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

[Martin Morgan]

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/",
        dirlistonly=TRUE)

This seems to sometimes work and sometimes not

 > urls[1]
[1] "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


>
> 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()
>


-- 
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