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Hi,
I tried to download the OrgDB object sourced by fungidb through annotationhub. Somehow it failed. See the commands and error below
library("AnnotationHub") hub <- AnnotationHub() > hub AnnotationHub with 46259 records # snapshotDate(): 2019-05-02 # $dataprovider: BroadInstitute, Ensembl, UCSC, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/, Haemcode, FungiDB, Inparanoid8, TriTrypDB, PlasmoDB, AmoebaDB # $species: Homo sapiens, Mus musculus, Drosophila melanogaster, Bos taurus, Rattus norvegicus, Pan troglodytes, Danio rerio, Gallus gallus, Mono... # $rdataclass: GRanges, BigWigFile, TwoBitFile, OrgDb, Rle, ChainFile, EnsDb, Inparanoid8Db, TxDb, data.frame # additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["AH5012"]]' title AH5012 | Chromosome Band AH5013 | STS Markers AH5014 | FISH Clones AH5015 | Recomb Rate AH5016 | ENCODE Pilot ... ... AH73812 | org.Plasmodium_vivax.eg.sqlite AH73813 | org.Burkholderia_mallei_ATCC_23344.eg.sqlite AH73814 | org.Bacillus_cereus_(strain_ATCC_14579_|_DSM_31).eg.sqlite AH73815 | org.Bacillus_cereus_ATCC_14579.eg.sqlite AH73816 | org.Schizosaccharomyces_cryophilus_OY26.eg.sqlite hub_subset <- query(hub , c("fungidb" ,"OrgDb")) > hub_subset AnnotationHub with 277 records # snapshotDate(): 2019-05-02 # $dataprovider: FungiDB # $species: Naganishia albida, Albugo candida 2VRR, Albugo laibachii Nc14, Allomyces macrogynus ATCC 38327, Aphanomyces astaci, Aphanomyces invad... # $rdataclass: OrgDb # additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags, # rdatapath, sourceurl, sourcetype # retrieve records with, e.g., 'object[["AH71411"]]' title AH71411 | Transcript information for Albugo candida 2VRR AH71412 | Transcript information for Albugo laibachii Nc14 AH71413 | Transcript information for Allomyces macrogynus ATCC 38327 AH71414 | Transcript information for Aspergillus aculeatus ATCC 16872 AH71415 | Transcript information for Aspergillus brasiliensis CBS 101740 ... ... AH71937 | Transcript information for Phytophthora sojae P6497 AH71938 | Transcript information for Pythium vexans DAOM BR484 AH71939 | Transcript information for Saccharomyces cerevisiae S288c AH71940 | Transcript information for Scedosporium apiospermum IHEM 14462 AH71941 | Transcript information for Yarrowia lipolytica CLIB89 W29 > hub_subset[["AH71940"]] downloading 1 resources retrieving 1 resource Downloading: 240 B Error: failed to load resource name: AH71940 title: Transcript information for Scedosporium apiospermum IHEM 14462 reason: 1 resources failed to download In addition: Warning messages: 1: download failed web resource path: ‘https://annotationhub.bioconductor.org/fetch/78686’ local file path: ‘/Users/chirag/Library/Caches/AnnotationHub/25d6f57295d_78686’ reason: Forbidden (HTTP 403). 2: bfcadd() failed; resource removed rid: BFC16 fpath: ‘https://annotationhub.bioconductor.org/fetch/78686’ reason: download failed 3: download failed hub path: ‘https://annotationhub.bioconductor.org/fetch/78686’ cache resource: ‘AH71940 : 78686’ reason: bfcadd() failed; see warnings() > hub_subset[["AH71412"]] downloading 1 resources retrieving 1 resource Downloading: 240 B Error: failed to load resource name: AH71412 title: Transcript information for Albugo laibachii Nc14 reason: 1 resources failed to download In addition: Warning messages: 1: download failed web resource path: ‘https://annotationhub.bioconductor.org/fetch/78158’ local file path: ‘/Users/chirag/Library/Caches/AnnotationHub/25d435cd1c6_78158’ reason: Forbidden (HTTP 403). 2: bfcadd() failed; resource removed rid: BFC17 fpath: ‘https://annotationhub.bioconductor.org/fetch/78158’ reason: download failed 3: download failed hub path: ‘https://annotationhub.bioconductor.org/fetch/78158’ cache resource: ‘AH71412 : 78158’ reason: bfcadd() failed; see warnings()
However, GRanges objects provided by fungidb are working fine.
Help would be highly appreciated.
Thanks.
The text was updated successfully, but these errors were encountered:
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Hi,
I tried to download the OrgDB object sourced by fungidb through annotationhub. Somehow it failed. See the commands and error below
However, GRanges objects provided by fungidb are working fine.
Help would be highly appreciated.
Thanks.
The text was updated successfully, but these errors were encountered: