Bug#1076552: ITP: libxpertmass -- Mass spectrometry-oriented libraries
Package: wnpp Severity: wishlist Owner: Filippo Rusconi X-Debbugs-Cc: debian-devel@lists.debian.org, lopi...@debian.org * Package name: libxpertmass Version : 1.0.0 Upstream Contact: Filippo Rusconi * URL : BLOCKEDmsxpertsuite[.]org/BLOCKED * License : GPL Programming Lang: C++ Description: GUI and non-GUI libraries for mass spectrometry (development files) . The libXpertMass and the libXpertMassGui shared libraries are designed to enshrine the non-GUI and the GUI functionalities needed by the following two mass spectrometry projects: . * msXpertSuite/massXpert2; * msXpertSuite/mineXpert2. . libXpertMass contains abstractions for all the chemical entities required to fully characterize a polymer chemistry definition, as shown below: . * Isotope * IsotopicData * Formula * Monomer * Oligomer * Polymer * Modif * CrossLinker * CrossLink * Aqueous chemical reactions (cleavages, enzymatic and non-enzymatic) * Gas-phase chemical reactions (fragmentations, with a sophisticated grammar to describe complex fragmentation patterns) * Isotopic cluster modelling/calculations for any chemical entity representable by an element composition formula and a charge. . libXpertMassGui contains classes useful: . * to display and manage isotopic data, * to configure isotopic cluster calculations, * to configure mass peak shaping processes (GAUSSIAN and LORENTZIAN), * to configure network communications between massXpert2 and mineXpert2. Description : Mass spectrometry-oriented libraries -- ⢀⣴⠾⠻⢶⣦⠀ Filippo Rusconi, PhD ⣾⠁⢠⠒⠀⣿⡁ Researcher at CNRS ⢿⡄⠘⠷⠚⠋⠀ Debian Developer ⠈⠳⣄ BLOCKEDmsxpertsuite[.]orgBLOCKED http://www.debian.org book: https://secure-web.cisco.com/1UXOc5OF7dQkkLfrbik_zF02sKC5moBbiSWQhbIT07wR1gpFPsme-ax3YAt213f9QN-H8KXn-ChehdH2Yt0N-QVDcMjZyAr5X1y4YaB-8s8J1BkZaYUfs6bLz1xfI3j6iOCrfNuna1_xTVJGqA-x6lFG_DH1ZpSBrJYPZ5hdxcPCvInFrvNbWfYQZeZAhMlPqBpayD7mTECYUGYUP1vmgHr5lI7e8uJ11-g-ba567jx7GbdBO9EV7X_JggplZq4h1Wi7SLbjVpBxhbQ3kn1TxlY564rZFWeAfMcYjzshyTE8GPJuZl6RbRVJJNjHhAiyH9bRQenVnSihuTQ_8YV23dV-IFwFtc8-FSKzMrarUw0iPm0Wi18vIk_2zEuBlmRAYwhYw5STKggDtKDsWEEVI_dpWH86xuhCrUZc-J_Dy7ouilGgY7cqbgMKkDEvtA35H/https%3A%2F%2Fwww.lavoisier.fr%2Flivre%2Fchimie%2Fmanuel-de-spectrometrie-de-masse-a-l-usage-des-biochimistes%2Frusconi%2Fdescriptif-9782743013417%3Fcombien%3D1 http://books.google.fr/books?id=2NmguxmEI1sC&printsec=frontcover&dq=rusconi+f+lavoisier&hl=fr&sa=X&ei=nGGOUt2SH_Ly0gX0uIHoBQ&ved=0CDUQ6AEwAA#v=onepage&q&f=false Institut Diversité, Écologie et Évolution du Vivant Unité Génétique Quantitative et Évolution Plateforme PAPPSO Université Paris-Saclay, INRAE, UMR CNRS 8120, AgroParisTech 12, route 128, Bâtiment 680 91272 Gif-sur-Yvette France http://moulon.inrae.fr/ & http://pappso.inrae.fr/ Tel : +33 (0)1 69 33 23 54 Fax : +33 (0)1 69 33 23 40
Bug#217094: Ongoing efforts with packaging of GNU polyxmass
Package: wnpp Followup-For: Bug #217094 The packaging of the GNU polyxmass software suite for simulation and analysis of mass spectrometric data of (bio-)polymers has improved dramatically these last days. The packages are available from http://www.polyxmass.org/debian and are currently reviewed by a Debian Developer. Sincerely, Filippo Rusconi Author/Maintainer GNU polyxmass (www.polyxmass.org) -- System Information: Debian Release: 3.1 APT prefers testing APT policy: (500, 'testing') Architecture: i386 (i686) Kernel: Linux 2.6.8-fr8 Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
Re: Bug#550817: ITP: gitolite -- standalone, souped-up version of gitosis
Greetings Debianists, On Tue, Oct 13, 2009 at 11:50:37AM +0200, Gerfried Fuchs wrote: > > Hi! > > * Stefano Zacchiroli [2009-10-13 11:03:00 CEST]: > > What if one has no idea of what "gitosis" is? For such a person, the > > above description will be close to meaningless. I suggest expanding in a > > couple of words what gitosis is, turning the reference to it as > > something like "similar to gitosis". > > Let me repeat my response that I sent already to the bugreport: > > | Of course it isn't [the final version of the description]; it's just > | the short blurb that can be seen on the upstream website about it. > | Having a full fledged description at ITP stage means that one already > | started at working on the package - and given that an ITP is meant to > | be there so that we don't duplicate work and /personally/ the package > | description is something that I rather *not* think as first of when > | starting to work on a package sending out the ITP with something > | final package description is backwards, counter-productive and > | anachronistic to me. :) Well, I think that ITP bugs are *more* useful when the person reading the bug report can tell what the intended-to-be-packaged software does. Sometimes, when I go through ITP bug reports, I find myself thinking "Hmmm, that's interesting stuff, I'll have to check that from time to time" (I also happen to discover software I did not know of this way). However, I'll never think something like that if I cannot figure what the software does, and that's a pity. My two cents ! Cheers, Filippo -- Filippo Rusconi, PhD - CNRS - public key C78F687C Author of ``massXpert'' at http://www.massxpert.org signature.asc Description: Digital signature
Bug#553622: ITP: colorcode -- advanced clone of the MasterMind game
Package: wnpp Severity: wishlist Owner: Filippo Rusconi * Package name: colorcode Version : 0.5.5 Upstream Author : Dirk Laebisch * URL : http://colorcode.laebisch.com/ * License : GPL-3 Programming Lang: C++ Description : advanced clone of the MasterMind game ColorCode is an advanced MasterMind clone with lots of different game variants, from the very easy up to really challenging ones. You can combine any color count from 2-10 with any column count from 2-5 and allow or not pegs of the same color. Or you may select one of the 5 predefined levels of difficulty. ColorCode has also a rather intelligent built in MasterMind solver - so you can let the computer guess for you (nope, he's not cheating - really). -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Bug#579796: ITP: othman -- electronic Quran browser in Python
On Tue, May 04, 2010 at 08:25:33PM +, brian m. carlson wrote: > On Tue, May 04, 2010 at 09:39:02PM +0200, Frank Lin PIAT wrote: > > I wonder who many people use the word "Coran" for Qur'an in English. If > > this is quite frequent, you might want insert this synonym somewhere in > > the description. > > In my experience, it's either "Qur'an" or "Koran." I think Gunnar used > "Coran" because TTBOMK that's the term that's used in Spanish (except > with an accent: Corán). > Well, in fact, in French that is "Le Coran", with a 'C' and not a 'K'. In Italian that is "Il Corano". Interestingly , the word is always accompanied by the definite article in both languages, although I do not know if the article should be necessarily be capitalized. -- Best regards, Filippo -- Filippo Rusconi, PhD - CNRS - public key C78F687C Author of ``massXpert'' at http://www.massxpert.org -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20100504220556.gb4...@biophypfr
Bug#527141: ITP: lutefisk -- Software for the de novo interpretation of peptide CID spectra
Package: wnpp Severity: wishlist Owner: Filippo Rusconi -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 * Package name: lutefisk Version : 1.0.5 Upstream Author : Richard S. Johnson * URL : http://sourceforge.net/projects/lutefiskxp/ * License : GPL Programming Lang: C Description : Software for the de novo interpretation of peptide CID spectra Lutefisk performs a de novo interpreation of CID spectra, providing the user with a file containing all the possible sequence candidates corresponding to the CID data fed to the program. Lutefisk Copyright: 1995-1999 Richard S. Johnson This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. - -- System Information: Debian Release: 5.0 APT prefers testing APT policy: (500, 'testing') Architecture: i386 (i686) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iEYEARECAAYFAkoAnqcACgkQTTOs5MePaHy4jgCfb9ag80WvQznyS6a8OhXh4ZtY ZKYAn16BqJM89cPNBF4/BbCE2Vx30qLM =7RyS -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Bug#529399: ITP: cb2bib -- extract bibliographic references from various sources
Package: wnpp Severity: wishlist Owner: Filippo Rusconi -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 * Package name: cb2bib Version : 1.2.3 Upstream Author : Pere Constans * URL : http://www.molspaces.com/cb2bib/ * License : GPL Programming Lang: C++ Description : extract bibliographic references from various sources cb2bib is a program to extract bibliographic references from unformatted and non standard sources, like: - email alerts; - journal Web pages; - and most interestingly PDF files. . Output references are written to BibTeX-formatted files. Other features include: - article files can be linked and renamed by dragging them onto the cb2Bib window; - editing and browsing BibTeX files; - citing references, searching references and the full contents of the referenced documents; - inserting bibliographic metadata to documents; - writing short notes that interrelate several references. Thanks, Filippo Rusconi - -- System Information: Debian Release: 5.0 APT prefers stable APT policy: (500, 'stable') Architecture: i386 (i686) -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.9 (GNU/Linux) iEYEARECAAYFAkoSX+UACgkQTTOs5MePaHxSKQCfY9/fa88ylRLsiO2ygEuSvMdp MVYAn2RdfteLO+KVINPPsKGkcp/1eqgT =bBKb -END PGP SIGNATURE- -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org
Re: Contact copyright holder / ask for free software license
Greetings, On Thu, Oct 09, 2014 at 01:51:31AM +0200, Michael Ole Olsen wrote: Contacting copyright holder and asking them to release under GPL or such is not a bad idea. even if they say no they might consider it in the future. Even better, in my experience, if the mail introducing the problem is well conceived, the authors are generally favourable. Especially if they did not license their software at all. Recently it took me one single mail to go from a proprietary license state to a GPL3+ licensed state. I usually offer two licenses as examples, even providing a short explanation of the choice between "permissive" (BSD-3-clause) and "restrictive" (GPL3). All of this also applies to documentation (and is part of my experience). Usually, making authors switch from the almost automatic "All rights reserved" motto to GPL (or similar) is not unfeasible. Cheers, Filippo -- Filippo Rusconi, PhD - public crypto key 7694CF42@ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20141009085327.GC3136@licorne
Bug#768058: ITP: comet-ms -- Tandem mass spectrometry (MS/MS) search engine
Package: wnpp Severity: wishlist Owner: Filippo Rusconi * Package name: comet-ms Version : 2014022 Upstream Author : Michael R. Hoopmann and colleagues * URL : http://sourceforge.net/projects/comet-ms/ * License : Apache Programming Lang: C++ Description : Tandem mass spectrometry (MS/MS) search engine . Comet is an open source tandem mass spectrometry (MS/MS) sequence database search engine. It identifies peptides by searching MS/MS spectra against sequences present in protein sequence databases. . This package ships a binary that does MS/MS database searches. Supported input formats are mzXML, mzML, and ms2 files. Supported output formats are .out, SQT, and pepXML. -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20141104153412.1526.33537.report...@roma.lcp.u-psud.fr
Bug#690177: ITP: python-mzml -- mzML mass spectrometric data parsing
Package: wnpp Severity: wishlist Owner: Filippo Rusconi * Package name: python-mzml Version : 0.7.4 Upstream Author : Christian Fufezan * URL : http://pymzml.github.com/ * License : LGPL Programming Lang: Python Description : mzML mass spectrometric data parsing python-mzml is an extension to Python that offers: - easy access to mass spectrometry (MS) data that allows the rapid development of tools; - a very fast parser for mzML data, the standard in mass spectrometry data format; - a set of functions to compare or handle spectra. -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121010195059.7864.84967.report...@licorne.clio.u-psud.fr
Bug#691129: ITP: openms -- package for LC/MS data management and analysis
Package: wnpp
Severity: wishlist
Owner: Filippo Rusconi
* Package name: openms
Version : 1.9.0
Upstream Author : Oliver Kohlbacher
* URL : http://open-ms.sourceforge.net
* License : (Artistic)
Programming Lang: (C++)
Description : software suite for LC/MS data management and analysis
OpenMS is a library for LC/MS data management and analysis. OpenMS
offers an infrastructure for the development of mass
spectrometry-related software and powerful 2D and 3D visualization
solutions.
.
TOPP (the OpenMS proteomic pipeline) is a pipeline for the analysis
of HPLC/MS data. It consists of a set of numerous small applications
that can be chained together to create analysis pipelines tailored
for a specific problem.
.
This package is a metapackage that depends on the OpenMS libraries
and TOPP binaries.
Package: libopenms1.9
Architecture: any
Depends: Depends: ${shlibs:Depends}, ${misc:Depends}
Suggests: openms-doc
Description: library for LC/MS data management and analysis - runtime
OpenMS is a library for LC/MS data management and analysis. OpenMS
offers an infrastructure for the development of mass
spectrometry-related software and powerful 2D and 3D visualization
solutions.
.
OpenMS offers analyses for various quantitation protocols, including
label-free quantitation, SILAC, iTRAQ, SRM, SWATH…
.
It provides built-in algorithms for de-novo identification and
database search, as well as adapters to other state-of-the art tools
like X!Tandem, Mascot, OMSSA…
.
OpenMS supports the Proteomics Standard Initiative (PSI) formats for
MS data and supports easy integration of tools into workflow engines
like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept
and a unified parameter handling.
.
This package ships the non-graphical user interface library.
Package: libopenms-dev
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, libopenms1.9 ( = ${binary:Version})
Suggests: openms-doc
Description: library for LC/MS data management and analysis - dev files
OpenMS is a library for LC/MS data management and analysis. OpenMS
offers an infrastructure for the development of mass
spectrometry-related software and powerful 2D and 3D visualization
solutions.
.
OpenMS offers analyses for various quantitation protocols, including
label-free quantitation, SILAC, iTRAQ, SRM, SWATH…
.
It provides built-in algorithms for de-novo identification and
database search, as well as adapters to other state-of-the art tools
like X!Tandem, Mascot, OMSSA…
.
OpenMS supports the Proteomics Standard Initiative (PSI) formats for
MS data and supports easy integration of tools into workflow engines
like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept
and a unified parameter handling.
.
This package ships the non-graphical user interface library
development files.
Package: libopenmsgui1.9
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}, libopenms1.9 ( = ${binary:Version})
Suggests: openms-doc
Description: gui library for LC/MS data management and analysis - runtime
OpenMS is a library for LC/MS data management and analysis. OpenMS
offers an infrastructure for the development of mass
spectrometry-related software and powerful 2D and 3D visualization
solutions.
.
OpenMS offers analyses for various quantitation protocols, including
label-free quantitation, SILAC, iTRAQ, SRM, SWATH…
.
It provides built-in algorithms for de-novo identification and
database search, as well as adapters to other state-of-the art tools
like X!Tandem, Mascot, OMSSA…
.
OpenMS supports the Proteomics Standard Initiative (PSI) formats for
MS data and supports easy integration of tools into workflow engines
like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept
and a unified parameter handling.
.
This package ships thee graphical user interface (gui) library.
Package: libopenmsgui-dev
Architecture: any
Depends: Depends: ${shlibs:Depends}, ${misc:Depends}, libopenms-dev
Suggests: openms-doc
Description: gui library for LC/MS data management and analysis - dev files
OpenMS is a library for LC/MS data management and analysis. OpenMS
offers an infrastructure for the development of mass
spectrometry-related software and powerful 2D and 3D visualization
solutions.
.
OpenMS offers analyses for various quantitation protocols, including
label-free quantitation, SILAC, iTRAQ, SRM, SWATH…
.
It provides built-in algorithms for de-novo identification and
database search, as well as adapters to other state-of-the art tools
like X!Tandem, Mascot, OMSSA…
.
OpenMS supports the Proteomics Standard Initiative (PSI) formats for
MS data and supports easy integration of tools into workflow engines
like Knime, Galaxy, WS-Pgrade, and TOPPAS via the TOPPtools concept
and a unified parameter handling.
.
This package ships the graphical user interface (gui) library
development files..
Package: topp
Architecture
Bug#693044: ITP: proteowizard -- library to perform proteomics data analyses
Package: wnpp Severity: wishlist Owner: Filippo Rusconi * Package name: proteowizard Version : 3.0.4098 Upstream Author : Spielberg Family Center for Applied Proteomics * URL : http://proteowizard.sourceforge.net/ * License : Apache License Version 2.0 Programming Lang: C++ Description : library to perform proteomics data analyses ProteoWizard provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations. . The primary goal of ProteoWizard is to eliminate the existing barriers to proteomic software development so that researchers can focus on the development of new analytic approaches, rather than having to dedicate significant resources to mundane (if important) tasks, like reading data files. -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121112123826.15045.72228.report...@licorne.clio.u-psud.fr
Re: Bug#693998: ITP: linux-minidisc -- Free software for accessing NetMD and HiMD MiniDisc devices
On Fri, Nov 23, 2012 at 02:26:34PM +0100, John Paul Adrian Glaubitz wrote: > On Fri, Nov 23, 2012 at 09:02:18AM +0800, Paul Wise wrote: > > On Fri, Nov 23, 2012 at 3:16 AM, John Paul Adrian Glaubitz wrote: > > > > > * Package name: linux-minidisc > > > > Thats a strange name considering it builds and runs on MacOS, Windows, > > Linux, FreeBSD and Haiku. > > Yes, the name is indeed somewhat confusing in that regard. But when we > first came up with the project, we were initially only concerned about > Linux, so the name was obvious. Finding a good name for such a project > is complicated because of possible trademark violations. > > If you have a better idea, I'd be happy to hear it ;). minidisk-intercessor minidisk-accessor ??? Ciao Filippo -- Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20121123133635.GA16316@licorne
Debian logo svg file is not loadable in Inkscape
Greetings, Fellow Debianists, this is not actually a bug report but something that might concern us all as a matter of Free Software use inside the Debian project: The Debian logo file at http://www.debian.org/logos/openlogo.svg fails to load in the much-respected SVG-based graphics editor Inkscape (which I use daily and which works fine also for svg files not produced by itself). The error is this: $ inkscape openlogo.svg openlogo.svg:18: namespace warning : xmlns: URI &ns_svg; is not absolute xmlns="&ns_svg;" xmlns:xlink="&ns_xlink;" xmlns:a="http://ns.adobe.com/AdobeSV ^ openlogo.svg:22: namespace warning : xmlns: URI &ns_vars; is not absolute ^ openlogo.svg:25: namespace warning : xmlns: URI &ns_custom; is not absolute ^ Note that The Gimp seems to load the file just fine, although also with an error message: Execution error for procedure 'gimp-vectors-import-from-file': Failed to import paths from 'openlogo.svg': Error on line 17: Entity name 'ns_extend' is not known Also, Iceweasel seems to load the file fine since it displays correctly. While I'm no expert in XML stuff, I see in the following lines at the top of the file that the problems might relate to some Adobe-specific namespace rules (or extensions, or whatever): http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd"; [ http://ns.adobe.com/Flows/1.0/";> http://ns.adobe.com/Extensibility/1.0/";> http://ns.adobe.com/AdobeIllustrator/10.0/";> http://ns.adobe.com/Graphs/1.0/";> http://ns.adobe.com/Variables/1.0/";> http://ns.adobe.com/ImageReplacement/1.0/";> http://ns.adobe.com/SaveForWeb/1.0/";> http://ns.adobe.com/GenericCustomNamespace/1.0/";> http://ns.adobe.com/XPath/1.0/";> http://www.w3.org/2000/svg";> http://www.w3.org/1999/xlink";> ]> Because opening the file in The Gimp transforms the svg graphics object into a raster graphics object, the vector benefits of svg are lost and thus The Gimp cannot be used as a substitute of Inkscape. We may want to make sure that this file loads fine in Free Software graphics svg-based programs and maybe convert it to either a more generic svg file, or at least something free (Inkscape might be a good candidate for this). Any thoughts ? Cheers, Filippo -- Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org signature.asc Description: Digital signature
Re: Debian logo svg file is not loadable in Inkscape
Hello Chris, thanks for bothering :-) On Thu, Jan 24, 2013 at 04:51:43PM +0100, Christoph Anton Mitterer wrote: > On Thu, 2013-01-24 at 16:35 +0100, Filippo Rusconi wrote: > > fails to load in the much-respected SVG-based graphics editor Inkscape > > (which I use daily and which works fine also for svg files not > > produced by itself). > In mine it loads, version 0.48.3.1-1.3. $ inkscape --version Inkscape 0.48.3.1 r9886 (Dec 29 2012) $ dpkg -l inkscape ii inkscape 0.48.3.1-1.3 amd64 So, I would say this is odd. $ sha1sum openlogo.svg f958ec1c5eaf8c8507e6830852292081fca1 openlogo.svg could you confirm this on a file that you have wget http://www.debian.org/logos/openlogo.svg Thanks, Filippo -- Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130124160824.GE5622@licorne
Re: Debian logo svg file is not loadable in Inkscape
Hello Stefano, On Thu, Jan 24, 2013 at 04:53:44PM +0100, Stefano Zacchiroli wrote: > On Thu, Jan 24, 2013 at 04:35:23PM +0100, Filippo Rusconi wrote: > > We may want to make sure that this file loads fine in Free Software > > graphics svg-based programs and maybe convert it to either a more > > generic svg file, or at least something free (Inkscape might be a good > > candidate for this). > > Agreed. > > > Any thoughts ? > > How about "patches welcome"? :) This is not meant to be tongue-in-cheek, > but a very pragmatic suggestion. I'm no SVG expert either, but AFAICT > all the "source" info are indeed in that .svg file, it is "just" that > due to some minor syntactic issues (I speculate: due to the age of the > .svg in question) it doesn't work properly with current version of > popular FOSS SVG editors. Investigating a bit, I found that http://www.adobe.com/AdobeSVGViewerExtensions/3.0/ gives a 404 in my browser. This url is at line 18 of the file. Same for http://www.adobe.com/Extensibility/1.0/ > Let's "just" find SVG experts in our community and ask them to fix the > source code. Posting a call for help about this on -dekstop might > actually be a useful way forward. We certainly need some experts knowing what they do :-) By the way, is the author of this file known ? Maybe he/she could help? Cheers, Filippo -- Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130124161346.GF5622@licorne
Re: Debian logo svg file is not loadable in Inkscape
[ CC: debian-...@lists.debian.org ] Greetings Jakub, On Thu, Jan 24, 2013 at 06:17:37PM +0100, Jakub Wilk wrote: > * Jakub Wilk , 2013-01-24, 17:48: > >here's how to fix the SVG: > > > >1) apt-get install libxml2-utils sgml-data > >2) xmllint --noent openlogo.svg > openlogo-fixed.svg > >(Yes it's "noent", not to be confused with "nonet".) > >3) Optionally, remove the DTD declaration from the resulting file. > > The last two steps could be merged into one: > > xmllint --dropdtd --noent openlogo.svg > openlogo-fixed.svg > That did the trick ! Thanks a lot. In fact I had set out to remove the DTD manually, but my first attempts failed. I can see that the DTD specif went away in the fixed file. For what it's worth, there is still some adobe-specific metadata cruft that can be removed with no harm apparently: http://ns.adobe.com/Variables/1.0/";> http://ns.adobe.com/GenericCustomNamespace/1.0/"; xmlns:v="http://ns.adobe.com/Variables/1.0/"/> http://ns.adobe.com/SaveForWeb/1.0/";> Attached to this mail is a version saved with inkscape and edited to remove any reference to adobe. This new file loads fine in Inkscape, The Gimp, Iceweasel and... GNU Emacs! Maybe the folks at debian-...@lists.debian.org might want to give it a test and replace the old file with this one? Anyhow I now have my Debian logo for my slides! Thanks all for helping with this issue. Cheers, Filippo -- Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org <>
mention of a truncated file in a build log
G3Zr/openms-1.9.0/source/APPLICATIONS/TOPPBase.C:538:38: warning: ignoring return value of 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result [-Wunused-result] /usr/bin/cmake -E cmake_progress_report /build/buildd-openms_1.9.0-2-s390x-IYG3Zr/openms-1.9.0/debian/build/CMakeFiles >8 My question is: is there a way to trigger rebuilding of the whole software so as to establish if the failure is reproducible ? If the failure is reproduced, given that the software builds fine on amd64, would that possibly mean that there are problems with zandonai.debian.org at the hardware level? Any idea on that matter? Cheers, Filippo -- Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20130308092536.GA4889@licorne
Re: Bug#729660: ITP: xemacs21 -- highly customizable text editor
[[ Not CC'ing bugs because this mail is not about technical stuff ]] Greetings Fellow Debianists, On Sat, Nov 16, 2013 at 01:30:01PM +0100, John Paul Adrian Glaubitz wrote: > On 11/16/2013 01:10 PM, Mark Brown wrote: > >> Your first mail came with the argument that you think that > >> xemacs is more visually appealing than emacs. Honestly, emacs > >> is primarily a tool and not an optical gimmick. Visual > >> appearance does not bother most users, I'd guess. Most emacs > >> users use the terminal (-nw) mode anyway. > > > > Your assertations here both seem rather strong and unsupported, > > especially the idea that people don't use Emacs in graphical mode - it > > I have yet to see someone who does. I'm a long-time emacs user > and so are many of other developers I work together with and everyone > I know of who uses emacs as their primary editor doesn't use X11 > support, you just don't need it in most cases. emacs is powerful through > it's keyboard shortcuts and you are much more efficient and > faster when using them as opposed to navigating through the > menus with your mouse. How about knowing the shortcuts while having emacs running in a window? > > > would be enormously surprising to me if people had abandoned X11 support > > en masse. As for people not caring about the appearence... if you're > > going to be looking at something for the best part of the day it seems > > strange that you'd not be interested in how it looks, it's a factor in > > usability. > > Well, as I said, if you're really using emacs for what it's renown > for, you don't care about the X11 user interface and the looks > because you use non-windowed mode anyway. Come on, John Paul Adrian, how can you assert all these things? Did you do any survey? Do you really think that your few colleagues actually are a mirror of a whole community of people using software for doing lots of different things? I do use plain GNU Emacs with a grahical interface (that is, with X11, not in console mode) the whole day, for doing either LaTeX, C/C++, Python, Bash, XML, WhatEver stuff... How about letting Mark do his job as a Debian Developer and judge him on his abilities to fix things? I have absolutely no interest in defining if XEmacs is worth it in Debian or not. The usage count should somehow help us. Can we assume that Mark will show a responsible behaviour? Also, may I ask how what he is trying to do is so detrimental to the project that we feel like spending time chirping about it? Don't we have other interesting Debian-Project-related things to discuss about ? > As I explained before, the problem with such packages is that they > can introduce unnecessary (RC) bugs which may delay the release > during the freeze. I am aware of the fact that the release team has > addressed the issue by removing packages from testing now which > have had RC bugs longer than a certain time frame, but I think we should > avoid such situations in the first place. And the fact that a very > limited group of users is using XEmacs doesn't justify the hassle. If there are RC bugs for unused software, the software needs to be removed and thus does not go into stable. Period. If this removal work is done well before the freeze, better. Again, let Mark do his job and check the package in due time. > If someone is so keen to actually prefer XEmacs over emacs, they > can just download and build the package from source. Selfish vision, to my humble opinion. That way of thinking defeats the whole idea of having software to help people do what they want the way they want. > > > At the end of the day if you're not interested in a leaf package just > > ignore it, work on something you do care about instead. > > > > No, I do care about the whole of Debian and not just about my particular > packages and honestly, it bothers me to no end when I see packages which > have dozens or hundreds of bugs unanswered because no one is stepping > in to fix that. And I think Paul feels the same. I rather prefer to > have a package removed than it being full of bugs, no matter whether > it's a leaf package or not. Mark is indeed trying to fix the bugs, if I understand correctly. Let's assume he is a responsible and technically sound DD. Ciao Filippo -- Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20131116183915.GC4166@licorne
Bug#736536: ITP: libwildmagic -- libraries for mathematics, physics, numerical methods
Package: wnpp Severity: wishlist Owner: Filippo Rusconi * Package name: libwildmagic Version : 5.11 Upstream Author : Dave Eberly * URL : http://geometrictools.com/ * License : Boostv1.0 Programming Lang: C++ Description : libraries for mathematics, physics, numerical methods The WildMagic5 libraries are meant to help developers perform computing tasks in the following specialties: . - computer graphics; - mathematics; - physics; - numerical methods; - image analysis. . This package ships these libraries: . - The LibCore library contains some basic support that applications need. Some of this support is for convenience during development; - The LibMathematics library; - The LibGraphics library; - The LibPhysics library; - The LibApplications library. -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20140124183548.19294.5329.report...@roma.lcp.u-psud.fr
Re: Conflict between debian/upstream (DEP-12) & debian/upstream/ (uscan)
Greetings Fellow Developers, I would like to put here some words that I had in mind since I discovered the problem with the upstream file/dir in debian/. It is already a respectable while that we use the debian/upstream *file* for the documentation of bibliographic data in packages that might have articles published about the software packaged. I discovered recently that upstream was to become a directory in debian/. While I think that such a choice might be a reasonably good idea, I have to admit my astonishment at the total absence of information/discussion around that matter, from the side of the devscripts folks, as this choice fell us--designers and happy users of debian/upstream as a file totally out of the blue. On Mon, Feb 10, 2014 at 09:21:02AM +0100, Andreas Tille wrote: On Fri, Feb 07, 2014 at 08:07:41PM -0500, James McCoy wrote: On Fri, Feb 07, 2014 at 10:32:52AM +0100, Daniel Leidert wrote: > James McCoy wrote: > >Part of the reason I chose to use debian/upstream/ is that an extensible > >location for upstream related information (similar in spirit to > >debian/source/) could be useful. > > I've really wondered, why you didn't use debian/source/ for this purpose > and introduced another directory? Why not put the key used to sign the > upstream source right into debian/source/? debian/source/ is for content related to the source package. debian/upstream/ would be for content related to upstream. There's a distinct separation there and as the signing key is, IMO, obviously upstream metadata it's not appropriate for debian/source/. The only relation it has to the source package is that it's used to verify one component of the source package. I wonder whether you have further files in mind which should end up in debian/upstream/ dir. Could your please give some reasons why you dropped the previously used location, debian/upstream-signing-key.pgp, in favour of introducing a directory which even conflicts with some other file name which is discussed in a DEP-12 without minding any discussion. IMHO, it is simply not the right way to to a grab into the name space without dicussion and creating work for your fellow DDs by doing so. +1 If I could see any vision behind your change I would have no problem to follow this vision but even if I have some very slight sympathy from the "esthetics" of naming I consider the principle of "never change a running system" as way more important than some slight esthetical change specifically introduced without any coordination / discussion in the first place. +1 In short: If there is some big plan for a debian/upstream/ dir please lay it out for public discussion. Otherwise I'd be in favour of reverting the change in devscripts. +1 Happy hacking, Filippo -- Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20140210090235.GB4274@licorne
Bug#622972: ITP: qonjugator -- Qonjugator conjugates verbs in different languages
Package: wnpp Severity: wishlist Owner: Filippo Rusconi * Package name: qonjugator Version : 0.17 Upstream Author : Glad Deschrijver * URL : http://qt-apps.org/content/show.php/Qonjugator?content=112575 * License : GPL Programming Lang: C++ Description : Qonjugator conjugates verbs in different languages The program allows one to conjugate verbs in a number of languages. The architecture of the software is plugin-based so that conjugation rules for new languages can be added with new plugins. . The software is made of the following components: - a library which loads the conjugation plugins for the different languages and which does the actual conjugation; - a GUI in which the user can conjugate verbs, the GUI uses the library; - a command-line interface; - modules for French, Spanish and Italian; - a plasmoid that can be used in KDE 4.x or later; - a QML application. -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/20110416095526.4762.22359.report...@licorne.clio.u-psud.fr
Re: packaging-dev meta package
Greetings, On Thu, May 26, 2011 at 02:14:28PM -0700, Russ Allbery wrote: > > Mackenzie Morgan writes: > > On Thu, May 26, 2011 at 4:49 PM, Benjamin Drung wrote: > > >> Recommends or Suggests: > >> cdbs > >> cmake > ... > > so coming across packages still using it will be common for a while. > > CMake is a corollary to autoconf and heavily used in KDE-land, which > > seems like a not-insignificant number of packages. > > It's a not-insigificant number of packages, but I think it's a lot fewer > in terms of number of developers, since I've never seen CMake used outside > of KDE-land. Many users of cmake are indeed KDE devs, but cmake is also used a lot in projects that use Qt only (massXpert is one example, but there are many). Ciao -- Filippo Rusconi, PhD - public crypto key C78F687C @ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org signature.asc Description: Digital signature
Re: delete my resume in your web site
Greetings, On Wed, Dec 03, 2014 at 02:48:33AM +, Jenny zhou wrote: HI, I requested many time. but my resume is still on your web site. Can you help me to delete that? https://lists.debian.org/debian-devel/2004/07/doc_9rK_X0lC5.doc I do not see how/why this would not be possible. However, you might try explaining us first how this file landed in our servers. If that was through a mail sent to one of our mailing lists, then you might provide us with a pointer to that post. Also, you might explain why we should think that you are the person owning that resume (your present email address differs from that of the file; is Yingwei somehow synonym for Jenny?). Fundamentally: are you entitled to ask for that file removal? The questions above might explain why nothing happened to date, even if you have asked "many time" to remove that file for our servers. Thank you, Filippo -- Filippo Rusconi, PhD - public crypto key 7694CF42@ pgp.mit.edu Researcher at CNRS and Debian Developer Author of ``massXpert'' at http://www.massxpert.org -- To UNSUBSCRIBE, email to debian-devel-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20141203144741.GA1995@licorne
Re: I resigned in 2004
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
Re: Opt-in to continue as DD/DM? (was: I resigned in 2004)
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
Bug#916218: ITP: isospec -- Isotopic fine structure calculator
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
Bug#919624: ITP: daps -- DocBook-based authoring and publishing system
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
Re: Package name discord ITP: discord a modern voice & text chat app
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: Questionable Package Present in Debian: fortune-mod
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: NEW queue almost empty
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: looking for debian friendly web app technology
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 signature.asc Description: PGP signature
dh_auto_test fails and I do not understand why
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: dh_auto_test fails and I do not understand why
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
signature.asc
Description: PGP signature
Re: GPL for package under MIT license upstream; repack?
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
Bug#961085: ITP: toppic -- Top-down proteoform identification and characterization
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
Bug#961805: ITP: libcustompwiz -- Library to load mzML/mzXML files (dev files)
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
Re: Pybliographer
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
Re: Next attempt to add Blends to Debian installer
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
Re: ISO download difficult (was: Debian Stretch new user report (vs Linux Mint))
On Fri, Dec 01, 2017 at 05:10:37PM +0100, W. Martin Borgert wrote: Quoting Andrey Rahmatullin : 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 ⢿⡄⠘⠷⠚⠋ ⠈⠳⣄
Bug#883538: ITP: libmsnumpress -- numerical compression in mass spectrometry data
Package: wnpp Severity: wishlist Owner: Filippo Rusconi * Package name: libmsnumpress Version : 1.0.0 Upstream Author : Johan Teleman et al * 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.
Re: Adding SONAME to a shared object in KLEE
libQtSvg.so.4 NEEDED 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
