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# Biomart server error
# Please also include the results of running the following in an R session
> biotype.fc<- getBM(attributes=c("gene_biotype","transcript_biotype","external_gene_name","ensembl_gene_id"),filters="ensembl_gene_id",values=fc.genes,mart=ensembl)
Error: biomaRt has encountered an unknown server error. HTTP error code: 405
Please report this on the Bioconductor support site at https://support.bioconductor.org/
Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)
> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 15.3.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicFeatures_1.54.4 AnnotationDbi_1.64.1 tximeta_1.20.3 tximport_1.30.0
[5] magrittr_2.0.3 lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1
[9] purrr_1.0.4 readr_2.1.5 tidyr_1.3.1 tibble_3.2.1
[13] tidyverse_2.0.0 biomaRt_2.58.2 dplyr_1.1.4 pcaExplorer_2.28.0
[17] DESeq2_1.42.1 ggplot2_3.5.2 pheatmap_1.0.12 R.utils_2.13.0
[21] R.oo_1.27.1 R.methodsS3_1.8.2 profileplyr_1.18.0 SummarizedExperiment_1.32.0
[25] GenomicRanges_1.54.1 GenomeInfoDb_1.38.8 IRanges_2.36.0 S4Vectors_0.40.2
[29] MatrixGenerics_1.14.0 matrixStats_1.5.0 Biobase_2.62.0 BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] dichromat_2.0-0.1 vroom_1.6.5
[3] GSEABase_1.64.0 progress_1.2.3
[5] tiff_0.1-12 DT_0.33
[7] Biostrings_2.70.3 TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0
[9] vctrs_0.6.5 digest_0.6.37
[11] png_0.1-8 shape_1.4.6.1
[13] shinyBS_0.61.1 registry_0.5-1
[15] ggrepel_0.9.6 mixsqp_0.3-54
[17] org.Mm.eg.db_3.18.0 deldir_2.0-4
[19] MASS_7.3-60.0.1 reshape2_1.4.4
[21] SQUAREM_2021.1 httpuv_1.6.16
[23] foreach_1.5.2 qvalue_2.34.0
[25] withr_3.0.2 xfun_0.52
[27] amap_0.8-20 ggfun_0.1.8
[29] survival_3.8-3 memoise_2.0.1
[31] tidytree_0.4.6 GlobalOptions_0.1.2
[33] gtools_3.9.5 prettyunits_1.2.0
[35] KEGGREST_1.42.0 promises_1.3.2
[37] httr_1.4.7 GreyListChIP_1.34.0
[39] restfulr_0.0.15 ashr_2.2-63
[41] rstudioapi_0.17.1 shinyAce_0.4.4
[43] generics_0.1.4 DOSE_3.28.2
[45] base64enc_0.1-3 curl_6.2.2
[47] zlibbioc_1.48.2 EnrichedHeatmap_1.32.0
[49] ggraph_2.2.1 polyclip_1.10-7
[51] ca_0.71.1 GenomeInfoDbData_1.2.11
[53] SparseArray_1.2.4 RBGL_1.78.0
[55] threejs_0.3.4 interactiveDisplayBase_1.40.0
[57] xtable_1.8-4 doParallel_1.0.17
[59] evaluate_1.0.3 S4Arrays_1.2.1
[61] systemPipeR_2.8.0 preprocessCore_1.64.0
[63] BiocFileCache_2.10.2 hms_1.1.3
[65] irlba_2.3.5.1 colorspace_2.1-1
[67] filelock_1.0.3 Rgraphviz_2.46.0
[69] later_1.4.2 viridis_0.6.5
[71] ggtree_3.10.1 lattice_0.22-7
[73] NMF_0.28 genefilter_1.84.0
[75] SparseM_1.84-2 XML_3.99-0.18
[77] shadowtext_0.1.4 cowplot_1.1.3
[79] pillar_1.10.2 nlme_3.1-168
[81] iterators_1.0.14 gridBase_0.4-7
[83] caTools_1.18.3 compiler_4.3.2
[85] stringi_1.8.7 Category_2.68.0
[87] TSP_1.2-4 dendextend_1.19.0
[89] GenomicAlignments_1.38.2 plyr_1.8.9
[91] crayon_1.5.3 abind_1.4-8
[93] BiocIO_1.12.0 truncnorm_1.0-9
[95] gridGraphics_0.5-1 emdbook_1.3.13
[97] locfit_1.5-9.12 graphlayouts_1.2.2
[99] org.Hs.eg.db_3.18.0 bit_4.6.0
[101] fastmatch_1.1-6 codetools_0.2-20
[103] TxDb.Mmusculus.UCSC.mm10.knownGene_3.10.0 crosstalk_1.2.1
[105] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GetoptLong_1.0.5
[107] plotly_4.10.4 mime_0.13
[109] splines_4.3.2 circlize_0.4.16
[111] Rcpp_1.0.14 dbplyr_2.5.0
[113] HDO.db_0.99.1 interp_1.1-6
[115] knitr_1.50 blob_1.2.4
[117] clue_0.3-66 BiocVersion_3.18.1
[119] AnnotationFilter_1.26.0 apeglm_1.24.0
[121] chipseq_1.52.0 fs_1.6.6
[123] ggplotify_0.1.2 rGREAT_2.4.0
[125] Matrix_1.6-5 statmod_1.5.0
[127] tzdb_0.5.0 tweenr_2.0.3
[129] pkgconfig_2.0.3 tools_4.3.2
[131] cachem_1.1.0 RSQLite_2.3.11
[133] viridisLite_0.4.2 DBI_1.2.3
[135] numDeriv_2016.8-1.1 fastmap_1.2.0
[137] rmarkdown_2.29 scales_1.4.0
[139] grid_4.3.2 shinydashboard_0.7.3
[141] Rsamtools_2.18.0 AnnotationHub_3.10.1
[143] patchwork_1.3.0 coda_0.19-4.1
[145] BiocManager_1.30.25 graph_1.80.0
[147] farver_2.1.2 tidygraph_1.3.1
[149] scatterpie_0.2.4 yaml_2.3.10
[151] AnnotationForge_1.44.0 latticeExtra_0.6-30
[153] rtracklayer_1.62.0 cli_3.6.5
[155] webshot_0.5.5 lifecycle_1.0.4
[157] mvtnorm_1.3-3 BiocParallel_1.36.0
[159] annotate_1.80.0 timechange_0.3.0
[161] gtable_0.3.6 rjson_0.2.23
[163] ChIPseeker_1.38.0 DiffBind_3.12.0
[165] parallel_4.3.2 ape_5.8-1
[167] limma_3.58.1 jsonlite_2.0.0
[169] seriation_1.5.7 bitops_1.0-9
[171] bit64_4.6.0-1 assertthat_0.2.1
[173] yulab.utils_0.2.0 heatmaply_1.5.0
[175] soGGi_1.34.0 bdsmatrix_1.3-7
[177] GOSemSim_2.28.1 lazyeval_0.2.2
[179] shiny_1.10.0 htmltools_0.5.8.1
[181] enrichplot_1.22.0 GO.db_3.18.0
[183] rappdirs_0.3.3 ensembldb_2.26.0
[185] glue_1.8.0 TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2
[187] XVector_0.42.0 RCurl_1.98-1.17
[189] treeio_1.26.0 BSgenome_1.70.2
[191] jpeg_0.1-11 gridExtra_2.3
[193] boot_1.3-31 igraph_2.1.4
[195] invgamma_1.1 R6_2.6.1
[197] gplots_3.2.0 labeling_0.4.3
[199] cluster_2.1.8.1 rngtools_1.5.2
[201] bbmle_1.0.25.1 aplot_0.2.5
[203] ProtGenerics_1.34.0 DelayedArray_0.28.0
[205] tidyselect_1.2.1 plotrix_3.8-4
[207] GOstats_2.68.0 ggforce_0.4.2
[209] xml2_1.3.8 KernSmooth_2.23-26
[211] topGO_2.54.0 data.table_1.17.2
[213] htmlwidgets_1.6.4 fgsea_1.28.0
[215] ComplexHeatmap_2.18.0 RColorBrewer_1.1-3
[217] hwriter_1.3.2.1 rlang_1.1.6
[219] ShortRead_1.60.0
