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

[Martin Morgan]

On 04/10/2015 03:31 AM, Rainer Johannes wrote:
> dear Thomas,
>
> still get the same error. Don't know why.
>
>> updateResources(AnnotationHubRoot=getWd(), BiocVersion=biocVersion(), preparerClasses="EnsemblGtfToEnsDbPreparer", insert=FALSE, metadataOnly=TRUE)
> INFO [2015-04-10 12:29:45] Preparer Class: EnsemblGtfToEnsDbPreparer
> 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
> Error in function (type, msg, asError = TRUE)  : Access denied: 530

Are these from AnnotationHubData, which has only been used internally and has 
hard-coded URLs to machines that are not available outside FHCRC. And in general 
updateResources requires that there is actually an AnnotationHub server instance 
that you have write access to.

What does traceback() say?

Martin

>
> I'll try to run that from within another network...
>
>> On 10 Apr 2015, at 12:09, Thomas Maurel <maurel at ebi.ac.uk> wrote:
>>
>> Dear Johannes,
>>
>> I had a look at our FTP site and it is working fine at the moment. Also, all the permissions on the Ensembl GTF 78 files are set properly.
>> Maybe it was a glitch with our FTP site, could you please try again?
>>
>> Regards,
>> Thomas
>>> On 10 Apr 2015, at 07:14, Rainer Johannes <Johannes.Rainer at eurac.edu> 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
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> --
>> Thomas Maurel
>> Bioinformatician - Ensembl Production Team
>> European Bioinformatics Institute (EMBL-EBI)
>> European Molecular Biology Laboratory
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge CB10 1SD
>> United Kingdom
>>
>
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