AnnotationHub, force update snapshot date?
Entering edit mode
Vang Le ▴ 80
Last seen 3.6 years ago

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/
LAPACK: /usr/lib/

[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           

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             
annotationhub • 1.4k views
Entering edit mode
shepherl 3.6k
Last seen 8 hours ago
United States

You will need to update your version of R to >= 3.5 and use the latest Bioconductor release 3.7 to see the most updated version of AnnotationHub. The snapshot date provided is the snapshot that is consistent with your version of R and the Bioconductor package version appropriate for that version/release (R 3.4.4 and Bioc release 3.6)

R 3.4 and Bioc release 3.6 uses snapshotDate(): 2017-10-27 
R 3.5 and Bioc release 3.7 uses snapshotDate(): 2018-04-30 
R 3.5 and Bioc devel 3.8 uses snapshotDate(): 2018-06-27
Entering edit mode

Not possible to upgrade to R 3.5 now, but I believe it will solve the problem as you suggested. Thanks


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