[Debian-med-packaging] Bug#859864: r-bioc-genomeinfodb: Reorganization of ftp://ftp.ncbi.nlm.nih.gov/genomes/all

[Balint Reczey]

Control: tags -1 pending

On Sat, 8 Apr 2017 10:10:06 +0200 Graham Inggs <ginggs at debian.org> wrote:
> Source: r-bioc-genomeinfodb
> Version: 1.10.2-1
> Severity: grave
> Affects: r-bioc-annotationhub
> Tags: upstream fixed-upstream

Hi Andreas,

I see you made all the uploads to this package but if you don't mind
I'll fix this bug with the new upstream later today under the team's
umbrella since we are very close to the release - both in Debian and Ubuntu.

Cheers,
Balint

> 
> Hi Maintainer
> 
> Autopkgtests of r-bioc-annotationhub started failing on 2017-0126 [1]
> with the following error:
> 
> Error in checkIdentical(setNames(rep(c(FALSE, TRUE), c(4, 1)), chr),
> GenomeInfoDb::isCircular(gr1)) :
>   FALSE
> 
> In addition: Warning messages:
> 1: 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'
> 2: 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'
> require("xxx_foo")
> 
> Upon investigation, I found that NCBI recently reorganized the data on
> the Genomes FTP site [2].
> A new upstream version 1.10.3 is available [3], and it seems the only
> changes relate to this reorganization.  I have not yet verified that
> this fixes r-bioc-annotationhub's autopkgtests, or that it is the only
> affected package.
> 
> Regards
> Graham
> 
> 
> [1] https://ci.debian.net/packages/r/r-bioc-annotationhub/unstable/amd64/
> [2] https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/README_change_notice.txt
> [3] https://bioconductor.org/packages/release/bioc/html/GenomeInfoDb.html
> 
>