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540014429
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@540014429-14445
Last seen 7.4 years ago
Deal all,
I encouter error in retrieve data from AnnotationHub:
> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2017-10-27
> query(ah, "oryza sativa")
AnnotationHub with 2 records
# snapshotDate(): 2017-10-27
# $dataprovider: Inparanoid8, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Oryza sativa, Oryza sativa_(japonica_cultivar-group)
# $rdataclass: Inparanoid8Db, OrgDb
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded,
# preparerclass, tags, rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH10561"]]'
title
AH10561 | hom.Oryza_sativa.inp8.sqlite
AH58059 | org.Oryza_sativa_(japonica_cultivar-group).eg.sqlite
> rice_ref <- ah[['AH58059']]
downloading from ‘https://annotationhub.bioconductor.org/fetch/64805’
retrieving 1 resource
Downloading: 230 B
Error: failed to load resource
name: AH58059
title: org.Oryza_sativa_(japonica_cultivar-group).eg.sqlite
reason: 1 resources failed to download
In addition: Warning message:
download failed
hub path: ‘https://annotationhub.bioconductor.org/fetch/64805’
cache path: ‘C:/Users/TanYongjun/Documents/AppData/.AnnotationHub/64805’
reason: Forbidden (HTTP 403).
while I try AH10561, it was OK, and the hub path of AH58059 can't open in webbrowser. is there something wrong with the source file of AH58059?
My R:
> sessionInfo() R version 3.4.2 (2017-09-28) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936 [3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C [5] LC_TIME=Chinese (Simplified)_China.936 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.28.0 clusterProfiler_3.6.0 DOSE_3.4.0 GenomicFeatures_1.30.0 [5] AnnotationDbi_1.40.0 biomaRt_2.34.0 ChIPseeker_1.14.0 ggsci_2.8 [9] AnnotationHub_2.10.1 rjson_0.2.15 readr_1.1.1 DESeq2_1.18.1 [13] SummarizedExperiment_1.8.0 DelayedArray_0.4.1 matrixStats_0.52.2 Biobase_2.38.0 [17] GenomicRanges_1.30.0 GenomeInfoDb_1.14.0 IRanges_2.12.0 S4Vectors_0.16.0 [21] BiocGenerics_0.24.0 tximport_1.6.0 RevoUtils_10.0.4 RevoUtilsMath_10.0.0 loaded via a namespace (and not attached): [1] fgsea_1.4.0 colorspace_1.3-2 [3] qvalue_2.10.0 htmlTable_1.9 [5] XVector_0.18.0 base64enc_0.1-3 [7] bit64_0.9-7 interactiveDisplayBase_1.16.0 [9] splines_3.4.0 GOSemSim_2.4.0 [11] geneplotter_1.56.0 knitr_1.17 [13] Formula_1.2-2 Rsamtools_1.30.0 [15] gridBase_0.4-7 annotate_1.56.1 [17] cluster_2.0.6 GO.db_3.5.0 [19] shiny_1.0.5 compiler_3.4.0 [21] httr_1.3.1 rvcheck_0.0.9 [23] backports_1.1.1 assertthat_0.2.0 [25] Matrix_1.2-12 lazyeval_0.2.1 [27] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 acepack_1.4.1 [29] htmltools_0.3.6 prettyunits_1.0.2 [31] tools_3.4.0 bindrcpp_0.2 [33] igraph_1.1.2 glue_1.2.0 [35] gtable_0.2.0 GenomeInfoDbData_0.99.1 [37] reshape2_1.4.2 DO.db_2.9 [39] dplyr_0.7.4 fastmatch_1.1-0 [41] Rcpp_0.12.13 Biostrings_2.46.0 [43] gdata_2.18.0 rtracklayer_1.38.0 [45] stringr_1.2.0 mime_0.5 [47] gtools_3.5.0 XML_3.98-1.9 [49] zlibbioc_1.24.0 scales_0.5.0 [51] hms_0.3 RColorBrewer_1.1-2 [53] yaml_2.1.14 curl_3.0 [55] memoise_1.1.0 gridExtra_2.3 [57] ggplot2_2.2.1 UpSetR_1.3.3 [59] rpart_4.1-11 latticeExtra_0.6-28 [61] stringi_1.1.6 RSQLite_2.0 [63] genefilter_1.60.0 plotrix_3.6-6 [65] RMySQL_0.10.13 checkmate_1.8.5 [67] caTools_1.17.1 boot_1.3-20 [69] BiocParallel_1.12.0 rlang_0.1.4 [71] pkgconfig_2.0.1 bitops_1.0-6 [73] lattice_0.20-35 purrr_0.2.4 [75] bindr_0.1 GenomicAlignments_1.14.1 [77] htmlwidgets_0.9 bit_1.1-12 [79] plyr_1.8.4 magrittr_1.5 [81] R6_2.2.2 gplots_3.0.1 [83] Hmisc_4.0-3 DBI_0.7 [85] foreign_0.8-69 survival_2.41-3 [87] RCurl_1.95-4.8 nnet_7.3-12 [89] tibble_1.3.4 KernSmooth_2.23-15 [91] progress_1.1.2 locfit_1.5-9.1 [93] grid_3.4.0 data.table_1.10.4-3 [95] blob_1.1.0 digest_0.6.12 [97] xtable_1.8-2 tidyr_0.7.2 [99] httpuv_1.3.5 munsell_0.4.3
Thanks!
The files are being regenerated. They should be fixed by Friday. Sorry for the inconvenience. I will post again when they are updated.