AnnotationHub, force update snapshot date?
1
0
Entering edit mode
Vang Le ▴ 80
@vang-le-6690
Last seen 3.9 years ago
Denmark

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             
annotationhub • 1.5k views
ADD COMMENT
1
Entering edit mode
shepherl 3.8k
@lshep
Last seen 14 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
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 618 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6