[Bioc-devel] GenomeInfoDb::Seqinfo() failing with 404 error

[Hervé Pagès]

Hi Raymond,

This should be fixed now in GenomeInfoDb 1.10.3 (release) and 1.11.8
(devel). Both packages should become available via biocLite() in the
next 24 hours or so.

Thanks again for reporting the issue and for your patience.

Cheers,
H.

On 02/01/2017 12:32 PM, Hervé Pagès wrote:
> Hi Raymond,
>
> On 02/01/2017 04:39 AM, Raymond Cavalcante wrote:
>> Hello,
>>
>> I was wondering if any progress has been made on fixing this? I looked
>> through recent commits for GenomeInfoDb, but there didn't seem to be
>> anything related to this problem.
>
> Not yet. Please expect a couple more days before this is resolved.
>
> Thanks for your patience,
> H.
>
>>
>> Thanks,
>> Raymond
>>
>>> On Jan 25, 2017, at 23:01, Obenchain, Valerie
>>> <Valerie.Obenchain at RoswellPark.org> wrote:
>>>
>>> Thanks for the report. It looks like the directory structure has
>>> changed. I'll work on this tomorrow and will post back when it's fixed.
>>>
>>> Valerie
>>>
>>>
>>>> On 01/25/2017 06:29 PM, Raymond Cavalcante wrote:
>>>> Hello,
>>>>
>>>> I'm suddenly encountering errors with GenomeInfoDb::Seqinfo():
>>>>
>>>>>> GenomeInfoDb::Seqinfo(genome='hg19')
>>>>> Error in file(file, "rt") : cannot open connection
>>>>> In addition: Warning message:
>>>>> In file(file, "rt") :
>>>>>  URL
>>>>> 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt':
>>>>> status was '404 Not Found'
>>>> I'm not sure how to fix this issue, as it seems to be more of an
>>>> NCBI problem. Any help would be greatly appreciated.
>>>>
>>>> Thanks,
>>>> Raymond Cavalcante
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>
>>>
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>

-- 
Hervé Pagès

Program in Computational Biology
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