Re: Questionable Package Present in Debian: fortune-mod

[Filippo Rusconi]

On Mon, Sep 25, 2023 at 08:32:29AM +0200, Sven Bartscher wrote:

Hi

Am 24.09.23 um 18:41 schrieb Salvo Tomaselli:

Without an ftpteam hat on, but my point of view -- I believe the team
would absolutely reject a package only based on its name (see:
#914179).


Not very consistently though:

$ apt search penis | grep penis | wc -l
2


Can you please clarify what problem you see with these package names? 
The results I get for this search are:


apt search penis | grep --color penis


Isn't penis the thing males hold in their hand when they urinate? Are we going
to exclude any term relating to fundamental biological functions in Debian? I
cannot believe I see this happening here.

As a (maybe already too old, for nowadays standards) biologist, I find this
upsetting that were are looking for this kind of silly things instead of doing
computer-related work.

Cheers,
Filippo

A Debian developer who is not sexist, rather, more inclined to altruism and
inclusiveness than not... but... not looking for things that do not deserve our
attention...

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Researcher at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
  http://www.debian.org

Re: Package name discord ITP: discord a modern voice & text chat app

[Filippo Rusconi]

Greetings,


On Sat, Jul 01, 2023 at 03:57:59AM +, matt quintanilla wrote:

Package name : discord
Severity: ITP
Package name: discord
Version: 0.0.27
Upstream Author: https://discord.com
URL: https://discord.com
License: custom
Description: All-in-one voice and text chat for gamers
Copyright: https://discord.com/terms#7 depends=('libnotify' 'libxss' 'nspr'
'nss' 'gtk3') optdepends=('libpulse: Pulseaudio support' 'ibappindicator:
Systray indicator support' 'xdg-utils: Open files') source=("
https://dl.discordapp.net/apps/linux/$pkgver/$pkgname-$pkgver.deb;
"LICENSE-$pkgver.html::https://discordapp.com/terms;
"OSS-LICENSES-$pkgver.html::https://discordapp.com/licenses;)
sha512sums=('285a0119b4740402a3fa94d3679a52bc8d883413ee32187e90087960a4d34aaf316788d2708bbccafe3f995c2b99767b45bc4b7c731704ef887a8de1b3d3926f'
'1f6e773b9c971aebd5391c22c5e2deea7aa222e0fda240aefbe91c4eb526305972d17302d1f5eb806a9d308c7f029ae8a0549f61d8c2adb53e4fe4ba9cd60a61'
'2adc1404b49930a419eb6c5fbb0c64ebd0a5d797e54357539a093cc99355b10e9c002750dd6d8ab84156593b7cbc8884c1b7e396ac0c2c2b59fcbda2368ebd1a
Please let me know if you need any more info
Matt Quintanilla
he/him
https://www.mattquintanilla.xyz/


I've never heard that Discord was Free Software. In fact, I heard that in my
university it has been flagged as non-Free Software and thus is not used.

The Licenses that you point at https://discordapp.com/licenses seem to be the
licenses of the software used by the software you intend to package.

I went to this place:

https://discord.com/terms#6

and I had a feeling that indeed, discord is not Free Software.

However, it might be that the specific software that you intend to package is
indeed Free Software, but we would like to see the explicit licence of that
software.

Would you post here the "custom" license that you describe in the stanza above,
please?

Sincerely,

Filippo Rusconi

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Researcher at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
  http://www.debian.org

Re: dh_auto_test fails and I do not understand why

[Filippo Rusconi]

Greetings, Niels,

On Thu, Dec 15, 2022 at 10:59:10AM +0100, Niels Thykier wrote:

Andrius Merkys:

Hello,

On 2022-12-15 11:20, Filippo Rusconi wrote:
I have uploaded a package yesterday. That package does not have 
any dh_auto_test

target in d/rules.

The builds all fail, as described here:
https://buildd.debian.org/status/package.php?p=minexpert2
and I do not understand why.
Any soul to help me with this question?


I have just stumbled on the same while building a new package with 
javahelper:


install: cannot change owner and permissions of 
‘debian/_jh_build.lucene9-9.4.2’: Operation not permitted
jh_build: error: install -m0755 -o 0 -g 0 -d 
debian/_jh_build.lucene9-9.4.2 returned exit code 1


However, I have no idea why '-o 0 -g 0' options are used. They do 
not seem to be used before.


Andrius



Long story short:

* Bug in fakeroot (#1023286 + #1024544)
* Me thinking it was a bug in debhelper so I tried to fix it
  (which did not work and broke on the way in)
* Me realizing it was a bug in fakeroot and my change did not
  even function as a work around, so I undid it (it broke on
  the way out as well).

And the winners are: All the people that have (and are) able to use 
"Rules-Requires-Root: no" as packages with that flag would have been

completely unaffected by this entire ordeal!

Your options include:

* Migrate to "Rules-Requires-Root: no" if you can
* Ensure you have debhelper (>= 13.11.3~) ("just uploaded") or
  debhelper/13.11.1 (or debhelper << 13.11)

I will now go back to looking more at my prototype for getting even 
more packages buildable with "Rules-Requires-Root: no".


Thank you so much for the explanation. I'll go the Rules-Requires-Root: no
route!

Sincerely,
Filippo

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
  http://www.debian.org



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Description: PGP signature

dh_auto_test fails and I do not understand why

[Filippo Rusconi]

Greetings, fellow Debianites,

I have uploaded a package yesterday. That package does not have any dh_auto_test
target in d/rules.

The builds all fail, as described here:
https://buildd.debian.org/status/package.php?p=minexpert2
and I do not understand why. 


Any soul to help me with this question?

Sincerely,
Filippo

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
  http://www.debian.org

Re: looking for debian friendly web app technology

[Filippo Rusconi]

Greetings,

On Tue, Dec 13, 2022 at 09:27:34PM +0100, Andreas Josef Heil wrote:

Well qt5 is fine too. I don't need fancy features. I will make a kde app.

On 13.12.22 05:22, Imre Nagy wrote:
The downside of these things, that current Debian does not seem to 
include Qt6 at all and I have no idea when it can go into the 
mainstream Debian, while there are a lot of project could be waiting 
for it. (Even my one is still pending for Debian). Qt6 for Debian is 
still in unstable/experimental state, which drives the developers 
like me to find other alternatives instead of Debian or for Debian.


Qt6 is very well usable in testing. I recently ported my (heavily graphical)
programs to Qt6 from Qt5 and that was pretty straightforward. I thinks there are
reasonable backports to stable, also. That might need some checking, though.

Sincerely,
Filippo

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
  http://www.debian.org



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Description: PGP signature

Re: NEW queue almost empty

[Filippo Rusconi]

On Mon, Nov 02, 2020 at 01:37:16PM +0100, Christian Kastner wrote:

The NEW queue length is down a single digit, from ~500 not all too long
ago. That's an amazing effort by ftp-master that must have consumed a
*lot* of energy.

THANK YOU!

https://ftp-master.debian.org/new.html


Awesome work !

I have two packages that have been rejected. I must say that the explanations
were always detailed and very courteously formulated.

Cheers,

Filippo

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
  http://www.debian.org

Re: Pybliographer

[Filippo Rusconi]

Greetings,

[ Sorry, I lost the message of the original poster ]

On Tue, Sep 01, 2020 at 09:19:14PM -0300, Henrique de Moraes Holschuh wrote:


On Sat, Aug 29, 2020, at 13:11, Ted To wrote:

Is there any chance of reviving pybliographer?  I understand that it was 
removed because it relied on old, unsupported Gnome libraries.  But the current 
version (1.4.0) has removed python-gnome2, python-gnome2-vfs, and python-glade2 
dependencies and instead uses pygtk and gettext 
(https://pybliographer.org/cgi-bin/moin.cgi/News/2018-04-03).  While there are 
alternatives like jabref and kbibtex, I prefer not to install the java and KDE 
dependencies.



I recommend you file a RFP bug as described here :
https://wiki.debian.org/RFP

And include the explanation above.


And also try cb2bib, which is in Debian. This is a robust solution to BibTeX
databases that I use since years with joy.

Sincerely,

Filippo

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
  http://www.debian.org

Bug#961805: ITP: libcustompwiz -- Library to load mzML/mzXML files (dev files)

[Filippo Rusconi]

Package: wnpp
Severity: wishlist
Owner: Filippo Rusconi 
 .
* Package name: libcustompwiz
  Version : 3.0.0
  Upstream Author : Filipo Rusconi and Proteowizard authors
* URL : https://salsa.debian.org/debichem-team/custompwiz
* License : GPL-3+
  Programming Lang: C++
  Description : Library to load mzML/mzXML files (dev files)
 .
 Description: Library to load mzML/mzXML files (dev files)
 .
 This library is a dumbed-down version of the Proteowizard library.
 This library only contains the required features to 
 load standard mzML/mzXML mass spectrometry data files.

 The original project, that I used to package has abandoned the autotools build
 system and the bjam-based build system is not acceptable by me for its
 unbearable complexity. 
 .
 The only features that are most often used by most projects  from the original
 library are the mass spectrometry data file loading features (files in the
 mzML/mzXML standard format). A number of projects have included this subset
 directly in their source tree. I want to be able to prune that code from these
 projects' source tree and link to this library when I package the projects for
 Debian (for example, the toppic project that I uploaded recently to NEW).
 .
 See http://proteowizard.sourceforge.net/ for the original project.

Ciao
Filippo

-- 

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
  http://www.debian.org

Bug#961085: ITP: toppic -- Top-down proteoform identification and characterization

[Filippo Rusconi]

Source: toppic
Section: science
Priority: optional
Maintainer: The Debichem Group 
Uploaders: Filippo Rusconi 
Build-Depends: debhelper-compat (= 12),
   dpkg-dev (>= 1.18.25),
   cmake (>= 3.12)
Standards-Version: 4.5.0
Homepage: http://proteomics.informatics.iupui.edu/software/toppic/index.html
Vcs-Browser: https://salsa.debian.org/debian/toppic
Vcs-Git: https://salsa.debian.org/debian/toppic.git

Package: wnpp
Severity: wishlist
Owner: Filippo Rusconi 


I intend to package the toppic software that is necessary to perform mass
spectrometry-based protein identifications. 

This software will become essential in my own laboratory research, along with
other software packages that I created and that I already maintain with the
debichem team.

I will maintain the package within the debichem team.

Package: toppic
Architecture: any
Depends: ${shlibs:Depends}, 
 ${misc:Depends}
Description: Top-down proteoform identification and characterization
 The TopPIC Suite consists of four software tools for the interpretation
 of top-down mass spectrometry data: TopFD, TopPIC, TopMG, and TopDiff.
 .
 - TopFD (Top-down mass spectral Feature Detection) is a software tool for
   top-down spectral deconvolution and a successor to MS-Deconv.  It groups
   top-down spectral peaks into isotopomer envelopes and converts isotopomer
   envelopes to monoisotopic neutral masses. In addition, it extracts proteoform
   features from LC-MS or CE-MS data.
.
 - TopPIC (Top-down mass spectrometry based Proteoform Identification and
   Characterization) identifies and characterizes proteoforms at the proteome
   level by searching top-down tandem mass spectra against a protein sequence
   database. TopPIC is a successor to MS-Align+. It efficiently identifies
   proteoforms with unexpected alterations, such as mutations and
   post-translational modifications (PTMs), accurately estimates the statistical
   significance of identifications, and characterizes reported proteoforms with
   unknown mass shifts. It uses several techniques, such as indexes, spectral
   alignment, generation function methods, and the modification identification
   score (MIScore), to increase the speed, sensitivity, and accuracy.
 .
 - TopMG (Top-down mass spectrometry based proteoform identification using Mass
   Graphs) is a software tool for identifying ultra-modified proteoforms by
   searching top-down tandem mass spectra against a protein sequence database. 
It
   is capable of identifying proteoforms with multiple variable PTMs and
   unexpected alterations, such as histone proteoforms and phosphorylated ones. 
It
   uses mass graphs, which efficiently represent candidate proteoforms with
   multiple variable PTMs, to increase the speed and sensitivity in proteoform
   identification. In addition, approximate spectrum-based filtering methods are
   employed for protein sequence filtering, and a Markov chain Monte Carlo 
method
   (TopMCMC) is used for estimating the statistical significance of
   identifications.  
 .
 - TopDiff (Top-down mass spectrometry-based identification of Differentially
   expressed proteoforms) compares the abundances of proteoforms and finds
   differentially expressed proteoforms by using identifications of top-down 
mass
   spectrometry data of several protein samples.

Regards,

Filippo

-- 

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Research scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
  http://www.debian.org

Accepted daps 3.0.0-4 (source) into unstable

[Filippo Rusconi]

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Date: Fri, 10 Jan 2020 14:58:49 +0100
Source: daps
Architecture: source
Version: 3.0.0-4
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Changes:
 daps (3.0.0-4) unstable; urgency=low
 .
   * Fake new package version to force the source package into unstable (see
 https://qa.debian.org/excuses.php?package=daps, with comment Not built on
 buildd: arch all binaries uploaded by lopippo, a new source-only upload is
 needed to allow migration).
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Re: GPL for package under MIT license upstream; repack?

[Filippo Rusconi]

Greetings,

On Tue, Sep 24, 2019 at 10:41:07AM +0200, Gard Spreemann wrote:

Hello,

A package I maintain (src:gudhi) was mostly under GPL-3+ up to and
including the current version in the archives. Since then, upstream has
switched to an MIT license, but with the caveat that many parts of the
code has GPL dependencies and that "for practical purposes this code is
GPL-3 for the user" [1].



From the page you provide a link to, the following shows little understanding of

licensing issues:

8< 

GPLv3 is a Copyleft license that gives the user the right to use, copy and
modify the code freely for non-commercial purposes.

 >8

Maybe you would like to ensure with them that they understand what they are
doing with this mixing of modules/licenses.

Ciao,

Filippo

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
 http://www.debian.org

Accepted libmsnumpress 1.0.0-5 (source all amd64) into unstable

[Filippo Rusconi]

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Date: Thu, 07 Mar 2019 16:38:58 +0100
Source: libmsnumpress
Binary: libmsnumpress-dev libmsnumpress-dev-doc libmsnumpress1 
libmsnumpress1-dbgsym
Architecture: source all amd64
Version: 1.0.0-5
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Description:
 libmsnumpress-dev - Numeric data compression for mass spectrometry (devel 
files)
 libmsnumpress-dev-doc - set of programs to perform proteomics data analyses 
(doc)
 libmsnumpress1 - Numeric data compression for mass spectrometry (runtime)
Changes:
 libmsnumpress (1.0.0-5) unstable; urgency=low
 .
   * Fix the mis-named qt compressed help file and add the QCH file to the doc
 base.
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Accepted libmsnumpress 1.0.0-3 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 07 Mar 2019 16:16:13 +0100
Source: libmsnumpress
Binary: libmsnumpress-dev libmsnumpress-dev-doc libmsnumpress1 
libmsnumpress1-dbgsym
Architecture: source all amd64
Version: 1.0.0-3
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Description:
 libmsnumpress-dev - Numeric data compression for mass spectrometry (devel 
files)
 libmsnumpress-dev-doc - set of programs to perform proteomics data analyses 
(doc)
 libmsnumpress1 - Numeric data compression for mass spectrometry (runtime)
Closes: 885240
Changes:
 libmsnumpress (1.0.0-3) unstable; urgency=low
 .
   * Standards-Version: 4.3.0.
   * d/copyright: fix order of stanzas.
 .
   * Add qttools5-dev-tools and qtchooser for qhelpgenerator.
   * Add graphviz for dot binary.
   * Closes: #885240 (thanks to "Aaron M. Ucko" ).
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Accepted isospec 1.9.1-5 (source) into unstable

[Filippo Rusconi]

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Hash: SHA256

Format: 1.8
Date: Wed, 06 Mar 2019 17:23:44 +0100
Source: isospec
Architecture: source
Version: 1.9.1-5
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Changes:
 isospec (1.9.1-5) unstable; urgency=low
 .
   * patch: Fix the IsoSpec++ build command line flags for riscv64 as it did not
 recognize the -march flag. I removed it, like I did before for m68k, for
 example.
 .
   * patch: Remove the -march=native compile flag for IsoSpec++ as it is
 considered erroneous to use if cross-builds are performed (Debian QA
 error: E march-native).
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Accepted msxpertsuite 5.8.6-2 (source) into unstable

[Filippo Rusconi]

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Format: 1.8
Date: Wed, 06 Mar 2019 12:40:54 +0100
Source: msxpertsuite
Architecture: source
Version: 5.8.6-2
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Changes:
 msxpertsuite (5.8.6-2) unstable; urgency=low
 .
   * d/control: +Homepage: http://www.msxpertsuite.org/ (not https).
 .
   * Fix the license mismatch output by lintian (appstream.xml file vs
 d/copyright).
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Accepted isospec 1.9.1-4 (source) into unstable

[Filippo Rusconi]

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Format: 1.8
Date: Wed, 06 Mar 2019 14:56:10 +0100
Source: isospec
Architecture: source
Version: 1.9.1-4
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Changes:
 isospec (1.9.1-4) unstable; urgency=low
 .
   * Remove -mtune -march build flags for the build of the C++ extension of the
 Python module.
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Accepted isospec 1.9.1-3 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 06 Mar 2019 11:41:44 +0100
Source: isospec
Binary: libisospec++-dev libisospec++-doc libisospec++1 libisospec++1-dbgsym 
python3-isospec python3-isospec-dbgsym r-cran-isospec r-cran-isospec-dbgsym
Architecture: source amd64 all
Version: 1.9.1-3
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 libisospec++-dev - Isotopic fine structure calculator (C++ development files)
 libisospec++-doc - Isotopic fine structure calculator (C++ API documentation)
 libisospec++1 - Isotopic fine structure calculator (C++ runtime)
 python3-isospec - Isotopic fine structure calculator for Python 3
 r-cran-isospec - Isotopic fine structure calculator for GNU R
Changes:
 isospec (1.9.1-3) unstable; urgency=low
 .
   * Add ifeq statements in IsoSpec++/Makefile's patch to fix many
 arch-specific problems with -march -mtune flags to the compiler
 command line.
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Accepted colorcode 0.8.5-2 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 05 Mar 2019 16:40:15 +0100
Source: colorcode
Binary: colorcode colorcode-dbgsym
Architecture: source amd64
Version: 0.8.5-2
Distribution: unstable
Urgency: medium
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 colorcode  - advanced clone of the MasterMind code-breaking game
Closes: 923116
Changes:
 colorcode (0.8.5-2) unstable; urgency=medium
 .
   * Modifications by Filippo Rusconi 
   Tue, 05 Mar 2019 16:40:15 +0100
 .
   * Fix d/copyright lintian warning.
   * Standards-Version: 4.3.0
   * Remove unused patch file.
 .
   * Upload (Closes: #923116):
   Thanks to Helmut Grohne  for the bug report and
   patch.
 .
   * Modifications by Helmut Grohne 
   Sun, 24 Feb 2019 10:37:41 +0100:
 .
   * Fix FTCBFS: (Closes: #-1)
 + Use QT_SELECT to select qt and avoid running qtchooser directly.
 + Let dh_auto_configure run qmake with appropriate flags.
 + Build-Depends qt5-qmake:native for running lrelease.
 .
   * Modifications by Ondřej Nový 
   Mon, 01 Oct 2018 10:38:09 +0200:
 .
   * d/copyright: Use https protocol in Format field
   * d/control: Deprecating priority extra as per policy 4.0.1
   * d/changelog: Remove trailing whitespaces
   * d/rules: Remove trailing whitespaces
   * d/control: Add Vcs-* field
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Accepted libodsstream 0.7.0-2 (source all amd64) into unstable

[Filippo Rusconi]

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Format: 1.8
Date: Fri, 15 Feb 2019 16:53:40 +0100
Source: libodsstream
Binary: libodsstream-doc libodsstream-qt5-0 libodsstream-qt5-0-dbgsym 
libodsstream-qt5-dev ods2tsv ods2tsv-dbgsym
Architecture: source all amd64
Version: 0.7.0-2
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Description:
 libodsstream-doc - doxygen documentation of the ODSstream library
 libodsstream-qt5-0 - C++ library to read or write ODS files
 libodsstream-qt5-dev - C++ library to read or write ODS files (development 
files)
 ods2tsv- ODS to TSV file converter
Changes:
 libodsstream (0.7.0-2) unstable; urgency=medium
 .
   * new API to read text files (TSV, CSV...)
 .
   * fixes to the packaging in various ways.
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Accepted msxpertsuite 5.8.6-1 (source) into unstable

[Filippo Rusconi]

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Hash: SHA256

Format: 1.8
Date: Thu, 14 Feb 2019 17:08:52 +0100
Source: msxpertsuite
Binary: msxpertsuite msxpertsuite-massxpert msxpertsuite-massxpert-data-doc 
msxpertsuite-minexpert msxpertsuite-minexpert-data-doc
Architecture: source
Version: 5.8.6-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Description:
 msxpertsuite - mass spectrometry software suite - metapackage
 msxpertsuite-massxpert - mass spectrometry software suite - massXpert
 msxpertsuite-massxpert-data-doc - mass spectrometry software suite - massXpert 
- data and doc
 msxpertsuite-minexpert - mass spectrometry software suite - mineXpert
 msxpertsuite-minexpert-data-doc - mass spectrometry software suite - mineXpert 
- data and doc
Closes: 922287
Changes:
 msxpertsuite (5.8.6-1) unstable; urgency=low
 .
   * Reinstate partially all the conflicts/breaks/replaces statements for the
 mspxertsuite-massxpert binary package. This ensures that upgrade of
 massxpert from stable's version to this version does not stumble upon
 overwriting blocks. Thanks to Andreas Beckmann
  for reporting the piuparts log (Closes: #922287).
 .
   * Took advantage to update the
 minexpert/org.msxpertsuite.minexpert.appdata.xml file (which justifies new
 upstream version.
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Accepted msxpertsuite 5.8.5-1 (source) into unstable

[Filippo Rusconi]

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Format: 1.8
Date: Tue, 12 Feb 2019 08:59:24 +0100
Source: msxpertsuite
Binary: msxpertsuite msxpertsuite-massxpert msxpertsuite-massxpert-data-doc 
msxpertsuite-minexpert msxpertsuite-minexpert-data-doc
Architecture: source
Version: 5.8.5-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Description:
 msxpertsuite - mass spectrometry software suite - metapackage
 msxpertsuite-massxpert - mass spectrometry software suite - massXpert
 msxpertsuite-massxpert-data-doc - mass spectrometry software suite - massXpert 
- data and doc
 msxpertsuite-minexpert - mass spectrometry software suite - mineXpert
 msxpertsuite-minexpert-data-doc - mass spectrometry software suite - mineXpert 
- data and doc
Changes:
 msxpertsuite (5.8.5-1) unstable; urgency=low
 .
   * appdata fixes to the gpl version number (lintian warning).
 .
   * d/rules: fix problem with the path to the .fop.xconf file not being found.
 This is a missing fix with respect to the other d/rules files that was
 working.
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msxpertsuite_5.8.5-1.debian.tar.xz
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Accepted daps 3.0.0-3 (source all) into unstable

[Filippo Rusconi]

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Hash: SHA256

Format: 1.8
Date: Tue, 12 Feb 2019 08:28:16 +0100
Source: daps
Binary: daps
Architecture: source all
Version: 3.0.0-3
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 daps   - DocBook Authoring and Publishing Suite (DAPS)
Changes:
 daps (3.0.0-3) unstable; urgency=low
 .
   * Fix in d/rules the .xsl file that is chmod'ed to +x while being installed.
 Sent bug report upstream.
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Accepted msxpertsuite 5.8.4-1 (source) into unstable

[Filippo Rusconi]

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Hash: SHA256

Format: 1.8
Date: Mon, 11 Feb 2019 13:46:36 +0100
Source: msxpertsuite
Architecture: source
Version: 5.8.4-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Changes:
 msxpertsuite (5.8.4-1) unstable; urgency=low
 .
   * Make the user manuals and install them under the control of CMake.
 .
   * Convert d/rules to the debhelper mini format.
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msxpertsuite_5.8.4-1.debian.tar.xz
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Accepted daps 3.0.0-2 (source all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 08 Feb 2019 19:55:51 +0100
Source: daps
Binary: daps
Architecture: source all
Version: 3.0.0-2
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 daps   - DocBook Authoring and Publishing Suite (DAPS)
Changes:
 daps (3.0.0-2) unstable; urgency=low
 .
   * Fix the Vcs fields for salsa location.
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Accepted msxpertsuite 5.8.3-1 (source) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 08 Feb 2019 17:02:20 +0100
Source: msxpertsuite
Architecture: source
Version: 5.8.3-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Closes: 921727
Changes:
 msxpertsuite (5.8.3-1) unstable; urgency=low
 .
   * Make sure CMake is called during dpkg-buildpackage -A (Closes: #921727).
 Thanks to Santiago Vila  for the report.
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Accepted msxpertsuite 5.8.2-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 06 Feb 2019 19:04:58 +0100
Source: msxpertsuite
Binary: msxpertsuite msxpertsuite-massxpert msxpertsuite-massxpert-data-doc 
msxpertsuite-massxpert-dbgsym msxpertsuite-minexpert 
msxpertsuite-minexpert-data-doc msxpertsuite-minexpert-dbgsym
Architecture: source all amd64
Version: 5.8.2-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Description:
 msxpertsuite - mass spectrometry software suite - metapackage
 msxpertsuite-massxpert - mass spectrometry software suite - massXpert
 msxpertsuite-massxpert-data-doc - mass spectrometry software suite - massXpert 
- data and doc
 msxpertsuite-minexpert - mass spectrometry software suite - mineXpert
 msxpertsuite-minexpert-data-doc - mass spectrometry software suite - mineXpert 
- data and doc
Changes:
 msxpertsuite (5.8.2-1) unstable; urgency=low
 .
   * New version with the daps dependency for the user manuals build.
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msxpertsuite-minexpert_5.8.2-1_amd64.deb
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Accepted daps 3.0.0-1 (source all) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 06 Feb 2019 21:43:14 +0100
Source: daps
Binary: daps
Architecture: source all
Version: 3.0.0-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 daps   - DocBook Authoring and Publishing Suite (DAPS)
Changes:
 daps (3.0.0-1) unstable; urgency=low
 .
   * Initial release with packaging starting from earlier work (see
 d/copyright).
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Accepted isospec 1.9.1-2 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 06 Feb 2019 10:07:16 +0100
Source: isospec
Binary: libisospec++-dev libisospec++-doc libisospec++1 libisospec++1-dbgsym 
python3-isospec python3-isospec-dbgsym r-cran-isospec r-cran-isospec-dbgsym
Architecture: source amd64 all
Version: 1.9.1-2
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 libisospec++-dev - Isotopic fine structure calculator (C++ development files)
 libisospec++-doc - Isotopic fine structure calculator (C++ API documentation)
 libisospec++1 - Isotopic fine structure calculator (C++ runtime)
 python3-isospec - Isotopic fine structure calculator for Python 3
 r-cran-isospec - Isotopic fine structure calculator for GNU R
Changes:
 isospec (1.9.1-2) unstable; urgency=low
 .
   * Fix Vcs URLs.
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Accepted isospec 1.9.1-1 (source amd64 all) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 19 Jan 2019 13:56:13 +0100
Source: isospec
Binary: libisospec++-dev libisospec++-doc libisospec++1 libisospec++1-dbgsym 
python3-isospec python3-isospec-dbgsym r-cran-isospec r-cran-isospec-dbgsym
Architecture: source amd64 all
Version: 1.9.1-1
Distribution: unstable
Urgency: medium
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 libisospec++-dev - Isotopic fine structure calculator (C++ development files)
 libisospec++-doc - Isotopic fine structure calculator (C++ API documentation)
 libisospec++1 - Isotopic fine structure calculator (C++ runtime)
 python3-isospec - Isotopic fine structure calculator for Python 3
 r-cran-isospec - Isotopic fine structure calculator for GNU R
Closes: 916218
Changes:
 isospec (1.9.1-1) unstable; urgency=medium
 .
   * Initial release (Closes: #916218).
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Accepted msxpertsuite 5.7.3.1-2 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 02 Feb 2019 02:26:08 +0100
Source: msxpertsuite
Binary: msxpertsuite msxpertsuite-massxpert msxpertsuite-massxpert-data-doc 
msxpertsuite-minexpert msxpertsuite-minexpert-data-doc
Architecture: source all amd64
Version: 5.7.3.1-2
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Description:
 msxpertsuite - mass spectrometry software suite - metapackage
 msxpertsuite-massxpert - mass spectrometry software suite - massXpert
 msxpertsuite-massxpert-data-doc - mass spectrometry software suite - massXpert 
- data and doc
 msxpertsuite-minexpert - mass spectrometry software suite - mineXpert
 msxpertsuite-minexpert-data-doc - mass spectrometry software suite - mineXpert 
- data and doc
Changes:
 msxpertsuite (5.7.3.1-2) unstable; urgency=low
 .
   * Fix libpwiz dependency version.
   * Remove unused dependency.
   * Standards-Version: 4.3.0 (no changes required).
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Accepted msxpertsuite 5.7.3.1-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 02 Feb 2019 00:32:22 +0100
Source: msxpertsuite
Binary: msxpertsuite msxpertsuite-massxpert msxpertsuite-massxpert-data-doc 
msxpertsuite-minexpert msxpertsuite-minexpert-data-doc
Architecture: source all amd64
Version: 5.7.3.1-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Description:
 msxpertsuite - mass spectrometry software suite - metapackage
 msxpertsuite-massxpert - mass spectrometry software suite - massXpert
 msxpertsuite-massxpert-data-doc - mass spectrometry software suite - massXpert 
- data and doc
 msxpertsuite-minexpert - mass spectrometry software suite - mineXpert
 msxpertsuite-minexpert-data-doc - mass spectrometry software suite - mineXpert 
- data and doc
Changes:
 msxpertsuite (5.7.3.1-1) unstable; urgency=low
 .
   * New version that makes use of the new /usr/include/proteowizard header
 directory that makes is easier to resolve the various subdirs. The
 previous hierarchy led to having  which is not intuitive.
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Accepted libpwiz 3.0.18342-2 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 01 Feb 2019 23:38:03 +0100
Source: libpwiz
Binary: libpwiz-dev libpwiz-doc libpwiz-tools libpwiz-tools-dbgsym libpwiz3 
libpwiz3-dbgsym
Architecture: source amd64 all
Version: 3.0.18342-2
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 libpwiz-dev - library to perform proteomics data analyses (devel files)
 libpwiz-doc - set of programs to perform proteomics data analyses (doc)
 libpwiz-tools - ProteoWizard command line tools
 libpwiz3   - library to perform proteomics data analyses (runtime)
Changes:
 libpwiz (3.0.18342-2) unstable; urgency=low
 .
   * Improve header path (move pwiz to proteowizard) to ease with nested
 directories.
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Bug#919624: ITP: daps -- DocBook-based authoring and publishing system

[Filippo Rusconi]

Package: wnpp
Severity: wishlist
Owner: Filippo Rusconi 

* Package name: daps
 Version : 3.0.0
 Upstream Author : Frank Sundermeyer 
* URL : http://opensuse.github.io/daps
* License : GPL-3.0
 Programming Lang: Shell, Python 
Description: DocBook Authoring and Publishing Suite (DAPS)

DAPS contains a set of stylesheets, scripts and makefiles that enable
you to create HTML, PDF, EPUB and other formats from DocBook XML with a
single command. It also contains tools to generate profiled source
tarballs for distributing your XML sources for translation or review.
.
DAPS also includes tools that assist you when writing DocBook XML:
linkchecker, validator, spellchecker, editor macros and stylesheets for
converting DocBook XML.

I was looking for some integrated solution to author the user manuals of my
msXpertSuite software and I tried publican, but felt it was a bit rough. Then I
discovered daps and I found it really well documented, really
well-functioning. In no time I had a workflow that worked flawlessly.

DocBook is now getting more and more traction even amongs non-technical writers.
I feel that having a bit of competition in Debian is useful.

When DAPS will be in Debian, I'll build the user manuals of mineXpert and
massXpert during package build.

Thanks
Filippo
--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
 http://www.debian.org

Accepted msxpertsuite 5.7.3-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 16 Jan 2019 19:14:57 +0100
Source: msxpertsuite
Binary: msxpertsuite msxpertsuite-massxpert msxpertsuite-massxpert-data-doc 
msxpertsuite-minexpert msxpertsuite-minexpert-data-doc
Architecture: source all amd64
Version: 5.7.3-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 msxpertsuite - mass spectrometry software suite - metapackage
 msxpertsuite-massxpert - mass spectrometry software suite - massXpert
 msxpertsuite-massxpert-data-doc - mass spectrometry software suite - massXpert 
- data and doc
 msxpertsuite-minexpert - mass spectrometry software suite - mineXpert
 msxpertsuite-minexpert-data-doc - mass spectrometry software suite - mineXpert 
- data and doc
Changes:
 msxpertsuite (5.7.3-1) unstable; urgency=low
 .
   * Fixes upstream.
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7h

Accepted msxpertsuite 5.7.2-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 15 Jan 2019 22:05:46 +0100
Source: msxpertsuite
Binary: msxpertsuite msxpertsuite-massxpert msxpertsuite-massxpert-data-doc 
msxpertsuite-minexpert msxpertsuite-minexpert-data-doc
Architecture: source all amd64
Version: 5.7.2-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 msxpertsuite - mass spectrometry software suite - metapackage
 msxpertsuite-massxpert - mass spectrometry software suite - massXpert
 msxpertsuite-massxpert-data-doc - mass spectrometry software suite - massXpert 
- data and doc
 msxpertsuite-minexpert - mass spectrometry software suite - mineXpert
 msxpertsuite-minexpert-data-doc - mass spectrometry software suite - mineXpert 
- data and doc
Changes:
 msxpertsuite (5.7.2-1) unstable; urgency=low
 .
   * Bug fixes in upstream massXpert.
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Accepted msxpertsuite 5.7.1-1 (source all amd64) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 21 Dec 2018 17:07:40 +0100
Source: msxpertsuite
Binary: msxpertsuite msxpertsuite-massxpert msxpertsuite-massxpert-data-doc 
msxpertsuite-minexpert msxpertsuite-minexpert-data-doc
Architecture: source all amd64
Version: 5.7.1-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 msxpertsuite - mass spectrometry software suite - metapackage
 msxpertsuite-massxpert - mass spectrometry software suite - massXpert
 msxpertsuite-massxpert-data-doc - mass spectrometry software suite - massXpert 
- data and doc
 msxpertsuite-minexpert - mass spectrometry software suite - mineXpert
 msxpertsuite-minexpert-data-doc - mass spectrometry software suite - mineXpert 
- data and doc
Changes:
 msxpertsuite (5.7.1-1) unstable; urgency=low
 .
   * Small fixes in upstream.
 .
   * Ship the data and doc (all-architecture) material in dedicated packages.
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msxpertsuite-massxpert_5.7.1-1_amd64.deb
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msxpertsuite-minexpert-dbgsym_5.7.1-1_amd64.deb
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msxpertsuite-minexpert_5.7.1-1_amd64.deb
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msxpertsuite_5.7.1-1_amd64.buildinfo
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Accepted msxpertsuite 5.6.1-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 11 Dec 2018 17:42:41 +0100
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc
Architecture: source all amd64
Version: 5.6.1-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.6.1-1) unstable; urgency=low
 .
   * New upstream release to cope with the libpwiz API change in the
 BinaryDataEncoder class, with the creation of the new BinaryData class to
 handle what used to be std::vector.
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Bug#916218: ITP: isospec -- Isotopic fine structure calculator

[Filippo Rusconi]

Package: wnpp
Severity: wishlist
Owner: Filippo Rusconi 

* Package name: isospec
 Version : 1.9.0
 Upstream Author : Micha Startek and Mateusz Lacki
* URL : https://github.com/MatteoLacki/IsoSpec
* License : (BSD-2-Clause)
 Programming Lang: (C++, Python and R)
 Description : Isotopic fine structure calculator
IsoSpec implements an algorithm for fast computation of isotopologues of
chemical substances that can alternate between joint probability and peak
height threshold.

This software piece will be central in the so-called "top/middle-down
proteomics" projects at it is used to model the isotopic cluster corresponding
to a polypeptide elemental formula. There does not seem to be such a standalone
library in Debian. I will make heavy use of that library in my msXpertSuite
software, packaged as msxpertsuite in Debian.

Filippo
--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
 http://www.debian.org



signature.asc
Description: PGP signature

Accepted libpwiz 3.0.18342-1 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 07 Dec 2018 13:27:42 +0100
Source: libpwiz
Binary: libpwiz-dev libpwiz3 libpwiz-tools libpwiz-doc
Architecture: source amd64 all
Version: 3.0.18342-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 libpwiz-dev - library to perform proteomics data analyses (devel files)
 libpwiz-doc - set of programs to perform proteomics data analyses (doc)
 libpwiz-tools - ProteoWizard command line tools
 libpwiz3   - library to perform proteomics data analyses (runtime)
Changes:
 libpwiz (3.0.18342-1) unstable; urgency=low
 .
   * New upstream release. Note that for this release (and later, probably),
 the pwiz package was crafted by me according to instructions and the bjam
 build system that is used upstream.
 .
   * Remove the nnls.h patch as this file is now shipped in the source tarball.
 .
   * debian/rules: update to tweak the Makefile (include directories) and
 BOOST_LDPATH.
 .
   * Update the Vcs-* fields to match the salsa-based URLs.
 .
   * Set Priority: to optional (not extra).
 .
   * Update d/copyright for the libraries/Eigen/nnls.h file.
 .
   * Standards-Version: 4.2.1: no changes required.
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Accepted comet-ms 2018012-1 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 18 Nov 2018 10:05:33 +0100
Source: comet-ms
Binary: comet-ms
Architecture: source amd64
Version: 2018012-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 comet-ms   - Tandem mass spectrometry (MS/MS) search engine
Changes:
 comet-ms (2018012-1) unstable; urgency=low
 .
   * New upstream release.
   * New version of the build system patch.
   * Bump-up Standards-Version to 4.2.1 (no changes needed).
   * Update the Vcs fields to match the salsa location.
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Accepted tandem-mass 1:201702011-1 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 18 Nov 2018 09:00:11 +0100
Source: tandem-mass
Binary: tandem-mass
Architecture: source amd64
Version: 1:201702011-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 tandem-mass - mass spectrometry software for protein identification
Changes:
 tandem-mass (1:201702011-1) unstable; urgency=low
 .
   * Exactly same package as the previous one that could not be uploaded
 because the package version number was not greater than the former NMU one
 (of version 1:20170201-0.1).
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Accepted openms 2.4.0-real-1 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 17 Nov 2018 17:24:48 +0100
Source: openms
Binary: libopenms2.4.0 libopenms-dev topp openms-common openms-doc openms
Architecture: source amd64 all
Version: 2.4.0-real-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 libopenms-dev - library for LC/MS data management and analysis - dev files
 libopenms2.4.0 - library for LC/MS data management and analysis - runtime
 openms - package for LC/MS data management and analysis
 openms-common - package for LC/MS data management and analysis - shared data
 openms-doc - package for LC/MS data management and analysis - documentation
 topp   - set of programs implementing The OpenMS Proteomic Pipeline
Closes: 816562 822412 906561 90
Changes:
 openms (2.4.0-real-1) unstable; urgency=low
 .
   * Really released 2.4.0 version with Qt5 port merged;
 .
   * d/control: update website url to http://www.openms.de (thanks to Adrian 
Bunk
 ; Closes: #906561);
 .
   * d/copyright: update website url and copyright years.
 add Design Science License (Thanks to Dmitry Smirnov
 , Closes: #822412);
 .
   * d/control: fix libqt5opengl5-dev (>= 5.7.0) to libqt5opengl5-desktop-dev
 (>= 5.7.0) because upstream won't support OpenGL ES anytime soon (thanks
 to Adrian Bunk , Closes: #90);
 .
   * Use secure copyright file specification URI.
   * Trim trailing whitespace.
 Jelmer Vernooij   Mon, 15 Oct 2018 06:59:37 +
 .
   * debian/control: Change "Conflicts:" to "Breaks:" (Closes:
 #816562);
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topp-dbg

Re: Opt-in to continue as DD/DM? (was: I resigned in 2004)

[Filippo Rusconi]

On Mon, Nov 12, 2018 at 09:43:20PM +0200, Lars Wirzenius wrote:

Tollef Fog Heen :

(I also wonder if we should just require people to opt in to their
DD-ship on a yearly basis instead of doing most of the WAT/MIA dance. If
people can't be bothered to reply to a single email saying «yup, another
year please» with some reasonable amount of pinging and time to reply,
they are effectively MIA, at least if they haven't let people know on
-private or similar.)


I support automatically retiring DDs and DMs that don't repond to a
ping, or don't upload, or don't vote, or otherwise show activity.


+1

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
 http://www.debian.org

Re: I resigned in 2004

[Filippo Rusconi]

Greetings Fellow Debianites,

On Fri, Nov 09, 2018 at 09:29:30PM +0100, Mattia Rizzolo wrote:

Hi,

On Fri, Nov 09, 2018 at 10:56:57AM -0800, Matthew Wilcox wrote:

For some reason, Debian as a project failed to notice that I had quit,


Probably because even at that time there were procedures that weren't
followed, and apparently nobody after then bothered to check your status
*and* follow up appropiately to clean it up.


even though my wi...@debian.org email address was deliberately forwarded
to a non-functional email address (in part because of the complete
catastrophe that was the Debian spam filtering system at the time).


I don't know what happened back then to your forwarding address (for
however strange your statement looks to me), so I can't quite comment
here.


Over the last couple of months, the MIA team has been trying to get me to
participate in some inane bureaucracy.  I have been ignoring their emails.


I can say that the MIA team didn't try to get you recently.  That was
Jonathan McDowell that apparently was in contact with you and -according
to the note he left- started on 2018-08-25 the process¹ to have you
properly retire. Missing the required follow up from your side² I sent
a follow up on 2018-09-30 completely out of curtesy as from my side it
just seemed like you missed the mail but you were interested in cleaning
your position.


Today, they took it to a new level by encouraging everybody who knows
me to pester me to answer my emails from them.  This is not acceptable.


Today, more than two months after Jonathan started the process, I
proceed to follow the "remove" route instead of the "retire" route,
which triggers an email in debian-private@.


Leave me alone.  Your project left me long ago.  Do not contact me with
regard to Debian bullshit.


ACK, we will have DAM remove you instead of retire.  I suppose there is
no harm as you don't seem interested in the "benefits" that the
"retired" DDs have over the "removed" ones.
I'm sorry to have bothered you more than necessary.


Good bye, and thank you for your contributions you made back then!



¹ https://nm.debian.org/process/539
² which would have consisted in following one link in that mail, and
 then click a single other button; really, nothing more

--
regards,
   Mattia Rizzolo

GPG Key: 66AE 2B4A FCCF 3F52 DA18  4D18 4B04 3FCD B944 4540  .''`.
more about me:  https://mapreri.org : :'  :
Launchpad user: https://launchpad.net/~mapreri  `. `'`
Debian QA page: https://qa.debian.org/developer.php?login=mattia  `-


+1 !

Cheers,
Fiilppo

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
 http://www.debian.org

Accepted msxpertsuite 5.6.0-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 13 Oct 2018 11:59:05 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc
Architecture: source all amd64
Version: 5.6.0-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.6.0-1) unstable; urgency=low
 .
   * New upstream version:
 .
 - Improve the interpreation of script lines;
 - Start implementation of a JavaScript script file to calibrate the Synapt
   data.
 - Improve the mass data integration in script mode;
 - When creating mass spectrum from clipboard, automatically trigger the
   computation of the actual mass spectrum plot without requiring a TIC
   to mass spectrum computation.
 - Provide Savitzky-Golay filtering to any trace in any plot widget with
   undo/redo feature.
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msxpertsuite-doc_5.6.0-1_all.deb
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msxpertsuite_5.6.0-1_amd64.buildinfo
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Accepted msxpertsuite 5.5.3-3 (source all amd64) into unstable

[Filippo Rusconi]

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Hash: SHA256

Format: 1.8
Date: Thu, 04 Oct 2018 20:08:06 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc
Architecture: source all amd64
Version: 5.5.3-3
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group 
Changed-By: Filippo Rusconi 
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.5.3-3) unstable; urgency=low
 .
   * Make sure we load the orig tar ball.
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massxpert_5.5.3-3_all.deb
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Accepted cb2bib 1.9.9-1 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 13 Sep 2018 16:14:02 +0200
Source: cb2bib
Binary: cb2bib
Architecture: source amd64
Version: 1.9.9-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 cb2bib - extract bibliographic references from various sources
Closes: 901535 906969
Changes:
 cb2bib (1.9.9-1) unstable; urgency=low
 .
   * New upstream release. Should fix bug (Closes: #906969); thanks to Santiago
 Vila  for reporting it.
 .
   * (From 1.9.7-3) Allow for cross-compilation (thanks to Helmut Grohne
  (Closes: #901535).
 .
   * Update the Vcs-Browser and Vcs-Git fields to point to the salsa.d.o
 science team location.
 .
   * Standards-Version: 4.2.1, no changes required.
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Accepted msxpertsuite 5.4.0-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 11 Sep 2018 19:31:02 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 5.4.0-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.4.0-1) experimental; urgency=low
 .
   * Port to the libqcustomplot 2.0.1 version. Mostly changes in the data
 format of the plot data in the QCustomPlot class.
 .
   * Fix bug that made the program crash when converting data from mzML to
 SQLite3-based db format when Synapt ion mobility data contained NaN
 values.
 .
   * Fix reporting in the console window of TIC intensity value calculations
 (no error on the result, only the reporting of that result).
 .
   Bump-up standards version to 4.2.0, no changes required.
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Accepted openms 2.4.0-1 (source amd64 all) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 16 Aug 2018 13:45:17 +0200
Source: openms
Binary: libopenms2.4.0 libopenms-dev topp openms-common openms-doc openms
Architecture: source amd64 all
Version: 2.4.0-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 libopenms-dev - library for LC/MS data management and analysis - dev files
 libopenms2.4.0 - library for LC/MS data management and analysis - runtime
 openms - package for LC/MS data management and analysis
 openms-common - package for LC/MS data management and analysis - shared data
 openms-doc - package for LC/MS data management and analysis - documentation
 topp   - set of programs implementing The OpenMS Proteomic Pipeline
Changes:
 openms (2.4.0-1) unstable; urgency=low
 .
   * New upstream version (release branch with Qt5 port merged).
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Re: Next attempt to add Blends to Debian installer

[Filippo Rusconi]

Greetings, Andreas, and everybody,


On Thu, Aug 16, 2018 at 10:34:36AM +0200, Andreas Tille wrote:

Hi,

to give some status information about how we can make Blends more
visible at installer stage:  Holger Levsen, Phil Hands, Steve McIntyre
and I had some discussion in DebCamp.  The conclusion was that adding
Blends to the installer tasksel menu would be perfectly possible if
tasksel itself would provide some menu hierarchy.  We all agreed that
the current selection of tasks needs some overhaul in general.  It
could provide some menu item:

  "Select Blend"   (or rather some better text here!)

and than you get a selection of Blends to pick (one or more) from.

For the Stretch release Phil even wrote some code in this direction that
needs some refresh. (Phil, can you give some pointer if there is
something to test?)

Any comments / code contributions are welcome.



Please, add some small strophe to explain what a blend is, as I can tell that
this is not something widely known even to seasoned Debian users/admins (have
examples from research labs).

Also, when I installed debian-science and debichem last time, the process
downloaded such an amount of software that it almost filled my disk (which I was
not suspecting). Maybe, a rough indication of the used disk space in front of
each blend might be useful, in this respect.

Just my 2 cents, along with my very best wishes,

Filippo

--

⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD
⣾⠁⢠⠒⠀⣿⡁   Scientist at CNRS
⢿⡄⠘⠷⠚⠋⠀   Debian Developer
⠈⠳⣄  http://msxpertsuite.org
 http://www.debian.org

Accepted msxpertsuite 5.3.3-1 (source all amd64) into unstable

[Filippo Rusconi]

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Hash: SHA256

Format: 1.8
Date: Wed, 20 Jun 2018 17:42:48 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 5.3.3-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Closes: 901154
Changes:
 msxpertsuite (5.3.3-1) unstable; urgency=low
 .
   * New upstream release.
 .
   * Fix the "ignore error" directive in the user manual documentation Makefile
 that drives the LaTeX-based compilation of the documents (Closes: #901154);
 .
   * Revert C++14 to C++11 to maintain compatibility with OSes that are less
 advanced with gcc;
 .
   * Fix problem with loading Agilent data because of drift bin count variable.
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Accepted msxpertsuite 5.3.2-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 04 Jun 2018 22:33:37 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 5.3.2-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.3.2-1) unstable; urgency=low
 .
   * New upstream release.
 .
   * General revision of the JavaScript reference documentation. Fixes and
 additions.
 .
   * Small fixes.
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Accepted msxpertsuite 5.3.0-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 31 May 2018 14:10:03 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 5.3.0-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.3.0-1) unstable; urgency=low
 .
   * New upstream release.
 .
   * Ensure that the QScript JavaScript environment works flawlessly even in
 the context of QThread-based code. Written JS-specific functions for
 where QThread would be a problem.
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Accepted msxpertsuite 5.2.1-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 29 May 2018 14:41:25 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 5.2.1-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi 
Changed-By: Filippo Rusconi 
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.2.1-1) unstable; urgency=low
 .
   * New upstream release.
 .
   * Fix integration help string that had bad keyboard key information to
 integrate to XIC chromatogram.
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Accepted msxpertsuite 5.2.0-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 25 May 2018 12:50:59 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 5.2.0-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.2.0-1) unstable; urgency=low
 .
   * New upstream release.
 .
   * Fix bug with the mzML to SQLite3 db conversion due to not allocation
 QCoreApplication before running the console-based conversion (MS Windows
 only bug, apparently).
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msxpertsuite_5.2.0-1_amd64.buildinfo
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msxpertsuite_5.2.0-1_amd64.deb

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Accepted msxpertsuite 5.1.1-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 24 May 2018 18:40:18 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 5.1.1-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.1.1-1) unstable; urgency=low
 .
   * New upstream release.
 .
   * Fix bug with the failing mass spectrometric data file slicer.
 .
   * Fix bug with the deconvolution of the isotopic cluster.
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msxpertsuite_5.1.1-1.debian.tar.xz
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massxpert-data_5.1.1-1_all.deb
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massxpert-doc_5.1.1-1_all.deb
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massxpert_5.1.1-1_all.deb
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msxpertsuite-data_5.1.1-1_all.deb
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msxpertsuite-dbgsym_5.1.1-1_amd64.deb
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msxpertsuite-doc_5.1.1-1_all.deb
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msxpertsuite_5.1.1-1_amd64.buildinfo
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msxpertsuite_5.1.1-1_amd64.deb

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Accepted msxpertsuite 5.1.0-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 23 May 2018 22:15:00 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 5.1.0-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.1.0-1) unstable; urgency=low
 .
   * New upstream release.
 .
   * Ensure the graphical user interface remains always snappy even when the
 computations are blocking by transferring all the integration tasks to
 QThread-based threads.
 .
   * Improved the feedback to the user when any integration is performed, be
 that integration to a TIC intensity value, a TIC chromatogram, a mass
 spectrum or a drift spectrum.
 .
   * Greatly improve the feedback to the user when integrations are performed
 to a MassSpectrum.
 .
   * Fix bug crashing mineXpert upon streamed mode integrations.
 .
   * Ensure that no binning is performed when a single spectrum is loaded from
 file.
 .
   * Make sure the user sees a help message when loading files. The message
 instructs the user about the way to configure the integrations to a mass
 spectrum.
 .
   * Updated all the tests.
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massxpert-data_5.1.0-1_all.deb
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massxpert-doc_5.1.0-1_all.deb
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massxpert_5.1.0-1_all.deb
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msxpertsuite-data_5.1.0-1_all.deb
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msxpertsuite-dbgsym_5.1.0-1_amd64.deb
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msxpertsuite-dev-doc_5.1.0-1_all.deb
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msxpertsuite-doc_5.1.0-1_all.deb
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Accepted openms 2.3-20180419-git-a0b7f650-1 (source amd64 all) into experimental, experimental

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 19 Apr 2018 11:02:39 +0200
Source: openms
Binary: libopenms2.3 libopenms-dev topp openms-common openms-doc openms
Architecture: source amd64 all
Version: 2.3-20180419-git-a0b7f650-1
Distribution: experimental
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libopenms-dev - library for LC/MS data management and analysis - dev files
 libopenms2.3 - library for LC/MS data management and analysis - runtime
 openms - package for LC/MS data management and analysis
 openms-common - package for LC/MS data management and analysis - shared data
 openms-doc - package for LC/MS data management and analysis - documentation
 topp   - set of programs implementing The OpenMS Proteomic Pipeline
Changes:
 openms (2.3-20180419-git-a0b7f650-1) experimental; urgency=low
 .
   * New upstream version (development branch with Qt5 port merged).
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openms_2.3-20180419-git-a0b7f650-1_amd64.buildinfo
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topp-dbgsym_2.3-20180419-git-a0b7f650-1_amd64.deb
 3410e377462fca3147bd55d24d70a8db 2714104 science optional 
topp_2.3-20180419-git-a0b7f650

Accepted msxpertsuite 5.0.2-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 24 Apr 2018 21:14:59 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 5.0.2-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.0.2-1) unstable; urgency=low
 .
   * New upstream release.
 .
   * Fix bug with failing charge state envelope-based mass spectral
 deconvolution.
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msxpertsuite_5.0.2.orig.tar.gz
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msxpertsuite_5.0.2-1.debian.tar.xz
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massxpert-data_5.0.2-1_all.deb
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massxpert-doc_5.0.2-1_all.deb
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massxpert_5.0.2-1_all.deb
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msxpertsuite-dbgsym_5.0.2-1_amd64.deb
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msxpertsuite-dev-doc_5.0.2-1_all.deb
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msxpertsuite-doc_5.0.2-1_all.deb
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msxpertsuite_5.0.2-1_amd64.buildinfo
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msxpertsuite_5.0.2-1_amd64.deb

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Accepted msxpertsuite 5.0.0-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 17 Apr 2018 14:46:46 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 5.0.0-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (5.0.0-1) unstable; urgency=low
 .
   * New upstream release.
 .
   * Bug fixes in quantities:
 * Add ability to trigger a TIC->MZ integration even without prior
   selection of a range in the TIC chrom plot widget;
 * Add XIC extraction feature for multi-plot widgets to be searched for;
 * Fix m_dragging-related bug;
 * Do not combine a DataPoint in a MassSpectrum if its val is 0;
 * Implement a statistics framework to compute statistical characteristics
   of the MassSpectrum instances in a list of spectra to combine.
 * Implement a MZ integration configuration system to ensure that all the
   files from different instruments/vendors can be handled properly. In
   this context, add a feature to filter a trace using Savitzky-Golay
   filtering. That needed an almost complete recoding of the
   binning/combination capabilities of MassSpectrum.
 * Major improvements to the JavaScript'ing capabilities of the software,
   that now cover almost all functionalities.
 * Improvements in the parallel code of spectrum combination.
 * Add JavaScript-specific code documentation with private code doc tags
   and a new doc extractor script. The JavaScript reference doc goes to
   scripting window reference tab and to the mineXpert user manual
   scripting reference chapter.
 * Many improvements to the scripting console;
 * Many many bugfixes, big and small.
 .
   * d/control: replace deprecated "extra" with "optional" software category.
 .
   * Fixes to the MacOSX build system.
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msxpertsuite_5.0.0.orig.tar.gz
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Accepted libmstoolkit 82-6 (source) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 05 Mar 2018 15:52:53 +0100
Source: libmstoolkit
Binary: libmstoolkit-dev libmstoolkit82 libmstoolkit-tools
Architecture: source
Version: 82-6
Distribution: unstable
Urgency: medium
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libmstoolkit-dev - libraries for manipulating mass spectrometry data - dev 
files
 libmstoolkit-tools - libraries for manipulating mass spectrometry data - tools
 libmstoolkit82 - libraries for manipulating mass spectrometry data - runtime
Changes:
 libmstoolkit (82-6) unstable; urgency=medium
 .
   * Fixing the linker command line such that the libs appear at the end of
 the link command. Thanks to Gianfranco Costamagna
 <locutusofb...@debian.org> for the patch.
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libmstoolkit_82-6.debian.tar.xz
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libmstoolkit_82-6_amd64.buildinfo

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Accepted comet-ms 2017014-2 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 02 Mar 2018 11:34:35 +0100
Source: comet-ms
Binary: comet-ms
Architecture: source amd64
Version: 2017014-2
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 comet-ms   - Tandem mass spectrometry (MS/MS) search engine
Closes: 891750
Changes:
 comet-ms (2017014-2) unstable; urgency=medium
 .
   * Fix problem with library linking in the Makefile. Thanks to Gianfranco
 Costamagna <locutusofb...@debian.org> for re-reporting that bug
 (Closes: #891750). In fact, he saw that the rules duplicated code and the
 Makefile such that the Makefile did not direct compilation, since that
 compilation was local.
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comet-ms_2017014-2_amd64.deb

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Accepted libmstoolkit 82-4 (source amd64) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 01 Mar 2018 17:34:08 +0100
Source: libmstoolkit
Binary: libmstoolkit-dev libmstoolkit82 libmstoolkit-tools
Architecture: source amd64
Version: 82-4
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libmstoolkit-dev - libraries for manipulating mass spectrometry data - dev 
files
 libmstoolkit-tools - libraries for manipulating mass spectrometry data - 
runtime
 libmstoolkit82 - libraries for manipulating mass spectrometry data - runtime
Changes:
 libmstoolkit (82-4) unstable; urgency=medium
 .
   * Fix the problem with linking MSSingleScan binary. And add it to the
 shipped material by creating a new binary package, libmstoolkit-tools.
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Accepted comet-ms 2017014-1 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 01 Mar 2018 11:37:59 +0100
Source: comet-ms
Binary: comet-ms
Architecture: source amd64
Version: 2017014-1
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 comet-ms   - Tandem mass spectrometry (MS/MS) search engine
Closes: 891750
Changes:
 comet-ms (2017014-1) unstable; urgency=medium
 .
   * New upstream version.
 .
   * Updated the patch that modifies the two Makefile_s such that
 libmstoolkitlite is used from the Debian package. Tested the comet-ms
 binary ok.
 .
   * Fix problem with library linking in the Makefile. Thanks to Gianfranco
 Costamagna <locutusofb...@debian.org> for reporting that bug
 (Closes: #891750).
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Accepted libmstoolkit 82-3 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 01 Mar 2018 09:13:48 +0100
Source: libmstoolkit
Binary: libmstoolkit-dev libmstoolkit82
Architecture: source amd64
Version: 82-3
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libmstoolkit-dev - libraries for manipulating mass spectrometry data - dev 
files
 libmstoolkit82 - libraries for manipulating mass spectrometry data - runtime
Closes: 891805
Changes:
 libmstoolkit (82-3) unstable; urgency=medium
 .
   * Fix the dpkg-gensymbols command line to produce a correct symbols file.
 Thanks to Adrian Bunk <b...@debian.org> for reporting the bug
 (Closes: #891805).
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Accepted libmstoolkit 82-2 (source amd64) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 26 Feb 2018 20:41:29 +0100
Source: libmstoolkit
Binary: libmstoolkit-dev libmstoolkit82
Architecture: source amd64
Version: 82-2
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libmstoolkit-dev - libraries for manipulating mass spectrometry data - dev 
files
 libmstoolkit82 - libraries for manipulating mass spectrometry data - runtime
Changes:
 libmstoolkit (82-2) unstable; urgency=medium
 .
   * Fix the missing license/copyright stanzas from a number of files. The
 stanzas have been added by Michael Hoopmann as a response to a private
 mail request by me. The files were modified on GitHub. I added these 
license
 stanzas to the files in the form of a patch. The version of the library
 was not updated and probably won't for some time. This is a compromise
 that should be acceptable.
 .
   * Update debian/copyright for the MSSingleScan.cpp file and all the others
 that got new license notices in the patch above.
 .
   * debian/compat 11.
 .
   * mv source.lintian-overrides source/lintian-overrides.
 .
   * debian/control: Standards-Version: 4.1.3
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Accepted cb2bib 1.9.7-2 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 25 Jan 2018 17:38:13 +0100
Source: cb2bib
Binary: cb2bib
Architecture: source amd64
Version: 1.9.7-2
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 cb2bib - extract bibliographic references from various sources
Closes: 887568
Changes:
 cb2bib (1.9.7-2) unstable; urgency=low
 .
   * Fix broken symbolic man page link. Although the bug report suggested an
 erroneous fix, I want to thanks Andreas Beckmann
 <a...@debian.org> for reporting the bug (Closes: #887568).
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Accepted libmsnumpress 1.0.0-2 (source all amd64) into unstable

[Filippo Rusconi]

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Hash: SHA256

Format: 1.8
Date: Wed, 10 Jan 2018 18:05:03 +0100
Source: libmsnumpress
Binary: libmsnumpress-dev libmsnumpress1 libmsnumpress-dev-doc
Architecture: source all amd64
Version: 1.0.0-2
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libmsnumpress-dev - Numeric data compression for mass spectrometry (devel 
files)
 libmsnumpress-dev-doc - set of programs to perform proteomics data analyses 
(doc)
 libmsnumpress1 - Numeric data compression for mass spectrometry (runtime)
Changes:
 libmsnumpress (1.0.0-2) unstable; urgency=low
 .
   Fix removal of files that are no present and that trigger an error.
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Accepted msxpertsuite 4.1.0-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 02 Jan 2018 18:52:11 +0100
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 4.1.0-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (4.1.0-1) unstable; urgency=low
 .
   * New upstream release with a greatly reworked build system to cope with
 the MacOSX build system.
 .
   * Reworked the configuration system to apply to massXpert and mineXpert
 independently (config.h file generated in the respective build
 directories).
 .
   * Fix problem with the VERSION that would adopt various values depending on
 the config.h file that is read (crufty config.h file residing in top
 source dir).
 .
   * Many fixes in the maintainer-scripts/ directory.
 .
   * Standards-Version: 4.1.3: no changes required.
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Accepted libmsnumpress 1.0.0-1 (source all amd64) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 04 Dec 2017 16:44:58 +0100
Source: libmsnumpress
Binary: libmsnumpress-dev libmsnumpress1 libmsnumpress-dev-doc
Architecture: source all amd64
Version: 1.0.0-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libmsnumpress-dev - Numeric data compression for mass spectrometry (devel 
files)
 libmsnumpress-dev-doc - set of programs to perform proteomics data analyses 
(doc)
 libmsnumpress1 - Numeric data compression for mass spectrometry (runtime)
Closes: 883538
Changes:
 libmsnumpress (1.0.0-1) unstable; urgency=low
 .
   * Initial release (Closes: #883538).
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Accepted msxpertsuite 4.0.0-1 (source all amd64) into unstable

[Filippo Rusconi]

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Hash: SHA256

Format: 1.8
Date: Thu, 14 Dec 2017 20:19:26 +0100
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 4.0.0-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (4.0.0-1) unstable; urgency=low
 .
   * New upstream release.
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msxpertsuite_4.0.0-1.debian.tar.xz
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msxpertsuite-dbgsym_4.0.0-1_amd64.deb
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msxpertsuite-doc_4.0.0-1_all.deb
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msxpertsuite_4.0.0-1_amd64.buildinfo
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msxpertsuite-dev-doc_4.0.0-1_all.deb
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msxpertsuite_4.0.0-1.debian.tar.xz
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massxpert-data_4.0.0-1_all.deb
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msxpertsuite-data_4.0.0-1_all.deb
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msxpertsuite-dbgsym_4.0.0-1_amd64.deb
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msxpertsuite-dev-doc_4.0.0-1_all.deb
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msxpertsuite-doc_4.0.0-1_all.deb
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msxpertsuite_4.0.0-1_amd64.buildinfo
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msxpertsuite_4.0.0-1_amd64.deb

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lTiTIduplmyzuL

Bug#883538: ITP: libmsnumpress -- numerical compression in mass spectrometry data

[Filippo Rusconi]

Package: wnpp
Severity: wishlist
Owner: Filippo Rusconi <lopi...@debian.org>

* Package name: libmsnumpress
  Version : 1.0.0
  Upstream Author : Johan Teleman et al <johan.tele...@immun.lth.se>
* URL : https://github.com/ms-numpress/ms-numpress  
* License : (Apache-2.0)
  Programming Lang: (C++)
  Description : numerical compression in mass spectrometry data

 Implementations of two compression schemes for numeric data from mass
 spectrometers.
 .
 The library provides implementations of 3 different algorithms, 1 designed to
 compress first order smooth data like retention time or M/Z arrays, and 2 for
 compressing non smooth data with lower requirements on precision like ion count
 arrays.

Accepted cb2bib 1.9.7-1 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 04 Dec 2017 11:36:28 +0100
Source: cb2bib
Binary: cb2bib
Architecture: source amd64
Version: 1.9.7-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 cb2bib - extract bibliographic references from various sources
Changes:
 cb2bib (1.9.7-1) unstable; urgency=low
 .
   * New upstream version.
Checksums-Sha1:
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cb2bib_1.9.7-1.debian.tar.xz
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cb2bib_1.9.7-1_amd64.buildinfo
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cb2bib_1.9.7-1.debian.tar.xz
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cb2bib-dbgsym_1.9.7-1_amd64.deb
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cb2bib_1.9.7-1_amd64.buildinfo
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Accepted comet-ms 2017012-1 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 03 Dec 2017 21:15:46 +0100
Source: comet-ms
Binary: comet-ms
Architecture: source amd64
Version: 2017012-1
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 comet-ms   - Tandem mass spectrometry (MS/MS) search engine
Changes:
 comet-ms (2017012-1) unstable; urgency=medium
 .
   * New upstream version.
Checksums-Sha1:
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Accepted msxpertsuite 3.8.1-2 (source all amd64) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 02 Dec 2017 08:30:55 +0100
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-dev-doc
Architecture: source all amd64
Version: 3.8.1-2
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-dev-doc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (3.8.1-2) unstable; urgency=low
 .
   * Forcing new debian package version to allow the package into Debian. No
 changes.
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msxpertsuite-dbgsym_3.8.1-2_amd64.deb
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msxpertsuite-dev-doc_3.8.1-2_all.deb
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msxpertsuite-doc_3.8.1-2_all.deb
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msxpertsuite_3.8.1-2_amd64.buildinfo
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msxpertsuite_3.8.1-2_amd64.deb
Files:
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 63d9c284848848204036ac31f81a6e17 30791805 science optional 
msxpertsuite_3.8.1.orig.tar.gz
 dd733522c1602fc69559862a2e78a847 15868 science optional 
msxpertsuite_3.8.1-2.debian.tar.xz
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massxpert-data_3.8.1-2_all.deb
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massxpert-doc_3.8.1-2_all.deb
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msxpertsuite-data_3.8.1-2_all.deb
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msxpertsuite-dbgsym_3.8.1-2_amd64.deb
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msxpertsuite-dev-doc_3.8.1-2_all.deb
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msxpertsuite-doc_3.8.1-2_all.deb
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msxpertsuite_3.8.1-2_amd64.buildinfo
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msxpertsuite_3.8.1-2_amd64.deb

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Re: ISO download difficult (was: Debian Stretch new user report (vs Linux Mint))

[Filippo Rusconi]

On Fri, Dec 01, 2017 at 05:10:37PM +0100, W. Martin Borgert wrote:

Quoting Andrey Rahmatullin <w...@debian.org>:


Of course, the stable amd64 netinst is useful only for VMs.


Why?


I suspect that this means that this image is useful to install a guest machine
in a virtualized environment.  Maybe because indeed it does not need specific
non-free drivers or binary blobs since related aspects are dealt with by the
host machine ?

Just a guess :-)

Filippo

--
⢀⣴⠾⠻⢶⣦⠀  Filippo Rusconi, PhD   
⣾⠁⢰⠒⠀⣿⡁  public crypto key B053 304E 17D6 D419 DD9B 4651 41AB 484D 7694 CF42 @ pgp.mit.edu 
⢿⡄⠘⠷⠚⠋
⠈⠳⣄ 

Accepted libpwiz 3.0.10827-4 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 01 Nov 2017 16:08:32 +0100
Source: libpwiz
Binary: libpwiz-dev libpwiz3 libpwiz-tools libpwiz-doc
Architecture: source amd64 all
Version: 3.0.10827-4
Distribution: unstable
Urgency: medium
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libpwiz-dev - library to perform proteomics data analyses (devel files)
 libpwiz-doc - set of programs to perform proteomics data analyses (doc)
 libpwiz-tools - ProteoWizard command line tools
 libpwiz3   - library to perform proteomics data analyses (runtime)
Closes: 878616
Changes:
 libpwiz (3.0.10827-4) unstable; urgency=medium
 .
   * debian/make-included-headers-hierarchy.sh: fix script to avoid adding
 non-useful h[pp] files. Thanks to Adam Borowski <kilob...@angband.pl>
 for reporting the bug (Closes:#878616).
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libpwiz-tools_3.0.10827-4_amd64.deb
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libpwiz3-dbgsym_3.0.10827-4_amd64.deb
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libpwiz_3.0.10827-4_amd64.buildinfo
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libpwiz-dev_3.0.10827-4_amd64.deb
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libpwiz-tools-dbgsym_3.0.10827-4_amd64.deb
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libpwiz_3.0.10827-4.debian.tar.xz
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libpwiz-dev_3.0.10827-4_amd64.deb
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libpwiz-doc_3.0.10827-4_all.deb
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libpwiz-tools_3.0.10827-4_amd64.deb
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libpwiz3_3.0.10827-4_amd64.deb
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Accepted msxpertsuite 3.7.0-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 13 Oct 2017 11:16:18 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-devdoc
Architecture: source all amd64
Version: 3.7.0-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-devdoc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (3.7.0-1) unstable; urgency=low
 .
   * New upstream package:
 .
   - small bug fixes;
   - unit testing code using the catch testing software;
   - regression testing using the scripting framework already coded into
 mineXpert.
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Accepted msxpertsuite 3.6.7-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 11 Sep 2017 12:14:45 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-devdoc
Architecture: source all amd64
Version: 3.6.7-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-devdoc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (3.6.7-1) unstable; urgency=low
 .
   * New upstream package with finished mineXpert developer documentation.
 .
   * Replace devdoc/html/jquery.js by a symbolic link to the same file of the
 libjs-jquery package.
 .
   * Standards-Version: 4.0.1
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msxpertsuite-dbgsym_3.6.7-1_amd64.deb
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Files:
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msxpertsuite_3.6.7.orig.tar.gz
 d98a2bc57ef8d5b2f8bcb3ca891f3284 15496 science optional 
msxpertsuite_3.6.7-1.debian.tar.xz
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massxpert-data_3.6.7-1_all.deb
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massxpert-doc_3.6.7-1_all.deb
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msxpertsuite-data_3.6.7-1_all.deb
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msxpertsuite-dbgsym_3.6.7-1_amd64.deb
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msxpertsuite-devdoc_3.6.7-1_all.deb
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msxpertsuite-doc_3.6.7-1_all.deb
 4a4aec9dbf145ac6230614c0a427319a 20539 science optional 
msxpertsuite_3.6.7-1_amd64.buildinfo
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msxpertsuite_3.6.7-1_amd64.deb

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Accepted python-pymzml 0.7.6-dfsg-5 (source all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 15 Sep 2017 14:05:47 +0200
Source: python-pymzml
Binary: python-pymzml python3-pymzml python-pymzml-doc
Architecture: source all
Version: 0.7.6-dfsg-5
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 python-pymzml - mzML mass spectrometric data parsing (Python 2.x)
 python-pymzml-doc - mzML mass spectrometric data parsing - documentation
 python3-pymzml - mzML mass spectrometric data parsing (Python 3.x)
Changes:
 python-pymzml (0.7.6-dfsg-5) unstable; urgency=low
 .
   * debian/control: update the dependencies latex-xcolor replaced with
 texlive-latex-recommended (bug number-865237 was closed by non-maintainer
 upload by Adrian Bunk <b...@debian.org> Tue, 18 Jul 2017 19:50:54 +0300.
 .
   * debian/compat: 9 (update dep to debhelper (>=9.20130630)).
 .
   * Standards-Version: 4.0.1 (no changes required).
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Files:
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python-pymzml_0.7.6-dfsg-5.dsc
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Accepted msxpertsuite 3.6.6-1 (source all amd64) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 11 Sep 2017 10:07:25 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc msxpertsuite-devdoc
Architecture: source all amd64
Version: 3.6.6-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-devdoc - mass spectrometry software suite - developer doc
 msxpertsuite-doc - mass spectrometry software suite - manuals
Closes: 874530
Changes:
 msxpertsuite (3.6.6-1) unstable; urgency=low
 .
   * New upstream release. Mainly updated the dev docs and now
 building html doxygen-based documentation
 (binary package msxpertsuite-devdoc).
 .
   * Occasional code cleanup and code improvements.
 .
   * Make sure that the arch vs indep build is ok and does not depend on the
 order of building. Thanks again to Aaron M. Ucko  <u...@debian.org> for
 reporting the building issue (Closes: 874530).
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msxpertsuite_3.6.6.orig.tar.gz
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msxpertsuite-dbgsym_3.6.6-1_amd64.deb
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msxpertsuite-doc_3.6.6-1_all.deb
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Accepted msxpertsuite 3.6.4-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 04 Sep 2017 15:35:05 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc
Architecture: source all amd64
Version: 3.6.4-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (3.6.4-1) unstable; urgency= low
 .
   * New upstream release. Mainly updated the dev-docs that sit in the code
 (based on doxygen).
 .
   * CMake-based project build system improved to better separate the build of
 the "binary" components of the project from the build of the "indep"
 compoments of the project (see below for rationale).
 .
   * debian packaging improved to fix build problems. Many thanks to by Aaron 
M. Ucko
 <u...@debian.org> for reporting them.
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Files:
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msxpertsuite_3.6.4.orig.tar.gz
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msxpertsuite_3.6.4-1.debian.tar.xz
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msxpertsuite-data_3.6.4-1_all.deb
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msxpertsuite-dbgsym_3.6.4-1_amd64.deb
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msxpertsuite-doc_3.6.4-1_all.deb
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msxpertsuite_3.6.4-1_amd64.buildinfo
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msxpertsuite_3.6.4-1_amd64.deb

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Accepted msxpertsuite 3.6.2-1 (source all amd64) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Fri, 30 Jun 2017 17:16:06 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc
Architecture: source all amd64
Version: 3.6.2-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (3.6.2-1) unstable; urgency= low
 .
   * New upstream release with name change;
 .
   * debian/control: bump up Standards version to 4.0.0 (no changes);
 .
   * debian/control: rework the software description to integrate the
 mineXpert and convXpert programs;
   * debian/control: add build-dep libboost-dev and libtclap-dev and gsfonts
 (required to succeed in converting splashscreen.svg to splashscreen.png).
 .
   * Entirely reworked the man page generation system, using docbook-to-man
 (added build-time dependency).
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msxpertsuite_3.6.2.orig.tar.gz
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msxpertsuite_3.6.2-1.debian.tar.xz
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massxpert-data_3.6.2-1_all.deb
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msxpertsuite-data_3.6.2-1_all.deb
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msxpertsuite-dbgsym_3.6.2-1_amd64.deb
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msxpertsuite-doc_3.6.2-1_all.deb
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msxpertsuite_3.6.2-1_amd64.buildinfo
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msxpertsuite_3.6.2-1_amd64.deb

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Accepted msxpertsuite 3.6.3-1 (source all amd64) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 17 Jul 2017 17:46:52 +0200
Source: msxpertsuite
Binary: massxpert msxpertsuite massxpert-data msxpertsuite-data massxpert-doc 
msxpertsuite-doc
Architecture: source all amd64
Version: 3.6.3-1
Distribution: unstable
Urgency: low
Maintainer: Filippo Rusconi <lopi...@debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - transitional package
 massxpert-data - transitional package
 massxpert-doc - transitional package
 msxpertsuite - mass spectrometry software suite - executable files
 msxpertsuite-data - mass spectrometry software suite - arch-indep data
 msxpertsuite-doc - mass spectrometry software suite - manuals
Changes:
 msxpertsuite (3.6.3-1) unstable; urgency= low
 .
   * New upstream release with bug fixes in the reporting of ranges for the
 "to tic intensity" integration.
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Files:
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msxpertsuite_3.6.3.orig.tar.gz
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msxpertsuite-dbgsym_3.6.3-1_amd64.deb
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msxpertsuite_3.6.3-1_amd64.buildinfo
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Accepted tandem-mass 1:20170201.1-1 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 22 Aug 2017 15:36:59 +0200
Source: tandem-mass
Binary: tandem-mass
Architecture: source amd64
Version: 1:20170201.1-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 tandem-mass - mass spectrometry software for protein identification
Changes:
 tandem-mass (1:20170201.1-1) unstable; urgency=low
 .
   * debian/control: add secure vcs-git url.
 StandardsVersion : 4.0.0 (no changes)
 debian/compat set to 9
 removed the dbg binary package stanza:
 thus, set debhelper (>= 9.20151219)
 .
   * debian/patches: add patch to fix pointer vs integer comparison (gcc
 7-spotted).
 .
* successful test of the patch by Olivier Langella
<olivier.lange...@u-psud.fr>.
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Accepted libpwiz 3.0.10827-3 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 05 Jul 2017 20:25:53 +0200
Source: libpwiz
Binary: libpwiz-dev libpwiz3 libpwiz-tools libpwiz-doc
Architecture: source amd64 all
Version: 3.0.10827-3
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libpwiz-dev - library to perform proteomics data analyses (devel files)
 libpwiz-doc - set of programs to perform proteomics data analyses (doc)
 libpwiz-tools - ProteoWizard command line tools
 libpwiz3   - library to perform proteomics data analyses (runtime)
Changes:
 libpwiz (3.0.10827-3) unstable; urgency=medium
 .
   * debian/control: Replace tabs with spaces.
 .
   * debian/control: fix libboost-dev dependency so that
 /usr/include/boost/lexical_cast.hpp is there although the library
 fine even without it, it is required by dependencies.
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Accepted libpwiz 3.0.10827-2 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sat, 01 Jul 2017 22:52:58 +0200
Source: libpwiz
Binary: libpwiz-dev libpwiz3 libpwiz-tools libpwiz-doc
Architecture: source amd64 all
Version: 3.0.10827-2
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libpwiz-dev - library to perform proteomics data analyses (devel files)
 libpwiz-doc - set of programs to perform proteomics data analyses (doc)
 libpwiz-tools - ProteoWizard command line tools
 libpwiz3   - library to perform proteomics data analyses (runtime)
Changes:
 libpwiz (3.0.10827-2) unstable; urgency=medium
 .
   * debian/control: add dependency to libbost-dev.
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Accepted libpwiz 3.0.10827-1 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 27 Jun 2017 10:17:49 +0200
Source: libpwiz
Binary: libpwiz-dev libpwiz3 libpwiz-tools libpwiz-doc
Architecture: source amd64 all
Version: 3.0.10827-1
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libpwiz-dev - library to perform proteomics data analyses (devel files)
 libpwiz-doc - set of programs to perform proteomics data analyses (doc)
 libpwiz-tools - ProteoWizard command line tools
 libpwiz3   - library to perform proteomics data analyses (runtime)
Changes:
 libpwiz (3.0.10827-1) unstable; urgency=medium
 .
   * New upstream version.
 .
   * debian/control Standards-Version: 4.0.0
 .
   * Use the trigger infrastructure to call ldconfig.
 .
   * debian/copyright: thorough rework using licensecheck  + manual checking.
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Accepted python-pymzml 0.7.6-dfsg-4 (source all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 01 Sep 2016 10:43:36 +0200
Source: python-pymzml
Binary: python-pymzml python3-pymzml python-pymzml-doc
Architecture: source all
Version: 0.7.6-dfsg-4
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 python-pymzml - mzML mass spectrometric data parsing (Python 2.x)
 python-pymzml-doc - mzML mass spectrometric data parsing - documentation
 python3-pymzml - mzML mass spectrometric data parsing (Python 3.x)
Changes:
 python-pymzml (0.7.6-dfsg-4) unstable; urgency=low
 .
   * debian/control: update the name of the git repository to match the new
 name of the package.
   * debian/control: set secure https protocol also for the vcs-git url.
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python-pymzml_0.7.6-dfsg-4.dsc
 a62f67000a73d54b888058ca24b71716 5872 python optional 
python-pymzml_0.7.6-dfsg-4.debian.tar.xz
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python-pymzml-doc_0.7.6-dfsg-4_all.deb
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python-pymzml_0.7.6-dfsg-4_all.deb
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Accepted python-pymzml 0.7.6-dfsg-3 (source all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 29 Aug 2016 14:12:31 +0200
Source: python-pymzml
Binary: python-pymzml python3-pymzml python-pymzml-doc
Architecture: source all
Version: 0.7.6-dfsg-3
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 python-pymzml - mzML mass spectrometric data parsing (Python 2.x)
 python-pymzml-doc - mzML mass spectrometric data parsing - documentation
 python3-pymzml - mzML mass spectrometric data parsing (Python 3.x)
Changes:
 python-pymzml (0.7.6-dfsg-3) unstable; urgency=low
 .
   * Fix problem with debian/control Replaces/Conflicts directives. Now
 python-mzml should be properly removed from the system upon installation
 of this replacing package.
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python-pymzml_0.7.6-dfsg-3.dsc
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python-pymzml_0.7.6-dfsg-3.debian.tar.xz
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Accepted python-pymzml 0.7.6-dfsg-2 (source all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 19 Jul 2016 16:23:38 +0200
Source: python-pymzml
Binary: python-pymzml python3-pymzml python-pymzml-doc
Architecture: source all
Version: 0.7.6-dfsg-2
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 python-pymzml - mzML mass spectrometric data parsing (Python 2.x)
 python-pymzml-doc - mzML mass spectrometric data parsing - documentation
 python3-pymzml - mzML mass spectrometric data parsing (Python 3.x)
Closes: 830331
Changes:
 python-pymzml (0.7.6-dfsg-2) unstable; urgency=low
 .
   * Fix bug reported by Lucas Nussbaum <lu...@debian.org> about iftex.sty not
 being found (add a texlive dependency to d/control). Closes: #830331.
   * Minor fixes to the debian packaging.
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Accepted massxpert 3.6.1-1 (source all amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 19 Jul 2016 12:16:20 +0200
Source: massxpert
Binary: massxpert massxpert-dbg massxpert-data massxpert-doc
Architecture: source all amd64
Version: 3.6.1-1
Distribution: unstable
Urgency: low
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 massxpert  - linear polymer mass spectrometry software
 massxpert-data - linear polymer mass spectrometry software - arch-indep data
 massxpert-dbg - linear polymer mass spectrometry software - debugging symbols
 massxpert-doc - Linear polymer mass spectrometry software - manual
Closes: 831089
Changes:
 massxpert (3.6.1-1) unstable; urgency=low
 .
   * New upstream version: Fix programming error detected by using GCC-6.
 Thanks to Lucas Nussbaum <lu...@debian.org> (Closes: 831089).
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Accepted mmass 5.5.0-5 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 20 Jun 2016 10:20:13 +0200
Source: mmass
Binary: mmass mmass-modules
Architecture: source amd64 all
Version: 5.5.0-5
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 mmass  - Mass spectrometry tool for proteomics
 mmass-modules - Mass spectrometry tool for proteomics - extension modules
Closes: 806078
Changes:
 mmass (5.5.0-5) unstable; urgency=medium
 .
   * Apply patch by Santiago Vila <sanv...@unex.es> (Closes:
 #806078):  FTBFS: when built with dpkg-buildpackage -A
 (No such file or directory) .
 .
   * Standards-Version: 3.9.8, no changes required.
 .
   * https:// secure protocol for VCS browser.
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Accepted openms 2.0.0-4 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Wed, 30 Mar 2016 12:06:31 +0200
Source: openms
Binary: libopenms2.0 libopenms2.0-dbg libopenms-dev topp topp-dbg openms-common 
openms-doc openms
Architecture: source amd64 all
Version: 2.0.0-4
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libopenms-dev - library for LC/MS data management and analysis - dev files
 libopenms2.0 - library for LC/MS data management and analysis - runtime
 libopenms2.0-dbg - library for LC/MS data management and analysis - debugging 
symbol
 openms - package for LC/MS data management and analysis
 openms-common - package for LC/MS data management and analysis - shared data
 openms-doc - package for LC/MS data management and analysis - documentation
 topp   - set of programs implementing The OpenMS Proteomic Pipeline
 topp-dbg   - set of programs implementing The OpenMS Proteomic Pipeline - debu
Closes: 816562
Changes:
 openms (2.0.0-4) unstable; urgency=medium
 .
   * debian/control: Change "Conflicts:" to "Breaks:" (Closes:
 #816562);
 .
   * debian/rules: fix the OPENMS_DATA_PATH value so that it points to
 /us/share/openms-common and not /usr/share/openms-common/OpenMS.
 .
   * debian/rules: Put dh_clean at the end of the clean target.
 .
   * switched doc_minimal doc_class_only targets around in the make call
 because the doxygen-based documentation for the classes did not get
 generated fully.
 .
   * Remove the git protocol URL for the repos and switch to secure http for
 the other URL.
 .
   * debian/control: Standards-Version: 3.9.7. No changes required.
 .
   * debian/rules: Reinstate DEB_BUILD_MAINT_OPTIONS along with the hardening
 flag +all..
 .
   * debian/rules: Make sure libSuperHirn and libOpenMS_GUI libraries are
 processed fine with respect to the symbols control file.
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libopenms-dev_2.0.0-4_amd64.deb
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libopenms2.0-dbg_2.0.0-4_amd64.deb
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libopenms2.0_2.0.0-4_amd64.deb
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openms-common_2.0.0-4_all.deb
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openms-doc_2.0.0-4_all.deb
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topp_2.0.0-4_amd64.deb

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Accepted tandem-mass 1:20151215-4 (source amd64) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Tue, 29 Mar 2016 09:31:24 +0200
Source: tandem-mass
Binary: tandem-mass tandem-mass-dbg
Architecture: source amd64
Version: 1:20151215-4
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 tandem-mass - mass spectrometry software for protein identification
 tandem-mass-dbg - mass spectrometry software for protein identification - 
debug sym
Closes: 819432
Changes:
 tandem-mass (1:20151215-4) unstable; urgency=medium
 .
   * debian/control: fix the URL that describes the format (thanks to Daniele
 Forsi <dfo...@gmail.com>) Closes: #819432.
 .
   * fix various packaging issues as detected by lintian.
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tandem-mass_20151215-4_amd64.deb
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tandem-mass_20151215-4.debian.tar.xz
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tandem-mass-dbg_20151215-4_amd64.deb
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tandem-mass_20151215-4_amd64.deb

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Accepted libpwiz 3.0.9393-1 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 21 Mar 2016 16:33:44 +0100
Source: libpwiz
Binary: libpwiz-dev libpwiz3 libpwiz-tools libpwiz-doc
Architecture: source amd64 all
Version: 3.0.9393-1
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libpwiz-dev - library to perform proteomics data analyses (devel files)
 libpwiz-doc - set of programs to perform proteomics data analyses (doc)
 libpwiz-tools - ProteoWizard command line tools
 libpwiz3   - library to perform proteomics data analyses (runtime)
Changes:
 libpwiz (3.0.9393-1) unstable; urgency=medium
 .
   * New upstream version.
 .
   * debian/rules: remove the clean target from the configure target.
 .
   * debian/control Standards-Version: 3.9.7 (no changes)
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Accepted tandem-mass 1:20151215-3 (source amd64) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Sun, 20 Mar 2016 10:58:33 +0100
Source: tandem-mass
Binary: tandem-mass tandem-mass-dbg
Architecture: source amd64
Version: 1:20151215-3
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 tandem-mass - mass spectrometry software for protein identification
 tandem-mass-dbg - mass spectrometry software for protein identification
Changes:
 tandem-mass (1:20151215-3) unstable; urgency=medium
 .
   * debian/copyright: add MIT licence for files expat* files.
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Re: Adding SONAME to a shared object in KLEE

[Filippo Rusconi]

   libQtGui.so.4
   NEEDED   libQtXml.so.4
   NEEDED   libQtCore.so.4
   NEEDED   libstdc++.so.6
   NEEDED   libm.so.6
   NEEDED   libgcc_s.so.1
   NEEDED   libc.so.6

Now, as you can see, the listed names are all SONAMES :
lib.so..

For example, if I now want to see the files relating to libQtCore.so.4:

ls /usr/lib/x86_64-linux-gnu/libQtCore.so* -l
  18 Jan 12 05:15 /usr/lib/x86_64-linux-gnu/libQtCore.so -> 
libQtCore.so.4.8.6
  18 Jan 12 05:15 /usr/lib/x86_64-linux-gnu/libQtCore.so.4 -> 
libQtCore.so.4.8.6
  18 Jan 12 05:15 /usr/lib/x86_64-linux-gnu/libQtCore.so.4.8 -> 
libQtCore.so.4.8.6
3033168 Jan 12 05:17 /usr/lib/x86_64-linux-gnu/libQtCore.so.4.8.6

You can see that the real library name is indeed libQtCore.so.4.8.6,
of size 3033168, and the other ones are only symbolic links.


OK, NOW THAT WE HAVE THESE FUNDAMENTALS HOW WOULD WE BE DOING WITH
libkleeRuntest library ?

The real name
=


Generate the library right from the build with the proper name:

libkleeRuntest.so.1.1

How would we do that ? We need to tell the linker how to create the
library file:

compilation flags to build your libkleeRuntest shared object lib:

-shared -fPIC -Wl,-soname,libkleeRuntest.so.1.1 -o libkleeRuntest.so.1.1

These flags need to go in the makefile that drives the build of the library.

This will build the properly-named lib file: libkleeRuntest.so.1.1.

You can check that by running this command:

readelf -d libkleeRuntest.so.1.1

will output something like:
Dynamic section at offset 0xb8c0 contains 26 entries:
   TagType Name/Value
  0x0001 (NEEDED) Shared library: [libgcc_s.so.1]
  0x0001 (NEEDED) Shared library: [libc.so.6]
  0x000e (SONAME) Library soname: [libkleeRuntest.so.1]
  0x000c (INIT)   0x4e68
  0x000d (FINI)   0x965c

As you can see, the SONAME is correctly mentioned now.

This is all we need to make real-world UNIX-based libs.

Now, we still need the symbolic links, and this is your debian
packager duty. How is this implemented in Debian and Debian-based
systems ?

When packaging libraries, we always start from a source package that
somehow only ships the original source tarball plus methods to build
the binary packages.

A random user will only want binary packages because she would not
even know what to do with a source package.

The software will be shipped as source in the debian source package
named libkleeruntest.

This source package will contain an attached archive file containing a
debian/ directory plus all of its contents.

In the debian/* files, we document how to process the source package
to actually build binary packages.

For each source package that contains a library (or set of libraries,
as is your case) we need to produce two different binary packages:

libkleeruntest1, which is the binary package that a user will have to
install if she ever needs to install a package that makes use of that
library. This package only contains the REAL-NAME file and the
SONAME-to-REAL-NAME symbolic link.

libkleeruntest-dev, which is the binary package that ships all the
files needed for the use of the library from a development
perspective. That is the package where the /usr/include/*.h[pp] files
are shipped. We also ship the second LINKER-NAME-to-REAL-NAME symbolic
link. In most cases, the -dev package is not versioned: it is
typically the last version of the library which in turn depends on the
other binary package of the same version, that of course ships the
real library file.

Hope this helps.

I tried to ./configure  the package, but I am missing a library on
this system and I cannot install it. If you cannot succeed with the
explanations above, send the makefile's (there are some, I saw) and
I'll try to see if I can help.

Ciao
Filippo

--
Filippo Rusconi, PhD - public crypto key 7694CF42@ pgp.mit.edu


pgpjehWCHZSLo.pgp
Description: PGP signature

Accepted openms 2.0.0-3 (source amd64 all) into unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Mon, 18 Jan 2016 21:35:18 +0100
Source: openms
Binary: libopenms2.0 libopenms2.0-dbg libopenms-dev topp topp-dbg openms-common 
openms-doc openms
Architecture: source amd64 all
Version: 2.0.0-3
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libopenms-dev - library for LC/MS data management and analysis - dev files
 libopenms2.0 - library for LC/MS data management and analysis - runtime
 libopenms2.0-dbg - library for LC/MS data management and analysis - debugging 
symbol
 openms - package for LC/MS data management and analysis
 openms-common - package for LC/MS data management and analysis - shared data
 openms-doc - package for LC/MS data management and analysis - documentation
 topp   - set of programs implementing The OpenMS Proteomic Pipeline
 topp-dbg   - set of programs implementing The OpenMS Proteomic Pipeline - debu
Changes:
 openms (2.0.0-3) unstable; urgency=medium
 .
   * Ship the dynamically generated cmake files to the -dev package.
 .
   * Improve the build system patch to state that we prefer libboost shared
 objects.
 .
   * debian/rules: Packaging (debian/*.install files) now uses the material
 that has been installed with make install DESTDIR=debian/build after
 cmake call with -DCMAKE_INSTALL_PREFIX=/usr.
Checksums-Sha1:
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libopenms2.0-dbg_2.0.0-3_amd64.deb
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openms_2.0.0-3.debian.tar.xz
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libopenms-dev_2.0.0-3_amd64.deb
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libopenms2.0-dbg_2.0.0-3_amd64.deb
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libopenms2.0_2.0.0-3_amd64.deb
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openms-common_2.0.0-3_all.deb
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topp-dbg_2.0.0-3_amd64.deb
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topp_2.0.0-3_amd64.deb

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Accepted openms 2.0.0-2 (source amd64 all) into unstable, unstable

[Filippo Rusconi]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA256

Format: 1.8
Date: Thu, 14 Jan 2016 12:36:43 +0100
Source: openms
Binary: libopenms2.0 libopenms2.0-dbg libopenms-dev topp topp-dbg openms-common 
openms-doc openms
Architecture: source amd64 all
Version: 2.0.0-2
Distribution: unstable
Urgency: medium
Maintainer: The Debichem Group <debichem-de...@lists.alioth.debian.org>
Changed-By: Filippo Rusconi <lopi...@debian.org>
Description:
 libopenms-dev - library for LC/MS data management and analysis - dev files
 libopenms2.0 - library for LC/MS data management and analysis - runtime
 libopenms2.0-dbg - library for LC/MS data management and analysis - debugging 
symbol
 openms - package for LC/MS data management and analysis
 openms-common - package for LC/MS data management and analysis - shared data
 openms-doc - package for LC/MS data management and analysis - documentation
 topp   - set of programs implementing The OpenMS Proteomic Pipeline
 topp-dbg   - set of programs implementing The OpenMS Proteomic Pipeline - debu
Closes: 810356
Changes:
 openms (2.0.0-2) unstable; urgency=medium
 .
   * Ship the code examples to the openms-doc package. These examples are
 partially described in the documentation (html format) but having the
 whole code files is more interesting.
 .
   * d/control: add "Replaces: libopenms-1.11" to fix upgrade problem
 (Closes: #810356), thanks to Andreas Beckmann <a...@debian.org> for
 the report.
 .
   * Bump-up debian/compat to 9.
 .
   * debian/watch: use sf redirector.
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Files:
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