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

[Graham Inggs]

Source: r-bioc-genomeinfodb
Version: 1.10.2-1
Severity: grave
Affects: r-bioc-annotationhub
Tags: upstream fixed-upstream

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