Debian Bug report logs - #859864
r-bioc-genomeinfodb: Reorganization of ftp://ftp.ncbi.nlm.nih.gov/genomes/all

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Message #5 received at submit@bugs.debian.org (full text, mbox, reply):

From: Graham Inggs <ginggs@debian.org>

To: Debian Bug Tracking System <submit@bugs.debian.org>

Subject: r-bioc-genomeinfodb: Reorganization of ftp://ftp.ncbi.nlm.nih.gov/genomes/all

Date: Sat, 8 Apr 2017 10:10:06 +0200

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

Message #10 received at 859864@bugs.debian.org (full text, mbox, reply):

From: Balint Reczey <balint@balintreczey.hu>

To: 859864@bugs.debian.org

Subject: Re: r-bioc-genomeinfodb: Reorganization of ftp://ftp.ncbi.nlm.nih.gov/genomes/all

Date: Sun, 9 Apr 2017 15:24:18 +0200

Control: tags -1 pending

On Sat, 8 Apr 2017 10:10:06 +0200 Graham Inggs <ginggs@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
> 
> 

Message #17 received at 859864@bugs.debian.org (full text, mbox, reply):

From: Andreas Tille <andreas@fam-tille.de>

To: Balint Reczey <balint@balintreczey.hu>, 859864@bugs.debian.org

Subject: Re: Bug#859864: r-bioc-genomeinfodb: Reorganization of ftp://ftp.ncbi.nlm.nih.gov/genomes/all

Date: Sun, 9 Apr 2017 21:20:19 +0200

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).

Thanks for caring for this

      Andreas.

-- 
http://fam-tille.de

Message #22 received at 859864@bugs.debian.org (full text, mbox, reply):

From: Balint Reczey <balint.reczey@canonical.com>

To: 859864@bugs.debian.org, 859864-done@bugs.debian.org

Subject: Re: Bug#859864: r-bioc-genomeinfodb: Reorganization of ftp://ftp.ncbi.nlm.nih.gov/genomes/all

Date: Mon, 10 Apr 2017 10:41:33 +0200

Contrlol: fixed -1 1.10.3-1


On Sun, 9 Apr 2017 21:20:19 +0200 Andreas Tille <andreas@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

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