[Debian-med-packaging] Your Debian package(s) will not migrate to testing

Andreas Tille andreas at an3as.eu
Thu Sep 5 09:55:51 BST 2019 

Hi,

it does not seem to be clear that we REALLY need to do source only
uploads since the release cycle for Debian 11 has been started.  Please
re-read the according mail on debian-devel-announce!

To make sure everybody is doing it the same way (or how to find out how
to create a source changes file easily) I added this to the Debian Med
team policy.  Please read

   https://med-team.pages.debian.net/policy/#to-make-gbp-buildpackage-build-the-package-with-pdebuild

carefully and adjust your ~/.gbp.conf file accordingly with

   pbuilder-options=--source-only-changes

This will create two changes file - one for the binary and one
for the source only upload.  You should

   debsign *_source.changes

when doing uploads to unstable (when uploading to new just sign the
binary changes file and upload this).

I have some remarks below - if it is to longish seek for your
name for specific comments.  All people in To: / CC: please
really read this mail.


On Wed, Sep 04, 2019 at 10:01:15PM +0100, Julian Gilbey wrote:
> 
> Source package: cnvkit
> Version: 0.9.6-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by moeller
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: kma
> Version: 1.2.11-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by moeller
> Transition verdict: REJECTED_PERMANENTLY
>
> Source package: biobambam2
> Version: 2.0.137+dfsg-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by moeller
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: libmaus2
> Version: 2.0.663-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by moeller
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: python-bids-validator
> Version: 1.2.4-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by yoh, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: bcbio
> Version: 1.1.5-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by moeller, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: subread
> Version: 1.6.5+dfsg-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by moeller
> Transition verdict: REJECTED_PERMANENTLY

Uploaded while doing Python3 migration and new upstream version.
 
> Source package: igdiscover
> Version: 0.11-2
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by moeller, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY

Beaten by #933527 against snakemake.

@Steffen:  You did it again and uploaded not using a chroot environment.
This is not helpful at all specifically if this is now catched by the
source-only uploads.  Just don't do that pretty please.
 
> Source package: shapeit4
> Version: 0.0.0+git20181214+dfsg-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by bob.dybian at gmail.com
> Transition verdict: REJECTED_PERMANENTLY

@Dylan: I did some minor updates but autopkgtest fails with:

Initialization:
[E::hts_open_format] Failed to open file unphased.bcf

ERROR: Problem opening index file for [unphased.bcf]
+ shapeit4 --input unphased.bcf --map chr20.b37.gmap.gz --region 20 --reference reference.bcf --scaffold scaffold.bcf --use-PS 0.0001 --thread 4 --log phased.log --output phased.bcf

SHAPEIT
  * Author        : Olivier DELANEAU, University of Lausanne
  * Contact       : olivier.delaneau at gmail.com
  * Version       : 4.0.0
  * Run date      : 05/09/2019 - 10:22:44

Files:
  * Input VCF     : [unphased.bcf]
  * Reference VCF : [reference.bcf]
  * Scaffold VCF  : [scaffold.bcf]
  * Genetic Map   : [chr20.b37.gmap.gz]
  * Output VCF    : [phased.bcf]
  * Output LOG    : [phased.log]

Parameters:
  * Seed    : 15052011
  * Threads : 4 threads
  * MCMC    : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
  * PBWT    : Store indexes every 8 variants
  * PBWT    : Depth of PBWT neighbours to condition on: 4
  * HMM     : K is variable / min W is 2.00Mb / Ne is 15000
  * HMM     : Inform phasing using VCF/PS field / Error rate of PS field is 0.0001

Initialization:
[E::hts_open_format] Failed to open file unphased.bcf

ERROR: Problem opening index file for [unphased.bcf]


Can you please have a look?


> Source package: python-pybedtools
> Version: 0.8.0-2
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by moeller, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: ragout
> Version: 2.1.1+dfsg-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by tille
> Transition verdict: REJECTED_PERMANENTLY

Taking over my responsibility here.  Update to new version as well as Python3
port are needed.
 
> Source package: orthanc-dicomweb
> Version: 1.0+dfsg-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by s.jodogne at gmail.com
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: orthanc
> Version: 1.5.7+dfsg-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by s.jodogne at gmail.com
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: tm-align
> Version: 20190708+dfsg-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by moeller
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: bioperl
> Version: 1.7.5-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by moeller, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: adapterremoval
> Version: 2.3.1-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by moeller
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: changeo
> Version: 0.4.6-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by moeller, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: obitools
> Version: 1.2.13+dfsg-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by moeller
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: q2-types
> Version: 2019.4.1-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by tille, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY

Just updated to latest upstream and uploaded.
 
> Source package: roary
> Version: 3.12.0+dfsg-3
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by satta at tetrinetsucht.de, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: libbigwig
> Version: 0.4.2+dfsg-2
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch amd64 binaries uploaded by moeller
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: biomaj3
> Version: 3.1.8-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by olivier.sallou at irisa.fr, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: biomaj3-core
> Version: 3.0.16-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by olivier.sallou at irisa.fr, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: biomaj3-daemon
> Version: 3.0.19-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by olivier.sallou at irisa.fr, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: biomaj3-download
> Version: 3.0.21-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by olivier.sallou at irisa.fr, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: biomaj3-process
> Version: 3.0.13-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by olivier.sallou at irisa.fr, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: biomaj3-user
> Version: 3.0.8-1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by olivier.sallou at irisa.fr, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY


The following packages are in a really bad state anyway.  For
the moment at least I will ignore these:
 
> Source package: freemedforms-project
> Version: 0.9.4-2
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by tille, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: sofa-framework
> Version: 1.0~beta4-12
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by tille, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY
> 
> Source package: sitplus
> Version: 1.0.3-5.1
> One relevant line of the excuse file (including the uploader):
>   Not built on buildd: arch all binaries uploaded by iwamatsu, a new source-only upload is needed to allow migration
> Transition verdict: REJECTED_PERMANENTLY


Please remember: Do NOT do binary uploads except when uploading to new!

Kind regards

      Andreas.

-- 
http://fam-tille.de

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