[Bioc-devel] error in stable AnnotationHub

[Obenchain, Valerie]

Hi Kasper,

This has been fixed. With the most current AnnotationHub (2.3.3 devel,
2.2.2 release) you should see a snapshot date of 2015-11-05.

> hub = AnnotationHub()
snapshotDate(): 2015-11-05
> hub[["AH28868"]]
require(“rtracklayer”)
loading from cache ‘/home/vobencha/.AnnotationHub/34308’
GRanges object with 412042 ranges and 2 metadata columns:
           seqnames               ranges strand   |        name     score
              <Rle>            <IRanges>  <Rle>   | <character> <numeric>
       [1]     chr1     [ 10148,  10277]      *   |        <NA>   15.1272
       [2]     chr1     [237721, 237783]      *   |        <NA>   12.5966
       [3]     chr1     [565271, 566061]      *   |        <NA>   11.8649
       [4]     chr1     [566736, 567271]      *   |        <NA>   16.7255
       [5]     chr1     [567455, 567889]      *   |        <NA>  427.2700
       ...      ...                  ...    ... ...         ...       ...
  [412038]     chrY [59022678, 59023002]      *   |        <NA>   4.15456
  [412039]     chrY [59023921, 59024217]      *   |        <NA>   2.02074
  [412040]     chrY [59025740, 59026020]      *   |        <NA>   4.93567
  [412041]     chrY [59027576, 59027857]      *   |        <NA>   3.10672
  [412042]     chrY [59030444, 59030771]      *   |        <NA>   3.11396
  -------
  seqinfo: 93 sequences (1 circular) from hg19 genome


FYI, some records in AH have been legitimately 'retired' (replaced with
new, had invalid tax ids, etc.). When you try to access those you'll see
something like,

> hub[["AH13960"]]
Error in .AnnotationHub_get1(x[idx]) : 'i' must be length 1

It's in the works to throw a more useful warning for these records and
suggest a replacement file if any.

Thanks.
Valerie


On 10/11/2015 03:30 AM, Morgan, Martin wrote:
>
>> -----Original Message-----
>> From: Bioc-devel [mailto:bioc-devel-bounces at r-project.org] On Behalf Of
>> Kasper Daniel Hansen
>> Sent: Saturday, October 10, 2015 11:04 PM
>> To: bioc-devel at r-project.org
>> Subject: [Bioc-devel] error in stable AnnotationHub
>>
>> Using Bioconductor 3.1 and the following code
>>
>> library(AnnotationHub)
>> ah <- AnnotationHub()
>> ah[["AH28868"]]
>>
>> I get an error like
> It seems like the record is expecting additional columns in the bed file, but it contains only ranges and score; spot checking on the hotspot.broad.bed files suggests that they all have this format. Will address, but in the mean time a workaround is
>
>   rtracklayer::import(cache(ah["AH28868"]), format="bed", genome="hg19")
>
> Martin
>
>> retrieving 1 resources
>>
>> |=========================================================
>> =============|
>> 100%
>> Error in value[[3L]](cond) :
>>   failed to load hub resource ‘E003-DNase.hotspot.broad.bed.gz’ of class
>>     EpigenomeRoadmapFile; reason: length of 'chrom' greater than length
>>     of 'ranges'
>> In addition: There were 50 or more warnings (use warnings() to see the first
>> 50)
>>
>> Best,
>> Kasper
>>
>> 	[[alternative HTML version deleted]]
>>
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