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

[Steve Lane]

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