Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Mon, Mar 24, 2014 at 10:09:45PM -0400, Stephen Smith wrote: I believe I have solved these issues and expanded the content to a more meaningful manpage. I think the synopsis was close but made some edits and the same for the description. I added some examples and more info for the commands. I also fixed the documentation bit. Hopefully that works. Fun editing man pages! If you would have called `lintian -I -i` it would have told you that there were some minus signes inside the manpage where hyphens are expected. Since I was fixing syntactical issues before I did so for now as well. Just a recommendation to use lintian extensively the next time. The package is uploaded and will hopefully accepted soon since Thorsten did some license checking in advance. If you now became addicted to Debian packaging you might like to have a look into http://code.google.com/p/prottest3/ (which has some start of packaging here: Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/prottest/trunk/ and can be moved to Git as well for sure) since the usage of phyutility inside this tool was my initial motivation to dive into phyutility. Kind regards Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140325080104.gh16...@an3as.eu
RM: bowtie2 [i386 hurd-i386 kfreebsd-i386] -- ANAIS; new release does not build on architectures other than amd64
X-Debbugs-Cc: a...@biotec.tu-dresden.de Package: ftp.debian.org Severity: normal Dear FTP Masters, New upstream release of bowtie2 doesn't build on mentioned in the subject architectures. In order to force transition from unstable to testing could you please consider removal of packages in testing with non amd64 architectures ? Also even if we could provide i386 builds in the past, it seems that nobody is using it on i386 because normally it requires big amounts of memory. Thank you, Alex Note: this was a request for a partial removal from testing, converted in one for unstable -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/53318bb3.8000...@biotec.tu-dresden.de
Re: Please consider relicensing maxflow 3.0 as free software
Dear Gert, I have put it under GPL (see version 3.03 on my homepage). Regards, Vladimir. On 03/17/2014 04:03 PM, Gert Wollny wrote: Dear Prof. Kolmogorov, dear Prof. Boykov, I'm writing to you on behalf of the Debian Med team. Debian Med is a collaborative effort to include all Free Software with relevance to medicine into the official Debian distribution. Here you can see the section of our work you might be interested in: http://blends.debian.org/med/tasks/imaging As you can see we also explicitly mention the publications of the authors who have written the software in question. Currently, I'm working on packaging a software for Multivariate Bayesian Image Segmentation that makes use of your maxflow library. Initially, the author of this segmentation software tried to make use of version 2.21 that is redistributable under the terms of the GNU GPL. However, already for normal sized brain data sets the software crashed, a problem that does not occur with maxflow version 3.0. Consequently, the author continued developing with the latter implementation, and to include the segmentation software into Debian, maxflow-3.0 would also needed to be included. Now, to include software into the official Debian distribution it must follow the Debian Free Software Guidelines [1], which, in its essence, means the software must be freely redistributable and usable in source and binary form. Therefore, in order to be able to include maxflow 3.0 in the official Debian distribution, I would kindly like to ask you to consider relicensing it to one of the Debian approved licenses, for example by licensing it the same way version 2.21 was licensed. Many thanks, Gert Wollny [1] https://www.debian.org/social_contract#guidelines -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/533186ae.8030...@ist.ac.at
Re: Please consider relicensing maxflow 3.0 as free software
Dear Vladimir, that's a very cool and quick move. Many thanks for this Andreas. On Tue, Mar 25, 2014 at 02:37:50PM +0100, Vladimir Kolmogorov wrote: Dear Gert, I have put it under GPL (see version 3.03 on my homepage). Regards, Vladimir. On 03/17/2014 04:03 PM, Gert Wollny wrote: Dear Prof. Kolmogorov, dear Prof. Boykov, I'm writing to you on behalf of the Debian Med team. Debian Med is a collaborative effort to include all Free Software with relevance to medicine into the official Debian distribution. Here you can see the section of our work you might be interested in: http://blends.debian.org/med/tasks/imaging As you can see we also explicitly mention the publications of the authors who have written the software in question. Currently, I'm working on packaging a software for Multivariate Bayesian Image Segmentation that makes use of your maxflow library. Initially, the author of this segmentation software tried to make use of version 2.21 that is redistributable under the terms of the GNU GPL. However, already for normal sized brain data sets the software crashed, a problem that does not occur with maxflow version 3.0. Consequently, the author continued developing with the latter implementation, and to include the segmentation software into Debian, maxflow-3.0 would also needed to be included. Now, to include software into the official Debian distribution it must follow the Debian Free Software Guidelines [1], which, in its essence, means the software must be freely redistributable and usable in source and binary form. Therefore, in order to be able to include maxflow 3.0 in the official Debian distribution, I would kindly like to ask you to consider relicensing it to one of the Debian approved licenses, for example by licensing it the same way version 2.21 was licensed. Many thanks, Gert Wollny [1] https://www.debian.org/social_contract#guidelines -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/533186ae.8030...@ist.ac.at -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140325144719.ga11...@an3as.eu
RM: bowtie2 [i386 hurd-i386 kfreebsd-i386] -- ANAIS; new release does not build on architectures other than amd64
Package: ftp.debian.org Severity: normal Dear FTP Masters, New upstream release of bowtie2 doesn't build on mentioned in the subject architectures. In order to force transition from unstable to testing could you please consider removal of packages in testing with non amd64 architectures ? Also even if we could provide i386 builds in the past, it seems that nobody is using it on i386 because normally it requires big amounts of memory. Thank you, Alex Note: this was a request for a partial removal from testing, converted in one for unstable -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/53318ed2.4010...@biotec.tu-dresden.de
Re: Please consider relicensing maxflow 3.0 as free software
Dear Vladimir, thanks a lot, we really appreciate this. Now that packaging can go forward. Best regards, Gert Wollny On 03/25/14 14:37, Vladimir Kolmogorov wrote: Dear Gert, I have put it under GPL (see version 3.03 on my homepage). Regards, Vladimir. On 03/17/2014 04:03 PM, Gert Wollny wrote: Dear Prof. Kolmogorov, dear Prof. Boykov, I'm writing to you on behalf of the Debian Med team. Debian Med is a collaborative effort to include all Free Software with relevance to medicine into the official Debian distribution. Here you can see the section of our work you might be interested in: http://blends.debian.org/med/tasks/imaging As you can see we also explicitly mention the publications of the authors who have written the software in question. Currently, I'm working on packaging a software for Multivariate Bayesian Image Segmentation that makes use of your maxflow library. Initially, the author of this segmentation software tried to make use of version 2.21 that is redistributable under the terms of the GNU GPL. However, already for normal sized brain data sets the software crashed, a problem that does not occur with maxflow version 3.0. Consequently, the author continued developing with the latter implementation, and to include the segmentation software into Debian, maxflow-3.0 would also needed to be included. Now, to include software into the official Debian distribution it must follow the Debian Free Software Guidelines [1], which, in its essence, means the software must be freely redistributable and usable in source and binary form. Therefore, in order to be able to include maxflow 3.0 in the official Debian distribution, I would kindly like to ask you to consider relicensing it to one of the Debian approved licenses, for example by licensing it the same way version 2.21 was licensed. Many thanks, Gert Wollny [1] https://www.debian.org/social_contract#guidelines -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/533199ac.5070...@gmail.com
ITP: maxflow - a library implementing a minimum cut/maximum flow algorithm
Package: wnpp Severity: wishlist * Package name: maxflow Version : 3.03 Upstream Author : Vladimir Kolmogorov and Yuri Boykov * URL : http://pub.ist.ac.at/~vnk/software.html * License : GPL3+ Programming Lang: C++ Description : This library implements the maxflow algorithm. This library implements an efficient minimum cut/maximum flow algorithms on graphs that can be used for exact or approximate energy minimization in low-level vision. The algorithm provides a high performance that makes near real-time performance possible. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/5331a0c3.3050...@gmail.com
Re: [MoM] incorporating phyutility into the packages
Hi Andreas, If you would have called `lintian -I -i` it would have told you that there were some minus signes inside the manpage where hyphens are expected. Since I was fixing syntactical issues before I did so for now as well. Just a recommendation to use lintian extensively the next time. Ah, sorry, I missed that. Still new to that tool. Getting there though. The package is uploaded and will hopefully accepted soon since Thorsten did some license checking in advance. Excellent! If you now became addicted to Debian packaging you might like to have a look into http://code.google.com/p/prottest3/ (which has some start of packaging here: Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/prottest/trunk/ and can be moved to Git as well for sure) since the usage of phyutility inside this tool was my initial motivation to dive into phyutility. Sounds good. I will take that as the next project. I have some other tools that I would love to get in there that have more complex dependencies so it will be good to get more under the belt before then. I will go ahead and dive into this. Take care, Stephen -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140325172217.GM4101@localhost.localdomain
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Tue, Mar 25, 2014 at 01:22:19PM -0400, Stephen Smith wrote: If you would have called `lintian -I -i` it would have told you that there were some minus signes inside the manpage where hyphens are expected. Since I was fixing syntactical issues before I did so for now as well. Just a recommendation to use lintian extensively the next time. Ah, sorry, I missed that. Still new to that tool. Getting there though. No problem. You will learn that lintian is one of your best friends when trying to prepare policy conform packages. http://code.google.com/p/prottest3/ (which has some start of packaging here: Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/prottest/trunk/ and can be moved to Git as well for sure) since the usage of phyutility inside this tool was my initial motivation to dive into phyutility. Sounds good. I will take that as the next project. I just ralised that the latest version is not using phyutility any more (for whatever reason). Just package it if it is interesting for you. I have some other tools that I would love to get in there that have more complex dependencies so it will be good to get more under the belt before then. Just a warning: prottest has some other binary jars which are not yet packaged for Debian and it needs to be sorted out which one are needed and thus need to be packaged or whether some of them might be dropped. I will go ahead and dive into this. Feel free to tackle other projects of yours if you might notice that it is not as simple as expected and the packages of your own agenda might seem more urgent for your personal work. Kind regards and thanks for your work on phyutility Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140325173259.gc11...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
In that case, I might like to try some other packages. Might try this one (treePL divergence time analysis for phylogenies) published here http://www.ncbi.nlm.nih.gov/pubmed/22908216 but will think about it. Also, I see there is a list of packages for debian as a whole that need help, but is there one for med? I might see if there are orphaned things that would also be interesting. Take care, Stephen On Tue, Mar 25, 2014 at 06:32:59PM +0100, Andreas Tille wrote: Hi Stephen, On Tue, Mar 25, 2014 at 01:22:19PM -0400, Stephen Smith wrote: If you would have called `lintian -I -i` it would have told you that there were some minus signes inside the manpage where hyphens are expected. Since I was fixing syntactical issues before I did so for now as well. Just a recommendation to use lintian extensively the next time. Ah, sorry, I missed that. Still new to that tool. Getting there though. No problem. You will learn that lintian is one of your best friends when trying to prepare policy conform packages. http://code.google.com/p/prottest3/ (which has some start of packaging here: Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/prottest/trunk/ and can be moved to Git as well for sure) since the usage of phyutility inside this tool was my initial motivation to dive into phyutility. Sounds good. I will take that as the next project. I just ralised that the latest version is not using phyutility any more (for whatever reason). Just package it if it is interesting for you. I have some other tools that I would love to get in there that have more complex dependencies so it will be good to get more under the belt before then. Just a warning: prottest has some other binary jars which are not yet packaged for Debian and it needs to be sorted out which one are needed and thus need to be packaged or whether some of them might be dropped. I will go ahead and dive into this. Feel free to tackle other projects of yours if you might notice that it is not as simple as expected and the packages of your own agenda might seem more urgent for your personal work. Kind regards and thanks for your work on phyutility Andreas. -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140325173259.gc11...@an3as.eu -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140325174449.GO4101@localhost.localdomain
Re: [tryton] Re: [Health-dev] Exception when building the package in a cleanroom Debian environment
* Luis Falcon: [tryton] Re: [Health-dev] Exception when building the package in a cleanroom Debian environment (Mon, 24 Mar 2014 19:02:30 -0300): Hi Emilien, hi all, On Mon, 24 Mar 2014 21:35:40 +0100 Emilien Klein emilien+gnuhealth@klein.st wrote: Hi GNU Health team, The Debian package has to pass a number of automated tests to validate a minimal level of quality. One of these tools is called piuparts. When running piuparts on the latest version of the Debian package, an exception was thrown. I would need some help figuring out how to fix this. See the output of the entire build process here, the Traceback is at the end: https://piuparts.debian.org/sid/fail/gnuhealth-server_2.4.1-2.log Extract: [Fri Mar 14 03:40:49 2014] INFO:modules:ir:loading lang.xml [Fri Mar 14 03:40:49 2014] [7mERROR [0m:convert:Error while parsing xml file: In tag record: model ir.lang with id lang_ca. Traceback (most recent call last): [...] File /usr/lib/python2.7/dist-packages/trytond/backend/postgresql/database.py, line 309, in execute return self.cursor.execute(sql, params) UnicodeEncodeError: 'ascii' codec can't encode character u'\xe0' in position 5: ordinal not in range(128) Seems like there is some character with accents in the Canadian language model, which can't be encoded using ASCII. The file ir/lang.xml is part of the core of Tryton server. I'm copying the Tryton community. The language that is making reference with this tag is Català (from Catalonia) . Tryton deals fine with non-ascii characters in xml files without the need for encoding it (like Catalagrave;) on the xml file. You should get this traceback at Tryton server tests, before the actual check GNU Health modules are loaded. It seems like it has to do with something on the test environment, since both Tryton core and GNU Health modules load just fine. Thanks a lot for reporting and for your great job on packaging GNU Health and Tryton in Debian. Best, Any idea how to fix this? Thanks, +Emilien I can not provide actually a fix withotu digging further into the gnuhealth package, but just some hints: 1) tryton-server [1] is passing piuparts and basically this seems also to apply for gnuhealth-server [2]. The error seems to be caused by the gnuhealth package scripts or the tools it uses. 2) Looking at the logs [3] the error occurs in the run of db-config-common: populating database via scriptfile... [Fri Mar 14 03:40:32 2014] INFO:server:using /etc/gnuhealth/gnuhealth-server.conf as configuration file So I would suggest to search in that direction, looking for something changing the environment to cause this error. [1] https://piuparts.debian.org/testing2sid/source/t/tryton-server.html [2] https://piuparts.debian.org/sid/state-failed-testing.html#gnuhealth-server [3] https://piuparts.debian.org/sid/state-failed-testing.html#gnuhealth-server -- Mathias Behrle MBSolutions Gilgenmatten 10 A D-79114 Freiburg Tel: +49(761)471023 Fax: +49(761)4770816 http://m9s.biz UStIdNr: DE 142009020 PGP/GnuPG key availabable from any keyserver, ID: 0x8405BBF6 signature.asc Description: PGP signature
Re: [MoM] incorporating phyutility into the packages
Hi Stephen On Tue, Mar 25, 2014 at 01:44:52PM -0400, Stephen Smith wrote: In that case, I might like to try some other packages. Might try this one (treePL divergence time analysis for phylogenies) published here http://www.ncbi.nlm.nih.gov/pubmed/22908216 but will think about it. That's perfectly fine. As a maintainer you are free to package what you need for your own work since this keeps you the most engaged to maintain it properly and up to date. When looking at its dependencies[1] I see two projects that do not sound familiar. It seems you need to package these first, right? Also, I see there is a list of packages for debian as a whole that need help, but is there one for med? I might see if there are orphaned things that would also be interesting. I have no idea at what page you are looking but I think the best overview can be obtained from the Maintainer dashboard[2] perhaps by adding the Debian Med maintainers list as maintainer[3]. There is quite some work to do left for any interested person. :-) Any you can try to scratch your own itch on any of these things - perhaps by announcing here what you want to do since you as a newcomer might not have the right feeling who usually touches what, There is some kind of natural sharing of the tasks. My most urgent endless issue is the stupid license issue of the aida part in libcolt-java were I expressed my deep frustration last time here[4]. The issue could either resolved by convincing the authors to drop the most boring clause in their license (GPL but not for military use) or to switch colt to a more recent replacement (which should be the technically better solution but costs some effort). In the consequence we could move beast into main which would bring back my motivation to work on this package. Kind regards Andreas. [1] https://github.com/blackrim/treePL/tree/master/deps [2] http://udd.debian.org/dmd/ [3] http://udd.debian.org/dmd/?email1=debian-med-packaging%40lists.alioth.debian.orgemail2=email3=packages=ignpackages=#todo [4] http://lists.alioth.debian.org/pipermail/debian-med-packaging/2014-February/025141.html -- http://fam-tille.de -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of unsubscribe. Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20140325194526.ga19...@an3as.eu
