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

Thomas Maurel maurel at ebi.ac.uk
Fri Apr 10 14:40:14 CEST 2015


Hi Martin,

> On 10 Apr 2015, at 13:23, Martin Morgan <mtmorgan at fredhutch.org> wrote:
> 
> On 04/10/2015 04:34 AM, Rainer Johannes wrote:
>> hi Martin,
>> 
>> but if that's true, then I will never have a way to test whether the recipe
>> actually works, right?
> 
> I guess I don't really know what I'm talking about, and that insert=FALSE is intended to not actually do the insertion so that the (immediate) problem is not with AnnotationHubData.
> 
> From the traceback below it seems like the error occurs in calls like the following
> 
> library(RCurl)
> getURL("ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/ <ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/>",
>       dirlistonly=TRUE)
> 
> This seems to sometimes work and sometimes not
> 
> > urls[1]
> [1] "ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/ <ftp://ftp.ensembl.org/pub/release-78/gtf/ailuropoda_melanoleuca/>"
> > getURL(urls[1], dirlistonly=TRUE)
> [1] "Ailuropoda_melanoleuca.ailMel1.78.gtf.gz\nCHECKSUMS\nREADME\n"
> > getURL(urls[1], dirlistonly=TRUE)
> [1] "Ailuropoda_melanoleuca.ailMel1.78.gtf.gz\nCHECKSUMS\nREADME\n"
> > getURL(urls[1], dirlistonly=TRUE)
> Error in function (type, msg, asError = TRUE)  : Access denied: 530
You are right, I’ve noticed the same thing.
I will investigate and see if there is something wrong with our FTP site machine.

Regards,
Thomas
> 
> 
>> 
>> that's the full traceback:
>> 
>> > updateResources(AnnotationHubRoot=getWd(), BiocVersion=biocVersion(),
>> preparerClasses="EnsemblGtfToEnsDbPreparer", insert=FALSE, metadataOnly=TRUE)
>> INFO [2015-04-10 13:32:18] 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
>> > traceback()
>> 17: fun(structure(list(message = msg, call = sys.call()), class = c(typeName,
>>         "GenericCurlError", "error", "condition")))
>> 16: function (type, msg, asError = TRUE)
>>     {
>>         if (!is.character(type)) {
>>             i = match(type, CURLcodeValues)
>>             typeName = if (is.na(i))
>>                 character()
>>             else names(CURLcodeValues)[i]
>>         }
>>         typeName = gsub("^CURLE_", "", typeName)
>>         fun = (if (asError)
>>             stop
>>         else warning)
>>         fun(structure(list(message = msg, call = sys.call()), class = c(typeName,
>>             "GenericCurlError", "error", "condition")))
>>     }(67L, "Access denied: 530", TRUE)
>> 15: .Call("R_curl_easy_perform", curl, .opts, isProtected, .encoding,
>>         PACKAGE = "RCurl")
>> 14: curlPerform(curl = curl, .opts = opts, .encoding = .encoding)
>> 13: getURL(url, dirlistonly = TRUE)
>> 12: strsplit(getURL(url, dirlistonly = TRUE), "\n")
>> 11: (function (url, filename, tag, verbose = TRUE)
>>     {
>>         df2 <- strsplit(getURL(url, dirlistonly = TRUE), "\n")[[1]]
>>         df2 <- df2[grep(paste0(filename, "$"), df2)]
>>         drop <- grepl("latest", df2) | grepl("00-", df2)
>>         df2 <- df2[!drop]
>>         df2 <- paste0(url, df2)
>>         result <- lapply(df2, function(x) {
>>             if (verbose)
>>                 message(basename(x))
>>             tryCatch({
>>                 h = suppressWarnings(GET(x, config = config(nobody = TRUE,
>>                     filetime = TRUE)))
>>                 nams <- names(headers(h))
>>                 if ("last-modified" %in% nams)
>>                     headers(h)[c("last-modified", "content-length")]
>>                 else c(`last-modified` = NA, `content-length` = NA)
>>             }, error = function(err) {
>>                 warning(basename(x), ": ", conditionMessage(err))
>>                 list(`last-modified` = character(), `content-length` = character())
>>             })
>>         })
>>         size <- as.numeric(sapply(result, "[[", "content-length"))
>>         date <- strptime(sapply(result, "[[", "last-modified"), "%a, %d %b %Y
>> %H:%M:%S",
>>             tz = "GMT")
>>         data.frame(fileurl = url, date, size, genome = tag, stringsAsFactors =
>> FALSE)
>>     })(dots[[1L]][[8L]], filename = dots[[2L]][[1L]], tag = dots[[3L]][[8L]])
>> 10: mapply(FUN = f, ..., SIMPLIFY = FALSE)
>> 9: Map(.ftpFileInfo, urls, filename = "gtf.gz", tag = basename(urls))
>> 8: do.call(rbind, Map(.ftpFileInfo, urls, filename = "gtf.gz", tag =
>> basename(urls)))
>> 7: .ensemblGtfSourceUrls(.ensemblBaseUrl, justRunUnitTest)
>> 6: makeAnnotationHubMetadataFunction(currentMetadata, justRunUnitTest =
>> justRunUnitTest,
>>        ...)
>> 5: .generalNewResources(importPreparer, currentMetadata,
>> makeAnnotationHubMetadataFunction,
>>        justRunUnitTest, ...)
>> 4: .local(importPreparer, currentMetadata, ...)
>> 3: newResources(preparerInstance, listOfExistingResources, justRunUnitTest =
>> justRunUnitTest)
>> 2: newResources(preparerInstance, listOfExistingResources, justRunUnitTest =
>> justRunUnitTest)
>> 1: updateResources(AnnotationHubRoot = getWd(), BiocVersion = biocVersion(),
>>        preparerClasses = "EnsemblGtfToEnsDbPreparer", insert = FALSE,
>>        metadataOnly = TRUE)
>> >
>> 
>> 
>>> On 10 Apr 2015, at 13:09, Martin Morgan <mtmorgan at fredhutch.org
>>> <mailto:mtmorgan at fredhutch.org <mailto:mtmorgan at fredhutch.org>>> wrote:
>>> 
>>> traceback()
>> 
> 
> 
> -- 
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> 
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793

--
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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