.0 sp_2.1-3 prettyunits_1.2.0
[19] gridExtra_2.3 progressr_0.14.0 cli_3.6.2
[22] spatstat.explore_3.2-6 askpass_1.2.0 ggridges_0.5.6
[25] pbapply_1.7-2 Rsamtools_2.18.0 foreign_0.8-86
[28] dichromat_2.0-0.1 parallelly_1.36.0 sessioninfo_1.2.2
[31] BSgenome_1.70.1 rstudioapi_0.15.0 RSQLite_2.3.5
[34] generics_0.1.3 BiocIO_1.12.0 ica_1.0-3
[37] spatstat.random_3.2-2 fansi_1.0.6 abind_1.4-5
[40] lifecycle_1.0.4 yaml_2.3.8 SparseArray_1.2.3
[43] BiocFileCache_2.10.1 grid_4.3.2 blob_1.2.4
[46] promises_1.2.1 ExperimentHub_2.10.0 crayon_1.5.2
[49] miniUI_0.1.1.1 lattice_0.22-5 beachmat_2.18.0
[52] KEGGREST_1.42.0 knitr_1.45 pillar_1.9.0
[55] rjson_0.2.21 future.apply_1.11.1 codetools_0.2-19
[58] fastmatch_1.1-4 leiden_0.4.3.1 glue_1.7.0
[61] data.table_1.15.0 remotes_2.4.2.1 vctrs_0.6.5
[64] png_0.1-8 gtable_0.3.4 cachem_1.0.8
[67] xfun_0.41 S4Arrays_1.2.0 mime_0.12
[70] survival_3.5-7 RcppRoll_0.3.0 interactiveDisplayBase_1.40.0 [73] ellipsis_0.3.2 fitdistrplus_1.1-11 ROCR_1.0-11
[76] nlme_3.1-164 bit64_4.0.5 progress_1.2.3
[79] filelock_1.0.3 RcppAnnoy_0.0.22 irlba_2.3.5.1
[82] rpart_4.1.23 KernSmooth_2.23-22 Hmisc_5.1-1
[85] colorspace_2.1-0 DBI_1.2.1 nnet_7.3-19
[88] tidyselect_1.2.0 processx_3.8.3 bit_4.0.5
[91] compiler_4.3.2 curl_5.2.0 htmlTable_2.4.2
[94] xml2_1.3.6 desc_1.4.3 DelayedArray_0.28.0
[97] plotly_4.10.4 rtracklayer_1.62.0 checkmate_2.3.1
[100] scales_1.3.0 lmtest_0.9-40 callr_3.7.3
[103] rappdirs_0.3.3 stringr_1.5.1 digest_0.6.34
[106] goftest_1.2-3 spatstat.utils_3.0-4 rmarkdown_2.25
[109] XVector_0.42.0 base64enc_0.1-3 htmltools_0.5.7
[112] pkgconfig_2.0.3 sparseMatrixStats_1.14.0 dbplyr_2.4.0
[115] fastmap_1.1.1 rlang_1.1.3 htmlwidgets_1.6.4
[118] shiny_1.8.0 DelayedMatrixStats_1.24.0 zoo_1.8-12
[121] jsonlite_1.8.8 BiocParallel_1.36.0 VariantAnnotation_1.48.1
[124] BiocSingular_1.18.0 RCurl_1.98-1.14 Formula_1.2-5
[127] GenomeInfoDbData_1.2.11 munsell_0.5.0 reticulate_1.35.0
[130] stringi_1.8.3 zlibbioc_1.48.0 MASS_7.3-60.0.1
[133] AnnotationHub_3.10.0 plyr_1.8.9 pkgbuild_1.4.3
[136] parallel_4.3.2 listenv_0.9.1 ggrepel_0.9.5
[139] deldir_2.0-2 Biostrings_2.70.2 splines_4.3.2
[142] tensor_1.5 hms_1.1.3 ps_1.7.6
[145] igraph_2.0.1.1 reshape2_1.4.4 biomaRt_2.58.2
[148] ScaledMatrix_1.10.0 pkgload_1.3.4 BiocVersion_3.18.1
[151] XML_3.99-0.16.1 evaluate_0.23 BiocManager_1.30.22
[154] tzdb_0.4.0 httpuv_1.6.14 openssl_2.1.1
[157] RANN_2.6.1 purrr_1.0.2 polyclip_1.10-6
[160] scattermore_1.2 rsvd_1.0.5 xtable_1.8-4
[163] restfulr_0.0.15 RSpectra_0.16-1 later_1.3.2
[166] viridisLite_0.4.2 tibble_3.2.1 memoise_2.0.1
[169] GenomicAlignments_1.38.2 cluster_2.1.6 globals_0.16.2
By the way,I run this online. Hope for your help and thanks in advance!