Processed: sourmash blocked by setuptools-scm-git-archive

[Debian Bug Tracking System]

Processing commands for cont...@bugs.debian.org:

> block 919681 by 910742
Bug #919681 [wnpp] ITP: sourmash -- tools for comparing DNA sequences with 
MinHash sketches
919681 was not blocked by any bugs.
919681 was not blocking any bugs.
Added blocking bug(s) of 919681: 910742
> thanks
Stopping processing here.

Please contact me if you need assistance.
-- 
919681: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919681
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems

Done! Re: fix for biojava4-live pending testing removal, requesting upload permissions

[Steffen Möller]

Done!

On 18.01.19 18:18, Michael Crusoe wrote:
dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow 
biojava4-live

Done! Re: another request for sponsorship: librcsb-core-wrapper

[Steffen Möller]

Done!

On 18.01.19 21:17, Michael Crusoe wrote:

This package is 436 days old (!)

https://salsa.debian.org/med-team/librcsb-core-wrapper/commit/004daf33a7d49c1abf4167ca69d51a0cca1a8313

Highlights from the changelog:

  * Adapt patches for latest boost version

dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow 
librcsb-core-wrapper


And I'm still waiting on hinge:

dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow hinge

https://salsa.debian.org/med-team/hinge/commit/5eb4a18ed46cf21a18cedb4a20d585ed3dcc8ecb

Thanks!

--
Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project 


Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
https://orcid.org/-0002-2961-9670 


m...@commonwl.org 

another request for sponsorship: librcsb-core-wrapper

[Michael Crusoe]

This package is 436 days old (!)

https://salsa.debian.org/med-team/librcsb-core-wrapper/commit/004daf33a7d49c1abf4167ca69d51a0cca1a8313

Highlights from the changelog:

  * Adapt patches for latest boost version

dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow
librcsb-core-wrapper

And I'm still waiting on hinge:

dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow hinge

https://salsa.debian.org/med-team/hinge/commit/5eb4a18ed46cf21a18cedb4a20d585ed3dcc8ecb

Thanks!

-- 
Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project

Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
https://orcid.org/-0002-2961-9670

m...@commonwl.org

Fwd: hinge_0.5.0-4_source.changes REJECTED

[Michael Crusoe]

Another request for upload permissions:

dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow hinge

* Added libspdlog-dev 1:1.3.0 compatibility, Closes: #909763

This package has been out of "testing" since October and the new version
has been waiting almost a year to clear the queue!

-- Forwarded message -
From: Debian FTP Masters 
Date: vin., 18 ian. 2019 la 21:22
Subject: hinge_0.5.0-4_source.changes REJECTED
To: Michael R. Crusoe , Debian Med Packaging Team





ACL dm: not allowed to upload source package 'hinge'



===

Please feel free to respond to this email if you don't understand why
your files were rejected, or if you upload new files which address our
concerns.



-- 
Michael R. Crusoe
Co-founder & Lead, Common Workflow Language project

Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania
https://orcid.org/-0002-2961-9670

m...@commonwl.org
+1 480 627 9108 / +370 653 11125

Re: fix for biojava4-live pending testing removal, requesting upload permissions

[Andreas Tille]

On Fri, Jan 18, 2019 at 07:18:24PM +0200, Michael Crusoe wrote:
> Looks like icedtea-netx isn't migrating to testing anytime soon, so to
> avoid the pending removal of biojava4-live from "testing" I switched to
> another netx implementation and did more package cleanup work:
> https://salsa.debian.org/med-team/biojava4-live/commits/master

Cool!  Thanks a lot.  That's really welcome.  I admit I'm a bit panicking
about the upcoming release and the number of packages not yet migrated to
testing.

I also wonder whether somebody could have a look at t-coffee (#917719).
 
> dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow biojava4-live

Done, Andreas.


-- 
http://fam-tille.de

fix for biojava4-live pending testing removal, requesting upload permissions

[Michael Crusoe]

Looks like icedtea-netx isn't migrating to testing anytime soon, so to
avoid the pending removal of biojava4-live from "testing" I switched to
another netx implementation and did more package cleanup work:
https://salsa.debian.org/med-team/biojava4-live/commits/master

dcut dm --uid 724D609337113C710550D7473C26763F6C67E6E2 --allow biojava4-live

Thanks!

-- 
Michael R. Crusoe

Bug#919681: ITP: sourmash -- tools for comparing DNA sequences with MinHash sketches

[Michael R. Crusoe]

Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: sourmash
  Version : 2.0.0~a11
  Upstream Author : C. Titus Brown , Luiz C. Irber, Jr 

* URL : http://sourmash.readthedocs.io/en/latest/
* License : BSD-3-Clause
  Programming Lang: Python, C++
  Description : tools for comparing DNA sequences with MinHash sketches

 Compute MinHash signatures for nucleotide (DNA/RNA) and protein sequences.
 .
 MinHash sketches provide a lightweight way to store “signatures” of large DNA
 or RNA sequence collections, and then compare or search them using a Jaccard
 index. MinHash sketches can be used to identify samples, find similar samples,
 identify data sets with shared sequences, and build phylogenetic trees
 (Ondov et al. 2015).
 .
 sourmash provides a command line script, a Python library, and a CPython
 module for MinHash sketches

Sourmash is team maintained by Debian-Med at 
https://salsa.debian.org/med-team/sourmash

Bug#919570: marked as done (ITP: python-mypy-extensions -- Experimental type system extensions for mypy typechecker (Python 3))

[Debian Bug Tracking System]

Your message dated Fri, 18 Jan 2019 13:00:11 +
with message-id 
and subject line Bug#919570: fixed in python-mypy-extensions 0.4.1-1
has caused the Debian Bug report #919570,
regarding ITP: python-mypy-extensions -- Experimental type system extensions 
for mypy typechecker (Python 3)
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
919570: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=919570
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: wnpp
Severity: wishlist
Owner: Debian Med team 

* Package name: python-mypy-extensions
  Version : 0.4.1
  Upstream Author : Jukka Lehtosalo and contributors
* URL : https://github.com/python/mypy_extensions/
* License : Expat
  Programming Lang: Python
  Description : Experimental type system extensions for mypy typechecker 
(Python 3)

(Include the long description here.
 Add type annotations to your Python programs, and use mypy to type check them.
 Mypy is essentially a Python linter on steroids, and it can catch many
 programming errors by analyzing your program, without actually having to run
 it. Mypy has a powerful type system with features such as type inference,
 gradual typing, generics and union types.
 .
 The "mypy_extensions" module defines experimental extensions to the
 standard "typing" module that are supported by the mypy typechecker.
 .
 This package provides the modules for Python 3.

This python module was previously part of the python3-mypy binary package from
the mypy source package as it came from the same PyPI source distribution. Now
it has been split into its own sdist/GitHub repo as of mypy v 0.660, so this
separate package is needed.

As with mypy, python-mypy-extensions will be team maintained by Debian Med.
--- End Message ---
--- Begin Message ---
Source: python-mypy-extensions
Source-Version: 0.4.1-1

We believe that the bug you reported is fixed in the latest version of
python-mypy-extensions, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 919...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Michael R. Crusoe  (supplier of updated 
python-mypy-extensions package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 17 Jan 2019 01:17:57 -0800
Source: python-mypy-extensions
Binary: python3-mypy-extensions
Architecture: source all
Version: 0.4.1-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 

Changed-By: Michael R. Crusoe 
Description:
 python3-mypy-extensions - Experimental type system extensions for mypy 
typechecker (Python
Closes: 919570
Changes:
 python-mypy-extensions (0.4.1-1) unstable; urgency=medium
 .
   * Initial release as standalone package. (Closes: #919570).
Checksums-Sha1:
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python-mypy-extensions_0.4.1-1.dsc
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python-mypy-extensions_0.4.1.orig.tar.gz
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python3-mypy-extensions_0.4.1-1_all.deb
Files:
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python-mypy-extensions_0.4.1-1.dsc
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python-mypy-extensions_0.4.1.orig.tar.gz
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python-mypy-extensions_0.4.1-1.debian.tar.xz
 3e81eb40a228d4e5d24bc87b230f2009 6298 utils optional 

Re: Should lambda-align v2 replace v1 or be its own Debian package?

[Sascha Steinbiss]

Hi Michael,

[...[
> Other than the lack of full test suite that we had with v1.0.x [1], I
> think this is ready for sponsorship for the NEW queue.

Hmm, but the rest of the tests (the ones currently run in your package
on salsa) are supposed to succeed? They fail for me:

[...]
   debian/rules override_dh_auto_test
make[1]: Entering directory '/build/lambda-align2-2.0.0'
for md5 in debian/*.md5sums; do gzip --keep ${md5}; done
cp --backup debian/*md5sums.gz tests/
cd build/tests && ctest . -j8 -I 1,10
Test project /build/lambda-align2-2.0.0/build/tests
  Start  1: test_mkindex_blastn_sa
  Start  2: test_mkindex_blastn_fm
  Start  3: test_mkindex_blastp_sa
  Start  4: test_mkindex_blastp_fm
  Start  5: test_mkindex_blastx_sa
  Start  6: test_mkindex_blastx_fm
  Start  7: test_mkindex_tblastn_sa
  Start  8: test_mkindex_tblastn_fm
 1/10 Test  #4: test_mkindex_blastp_fm ...***Failed0.48 sec
  Start  9: test_mkindex_tblastx_sa
 2/10 Test  #3: test_mkindex_blastp_sa ...***Failed0.49 sec
  Start 10: test_mkindex_tblastx_fm
 3/10 Test  #6: test_mkindex_blastx_fm ...***Failed0.65 sec
 4/10 Test  #5: test_mkindex_blastx_sa ...***Failed0.72 sec
 5/10 Test  #1: test_mkindex_blastn_sa ...***Failed1.23 sec
 6/10 Test  #2: test_mkindex_blastn_fm ...***Failed1.25 sec
 7/10 Test  #8: test_mkindex_tblastn_fm ..***Failed1.26 sec
 8/10 Test  #7: test_mkindex_tblastn_sa ..***Failed1.29 sec
 9/10 Test  #9: test_mkindex_tblastx_sa ..***Failed0.83 sec
10/10 Test #10: test_mkindex_tblastx_fm ..***Failed0.82 sec

0% tests passed, 10 tests failed out of 10

Total Test time (real) =   1.31 sec

The following tests FAILED:
  1 - test_mkindex_blastn_sa (Failed)
  2 - test_mkindex_blastn_fm (Failed)
  3 - test_mkindex_blastp_sa (Failed)
  4 - test_mkindex_blastp_fm (Failed)
  5 - test_mkindex_blastx_sa (Failed)
  6 - test_mkindex_blastx_fm (Failed)
  7 - test_mkindex_tblastn_sa (Failed)
  8 - test_mkindex_tblastn_fm (Failed)
  9 - test_mkindex_tblastx_sa (Failed)
 10 - test_mkindex_tblastx_fm (Failed)
Errors while running CTest
[...]

Any ideas?

Cheers
Sascha