Your message dated Mon, 10 Apr 2017 10:41:33 +0200
with message-id <6729c16a-2cde-d582-ee22-5d54e615d...@ubuntu.com>
and subject line Re: Bug#859864: r-bioc-genomeinfodb: Reorganization of
ftp://ftp.ncbi.nlm.nih.gov/genomes/all
has caused the Debian Bug report #859864,
regarding r-bioc-genomeinfodb: Reorganization of
ftp://ftp.ncbi.nlm.nih.gov/genomes/all
to be marked as done.
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859864: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=859864
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--- Begin Message ---
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
--- End Message ---
--- Begin Message ---
Contrlol: fixed -1 1.10.3-1
On Sun, 9 Apr 2017 21:20:19 +0200 Andreas Tille <andr...@fam-tille.de>
wrote:
> Hi Balint,
>
> On Sun, Apr 09, 2017 at 03:24:18PM +0200, Balint Reczey wrote:
> > Control: tags -1 pending
> >
> > 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.
>
> I can confirm that I checked the issue and I think that the new upstream
> version is a sensible approach. Please note that r-cran-rcurl is needed
> as new Build-Depends.
>
> If you upload please commit your changes to SVN (writable for any DD).
Done, but made a typo in changelog and it did not close the bug. :-(
Cheers,
Balint
--- End Message ---
