Entering edit mode
Somehow I can't get the latest date:
> library(AnnotationHub) > ah <- AnnotationHub() snapshotDate(): 2017-10-27 > query(ah, c("norvegicus", "release-92")) AnnotationHub with 0 records # snapshotDate(): 2017-10-27
Is there cache data somewhere that I need to delete?
> sessionInfo() R version 3.4.4 (2018-03-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.4 LTS Matrix products: default BLAS: /usr/lib/openblas-base/libblas.so.3 LAPACK: /usr/lib/libopenblasp-r0.2.18.so 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 [6] LC_MESSAGES=en_GB.UTF-8 LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base other attached packages: [1] bindrcpp_0.2.2 reshape2_1.4.3 ggplot2_3.0.0 BSgenome.Rnorvegicus.UCSC.rn6_1.4.1 [5] BSgenome_1.46.0 Rsamtools_1.30.0 Biostrings_2.46.0 XVector_0.18.0 [9] dplyr_0.7.6 Rsubread_1.28.1 GenomicFeatures_1.30.3 AnnotationDbi_1.40.0 [13] Biobase_2.38.0 rtracklayer_1.38.3 GenomicRanges_1.30.3 GenomeInfoDb_1.14.0 [17] IRanges_2.12.0 S4Vectors_0.16.0 biomaRt_2.34.2 AnnotationHub_2.10.1 [21] BiocGenerics_0.24.0 vimcom_1.2-5 setwidth_1.0-4 colorout_1.1-0 loaded via a namespace (and not attached): [1] httr_1.3.1 RMySQL_0.10.15 bit64_0.9-7 shiny_1.1.0 assertthat_0.2.0 [6] interactiveDisplayBase_1.16.0 blob_1.1.1 GenomeInfoDbData_1.0.0 yaml_2.1.19 progress_1.2.0 [11] pillar_1.2.3 RSQLite_2.1.1 lattice_0.20-35 glue_1.2.0 digest_0.6.15 [16] promises_1.0.1 colorspace_1.3-2 htmltools_0.3.6 httpuv_1.4.4.2 Matrix_1.2-14 [21] plyr_1.8.4 XML_3.98-1.11 pkgconfig_2.0.1 zlibbioc_1.24.0 purrr_0.2.5 [26] xtable_1.8-2 scales_0.5.0 later_0.7.3 BiocParallel_1.12.0 tibble_1.4.2 [31] withr_2.1.2 SummarizedExperiment_1.8.1 lazyeval_0.2.1 magrittr_1.5 crayon_1.3.4 [36] mime_0.5 memoise_1.1.0 BiocInstaller_1.28.0 tools_3.4.4 prettyunits_1.0.2 [41] hms_0.4.2 matrixStats_0.53.1 stringr_1.3.1 munsell_0.5.0 DelayedArray_0.4.1 [46] compiler_3.4.4 rlang_0.2.1 grid_3.4.4 RCurl_1.95-4.10 rstudioapi_0.7 [51] bitops_1.0-6 gtable_0.2.0 curl_3.2 DBI_1.0.0 R6_2.2.2 [56] GenomicAlignments_1.14.2 bit_1.1-14 bindr_0.1.1 stringi_1.2.3 Rcpp_0.12.17 [61] tidyselect_0.2.4
Not possible to upgrade to R 3.5 now, but I believe it will solve the problem as you suggested. Thanks