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

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