[Debian-med-packaging] Bug#758987: qiime: Can't upgrade - pynast 1.2.2 does not exist

[Andreas Tille]

Hi Steve,

thanks for your bug report.  I was woncering myself why pynast 1.2.2 is
not yet available.  At first I thought I would have missed the final
upload and uploaded again - than I notices that the package is in new
queue since I renamed the source package to reflect the binary name
(source was python-pynast for no good reason and I renamed it to
pynast).

I guess it will be available soon and will close the bug than.

Kind regards

      Andreas.

PS: Thorsten, a similarly simple package is r-cran-qtl which is also
    only renamed (from qtl).

On Sat, Aug 23, 2014 at 07:35:06AM -0700, Steve Lane wrote:
> Package: qiime
> Version: 1.8.0+dfsg-2
> Severity: normal
> 
> Dear Maintainer Folks,
> 
> I am trying to upgrade qiime to 1.8.0+dfsg-4, but I get:
> 
> qiime : Depends: pynast (>= 1.2.2) but 1.2-1 is to be installed
> 
> and:
> 
> # apt-show-versions -a pynast
> pynast 1.2-1 install ok installed
> pynast 1.1-3 stable   ftp.debian.org
> pynast 1.2-1 testing  ftp.debian.org
> pynast 1.2-1 unstable ftp.debian.org
> pynast/testing uptodate 1.2-1
> 
> (which is also what packages.debian.org reports)
> 
> I also see the following on packages.debian.org:
> 
> testing migration
> excuses:
> 9 days old (needed 5 days)
> qiime/i386 unsatisfiable Depends: pynast (>= 1.2.2)
> qiime/amd64 unsatisfiable Depends: pynast (>= 1.2.2)
> qiime/armel unsatisfiable Depends: pynast (>= 1.2.2)
> qiime/armhf unsatisfiable Depends: pynast (>= 1.2.2)
> qiime/kfreebsd-amd64 unsatisfiable Depends: pynast (>= 1.2.2)
> qiime/kfreebsd-i386 unsatisfiable Depends: pynast (>= 1.2.2)
> qiime/mips unsatisfiable Depends: pynast (>= 1.2.2)
> qiime/mipsel unsatisfiable Depends: pynast (>= 1.2.2)
> qiime/powerpc unsatisfiable Depends: pynast (>= 1.2.2)
> qiime/s390x unsatisfiable Depends: pynast (>= 1.2.2)
> Valid candidate
> 
> so perhaps you already know about this.
> 
> Thanks much/best,
> 
> --
> Steve Lane
> System Administrator, Scientific Computing
> Joint BioEnergy Institute
> Lawrence Berkeley National Laboratory
> 
> 
> -- System Information:
> Debian Release: 7.6
>   APT prefers stable
>   APT policy: (990, 'stable'), (900, 'testing'), (800, 'unstable')
> Architecture: amd64 (x86_64)
> 
> Kernel: Linux 3.2.0-4-amd64 (SMP w/64 CPU cores)
> Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
> Shell: /bin/sh linked to /bin/dash
> 
> Versions of packages qiime depends on:
> ii  king                2.21.120420-2
> ii  libc6               2.19-9
> ii  libffi6             3.1-2
> ii  libgmp10            2:6.0.0+dfsg-6
> ii  pynast              1.2-1
> ii  python              2.7.8-1
> ii  python-biom-format  2.1+dfsg-1
> ii  python-cogent       1.5.3-2
> ii  python-qcli         0.1.0-1
> 
> Versions of packages qiime recommends:
> pn  ampliconnoise      <none>
> ii  blast2             1:2.2.26.20120620-2
> pn  cd-hit             <none>
> pn  chimeraslayer      <none>
> pn  fasttree           <none>
> pn  infernal           <none>
> ii  libjs-jquery       1.7.2+dfsg-1
> ii  muscle             1:3.8.31-1
> ii  python-matplotlib  1.3.1-2
> pn  python-mpi4py      <none>
> ii  python-numpy       1:1.8.2-1
> 
> Versions of packages qiime suggests:
> pn  cytoscape       <none>
> pn  rdp-classifier  <none>
> pn  t-coffee        <none>
> pn  torque-client   <none>
> 
> -- no debconf information
> 
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-- 
http://fam-tille.de