[Bioc-devel] AnnotationHubData Error: Access denied: 530

[Arora, Sonali]

Hi Rainer,

Just to be clear - what do you want to be available from AnnotationHub() 
in the end?

Currently the GTF files from Ensembl are already present inside the 
AnnotationHub

library(AnnotationHub)
ah = AnnotationHub()
gtf <- query(ah, "GTF")
gtf <- query(gtf, "Ensembl")
gtf[1]
gtf[[1]] # returned to you as  GenomicRanges object.

- why not get the GTF files directly from AnnotationHub instead of 
getting them from the ftp site? Then you can make your EnsDb classes 
from these GRanges.
It will also make your recipe faster because you will not have to 
download the file and parse the object.

Thanks,
Sonali.


On 4/9/2015 11:14 PM, Rainer Johannes wrote:
> dear all,
>
> I have added a recipe to the AnnotationHubData to provide EnsDb classes (from my ensembldb package) based on GTF files from Ensembl. Now, after adding the recipe to the AnnotationHubData package and installing it (following the vignettes from the AnnotationHub and AnnotationHubData) I called
>
> updateResources(AnnotationHubRoot=getWd(), BiocVersion=biocVersion(), preparerClasses="EnsemblGtfToEnsDbPreparer", insert=FALSE, metadataOnly=TRUE)
>
> and got the output:
>
> Ailuropoda_melanoleuca.ailMel1.78.gtf.gz
> Anas_platyrhynchos.BGI_duck_1.0.78.gtf.gz
> Anolis_carolinensis.AnoCar2.0.78.gtf.gz
> Astyanax_mexicanus.AstMex102.78.gtf.gz
> Bos_taurus.UMD3.1.78.gtf.gz
> Caenorhabditis_elegans.WBcel235.78.gtf.gz
> Callithrix_jacchus.C_jacchus3.2.1.78.gtf.gz
> Canis_familiaris.CanFam3.1.78.gtf.gz
> Cavia_porcellus.cavPor3.78.gtf.gz
> Chlorocebus_sabaeus.ChlSab1.1.78.gtf.gz
> Choloepus_hoffmanni.choHof1.78.gtf.gz
> Ciona_intestinalis.KH.78.gtf.gz
> Ciona_savignyi.CSAV2.0.78.gtf.gz
> Danio_rerio.Zv9.78.gtf.gz
> Dasypus_novemcinctus.Dasnov3.0.78.gtf.gz
> Dipodomys_ordii.dipOrd1.78.gtf.gz
> Drosophila_melanogaster.BDGP5.78.gtf.gz
> Error in function (type, msg, asError = TRUE)  : Access denied: 530
>
> I guess that must be related to the Ensembl ftp? Is anybody else experiencing this error?
>
> cheers, jo
>
>
> my session info:
>
>> sessionInfo()
> R Under development (unstable) (2015-03-04 r67940)
> Platform: x86_64-apple-darwin14.3.0/x86_64 (64-bit)
> Running under: OS X 10.10.3 (Yosemite)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
> [8] methods   base
>
> other attached packages:
> [1] AnnotationHubData_0.0.205 futile.logger_1.4
> [3] AnnotationHub_1.99.81     GenomicRanges_1.19.52
> [5] GenomeInfoDb_1.3.16       IRanges_2.1.43
> [7] S4Vectors_0.5.22          BiocGenerics_0.13.11
>
> loaded via a namespace (and not attached):
>   [1] Rcpp_0.11.5                  BiocInstaller_1.17.7
>   [3] XVector_0.7.4                futile.options_1.0.0
>   [5] GenomicFeatures_1.19.37      bitops_1.0-6
>   [7] tools_3.2.0                  zlibbioc_1.13.3
>   [9] biomaRt_2.23.5               digest_0.6.8
> [11] BSgenome_1.35.20             jsonlite_0.9.15
> [13] RSQLite_1.0.0                shiny_0.11.1
> [15] DBI_0.3.1                    rtracklayer_1.27.11
> [17] httr_0.6.1                   stringr_0.6.2
> [19] Biostrings_2.35.12           Biobase_2.27.3
> [21] R6_2.0.1                     AnnotationDbi_1.29.21
> [23] XML_3.98-1.1                 BiocParallel_1.1.24
> [25] RJSONIO_1.3-0                ensembldb_0.99.15
> [27] lambda.r_1.1.7               Rsamtools_1.19.50
> [29] htmltools_0.2.6              GenomicAlignments_1.3.34
> [31] AnnotationForge_1.9.7        mime_0.3
> [33] interactiveDisplayBase_1.5.6 xtable_1.7-4
> [35] httpuv_1.3.2                 RCurl_1.95-4.5
> [37] VariantAnnotation_1.13.47
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