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

[Rainer Johannes]

hi Martin,

but if that's true, then I will never have a way to test whether the recipe actually works, right?

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>> wrote:

traceback()


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