Dear all,
I'm currently struggling to fetch data from AnnotationHub:
> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2018-04-30
> query(ah, "coprinopsis cinerea")
AnnotationHub with 2 records
# snapshotDate(): 2018-04-30
# $dataprovider: Inparanoid8, ftp:...
# $species: Coprinopsis cinerea, C...
# $rdataclass: Inparanoid8Db, OrgDb
# additional mcols(): taxonomyid,
# genome, description,
# coordinate_1_based, maintainer,
# rdatadateadded, preparerclass,
# tags, rdatapath, sourceurl,
# sourcetype
# retrieve records with, e.g.,
# 'object[["AH10386"]]'
title
AH10386 | hom.Coprinopsis_cinere...
AH62557 | org.Coprinopsis_cinere...
> query(ah, "coprinopsis cinerea")
AnnotationHub with 2 records
# snapshotDate(): 2018-04-30
# $dataprovider: Inparanoid8, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Coprinopsis cinerea, Coprinopsis cinerea_okayama7#130
# $rdataclass: Inparanoid8Db, OrgDb
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer,
# rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH10386"]]'
title
AH10386 | hom.Coprinopsis_cinerea.inp8.sqlite
AH62557 | org.Coprinopsis_cinerea_okayama7#130.eg.sqlite
> ccin <- ah [['AH62557']]
downloading 1 resources
retrieving 1 resource
Downloading: 240 B
Error: failed to load resource
name: AH62557
title: org.Coprinopsis_cinerea_okayama7#130.eg.sqlite
reason: 1 resources failed to download
In addition: Warning message:
download failed
hub path: 'https://annotationhub.bioconductor.org/fetch/69303'
cache path: '/Users/kathy_chan//.AnnotationHub/69303'
reason: Forbidden (HTTP 403).
while I try AH10386, it was OK, and the hub path of AH62557 can't open in webbrowser. is there something wrong with the source file of AH62557?
My R:
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] AnnotationHub_2.12.1 BiocInstaller_1.30.0 XML_3.98-1.16 pathview_1.20.0
[5] org.Hs.eg.db_3.6.0 AnnotationDbi_1.42.1 IRanges_2.14.12 S4Vectors_0.18.3
[9] Biobase_2.40.0 BiocGenerics_0.26.0 KEGGREST_1.20.2 gage_2.30.0
[13] dplyr_0.7.6 clusterProfiler_3.8.1
loaded via a namespace (and not attached):
[1] enrichplot_1.0.2 bit64_0.9-7 httr_1.3.1
[4] UpSetR_1.3.3 Rgraphviz_2.24.0 tools_3.5.0
[7] R6_2.3.0 DBI_1.0.0 lazyeval_0.2.1
[10] colorspace_1.3-2 tidyselect_0.2.4 gridExtra_2.3
[13] bit_1.1-14 curl_3.2 compiler_3.5.0
[16] graph_1.58.1 labeling_0.3 KEGGgraph_1.40.0
[19] scales_1.0.0 ggridges_0.5.1 stringr_1.3.1
[22] digest_0.6.17 DOSE_3.6.1 XVector_0.20.0
[25] htmltools_0.3.6 pkgconfig_2.0.2 rlang_0.2.2.9000
[28] rstudioapi_0.8 RSQLite_2.1.1 shiny_1.1.0
[31] bindr_0.1.1 BiocParallel_1.14.2 GOSemSim_2.6.2
[34] magrittr_1.5 GO.db_3.6.0 Matrix_1.2-14
[37] Rcpp_0.12.19 munsell_0.5.0 viridis_0.5.1
[40] yaml_2.2.0 stringi_1.2.4 ggraph_1.0.2
[43] MASS_7.3-50 zlibbioc_1.26.0 plyr_1.8.4
[46] qvalue_2.12.0 grid_3.5.0 blob_1.1.1
[49] promises_1.0.1 ggrepel_0.8.0 DO.db_2.9
[52] crayon_1.3.4 lattice_0.20-35 Biostrings_2.48.0
[55] cowplot_0.9.3 splines_3.5.0 pillar_1.3.0
[58] fgsea_1.6.0 igraph_1.2.2 reshape2_1.4.3
[61] fastmatch_1.1-0 glue_1.3.0 data.table_1.11.8
[64] httpuv_1.4.5 png_0.1-7 tweenr_1.0.0
[67] gtable_0.2.0 purrr_0.2.5 tidyr_0.8.1
[70] assertthat_0.2.0 ggplot2_3.0.0 ggforce_0.1.3
[73] mime_0.6 xtable_1.8-3 later_0.7.5
[76] viridisLite_0.3.0 tibble_1.4.2 rvcheck_0.1.1
[79] memoise_1.1.0 units_0.6-1 bindrcpp_0.2.2
[82] interactiveDisplayBase_1.18.0
looking forward to your reply, thank you!!
Thank you and looking forward to your reply.