Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Tue, Apr 08, 2014 at 10:19:07PM -0400, Stephen Smith wrote: > Hi Thorsten > No, libmatrixExp.so isn't used for anything here. Is there a way to > remove that in the debian package or do I need to do it in the original > phyutilty and push a new version? There is the option to use "Files-Excluded" with uscan from latest devscripts. However, if I would be in your shoes I would simply remove this from the upstream source since there is no real point in carrying unneeded binary data in there. You might ask ftpmaster whether they accept this if you promise that there will be a new release soon without this file. :-) Thanks for the clarification Andreas. > On Tue, Apr 01, 2014 at 02:55:44PM +0200, Thorsten Alteholz wrote: > > Hi Stephen, > > > > lintian tells me something about: > > W: phyutility: incompatible-java-bytecode-format Java7 version (Class > > format: 51 > > I am not a Java expert, but wouldn't this make the package unusable on > > standard Debian? > > > > Do you need src/jade/lib/libmatrixExp.so for anything? > > > >Thorsten > > > > > > -- > > 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/pine.lnx.4.64.1404011451530.29...@tor.gallien.in-chemnitz.de > > > > -- > Dr. Stephen A. Smith > http://blackrim.org > Assistant Professor, Dept. Ecology and Evolutionary Biology > University of Michigan > 2071A Kraus Natural Science Building > 830 North University > Ann Arbor, MI 48109-1048 > > > -- > 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/20140409021905.GE4009@localhost.localdomain > > -- 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/20140409061206.ga28...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Thorsten No, libmatrixExp.so isn't used for anything here. Is there a way to remove that in the debian package or do I need to do it in the original phyutilty and push a new version? Take care, Stephen On Tue, Apr 01, 2014 at 02:55:44PM +0200, Thorsten Alteholz wrote: > Hi Stephen, > > lintian tells me something about: > W: phyutility: incompatible-java-bytecode-format Java7 version (Class > format: 51 > I am not a Java expert, but wouldn't this make the package unusable on > standard Debian? > > Do you need src/jade/lib/libmatrixExp.so for anything? > >Thorsten > > > -- > 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/pine.lnx.4.64.1404011451530.29...@tor.gallien.in-chemnitz.de > -- Dr. Stephen A. Smith http://blackrim.org Assistant Professor, Dept. Ecology and Evolutionary Biology University of Michigan 2071A Kraus Natural Science Building 830 North University Ann Arbor, MI 48109-1048 -- 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/20140409021905.GE4009@localhost.localdomain
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, I guess Thorsten was asking this question wearing his ftpmaster hat. Any comment to his question? Kind regards Andreas. On Tue, Apr 01, 2014 at 02:55:44PM +0200, Thorsten Alteholz wrote: > Hi Stephen, > > lintian tells me something about: > W: phyutility: incompatible-java-bytecode-format Java7 version (Class > format: 51 > I am not a Java expert, but wouldn't this make the package unusable > on standard Debian? > > Do you need src/jade/lib/libmatrixExp.so for anything? > >Thorsten > > > -- > 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/pine.lnx.4.64.1404011451530.29...@tor.gallien.in-chemnitz.de > > -- 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/20140404135401.gb27...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, lintian tells me something about: W: phyutility: incompatible-java-bytecode-format Java7 version (Class format: 51 I am not a Java expert, but wouldn't this make the package unusable on standard Debian? Do you need src/jade/lib/libmatrixExp.so for anything? Thorsten -- 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/pine.lnx.4.64.1404011451530.29...@tor.gallien.in-chemnitz.de
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.org&email2=&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
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: [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
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 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
Re: [MoM] incorporating phyutility into the packages
Hi Andreas, > So far for the syntactical things in the manpage, but there is some > missing content. The DESCRIPTION section is somehow suboptimal and you > are refering to "the documentation" - but where is this. At least not > in the package and thus a link would be helpful. Please also provide a > simple example since I'm not sure whether I've got the SYNOPSIS correct > (please also check this). The goal of the manpage should be to provide > some quick entry for users or some reminder how to use it after having > read the extensive docs without forcing them to reread the docs over and > over. > 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 the manpage is fixed I will upload the package. If you are unsure > about the syntax please just inject the content and remind me to check > again. > Excellent! > For future upstream versions I would like you to consider two things: > > 1. It might make sense to rely on the maintained jebl2 instead of > maintaining a private jebl (otherwise I's recommend to explain > your reasons for sticking to jebl in some README to let others > understand. > > 2. We try to provide unit tests as much as possible (see the current > discussion about reproducible science on the Debian Med mailing > list). These could be run at package build time and also later > using autopkgtest in an automated process. So if you could provide > such tests this would be really great (independently from the > Debian packaging for sure to let others profit from it as well) Will do. 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/20140325020943.GA8298@localhost.localdomain
Re: [MoM] incorporating phyutility into the packages
Hi Thorsten There were a number of others and they have been added to the copyright file. Thanks for the catch. Take care, Stephen On Sun, Mar 23, 2014 at 03:47:18PM +0100, Thorsten Alteholz wrote: > Hi Stephen, > > On Thu, 20 Mar 2014, Stephen Smith wrote: > > >Hopefully, yes! I have tracked down as best I can, all the authors of > >the original JEBL and the LGPL version that it was under. These have > >been added to the copyright. > > sorry for not being more verbose, the jebl directory was just one example. > There are more files that need to be added to debian/copyright: > src/phyutility/drb/WwdUtils.java <- Apache 2.0 > src/jade/data/TransitionPenaltyTable.java -> LGPL > (and maybe there are others) > > Thorsten > -- 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/20140325005244.GA4202@localhost.localdomain
Re: [MoM] incorporating phyutility into the packages
Hi Thorsten Ah! Sorry, missed those. Will add and look closer for any others. Take care, Stephen On Sun, Mar 23, 2014 at 03:47:18PM +0100, Thorsten Alteholz wrote: > Hi Stephen, > > On Thu, 20 Mar 2014, Stephen Smith wrote: > > >Hopefully, yes! I have tracked down as best I can, all the authors of > >the original JEBL and the LGPL version that it was under. These have > >been added to the copyright. > > sorry for not being more verbose, the jebl directory was just one example. > There are more files that need to be added to debian/copyright: > src/phyutility/drb/WwdUtils.java <- Apache 2.0 > src/jade/data/TransitionPenaltyTable.java -> LGPL > (and maybe there are others) > > Thorsten > -- 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/20140323221257.GE3819@localhost.localdomain
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Thu, 20 Mar 2014, Stephen Smith wrote: Hopefully, yes! I have tracked down as best I can, all the authors of the original JEBL and the LGPL version that it was under. These have been added to the copyright. sorry for not being more verbose, the jebl directory was just one example. There are more files that need to be added to debian/copyright: src/phyutility/drb/WwdUtils.java <- Apache 2.0 src/jade/data/TransitionPenaltyTable.java -> LGPL (and maybe there are others) Thorsten -- 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/pine.lnx.4.64.1403231415590.24...@tor.gallien.in-chemnitz.de
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Thu, Mar 20, 2014 at 10:05:16PM -0400, Stephen Smith wrote: > Hopefully, yes! I have tracked down as best I can, all the authors of > the original JEBL and the LGPL version that it was under. These have > been added to the copyright. Looks good to me. > The removal of the dep of jebl2 was pushed > and the adding of the bug number was done. So, I think that is it? Nearly. I stumbled upon the manpage where help2man did a bad job. Due to a bug it did a repeated output (which I deleted). You should also always call help2man with '--no-info' option since otherwise it appends a paragraph which directs to a texinfo manual which usually never exists. Help2man was also unable to detect the proper name of the program and in the NAME section it added "don't" as name. This is fixed. I did some more syntactical fixes since I could imagine that you might not be that used to manpage editing. As a hint for editing manpages: I'm usually using mc (MidnightCommander) and when pressing F3 on a manpage it is rendered like with man - so you can quickly check your edits. So far for the syntactical things in the manpage, but there is some missing content. The DESCRIPTION section is somehow suboptimal and you are refering to "the documentation" - but where is this. At least not in the package and thus a link would be helpful. Please also provide a simple example since I'm not sure whether I've got the SYNOPSIS correct (please also check this). The goal of the manpage should be to provide some quick entry for users or some reminder how to use it after having read the extensive docs without forcing them to reread the docs over and over. > Let > me know if there are additional things that need to be done or other > testing that I should do. If the manpage is fixed I will upload the package. If you are unsure about the syntax please just inject the content and remind me to check again. For future upstream versions I would like you to consider two things: 1. It might make sense to rely on the maintained jebl2 instead of maintaining a private jebl (otherwise I's recommend to explain your reasons for sticking to jebl in some README to let others understand. 2. We try to provide unit tests as much as possible (see the current discussion about reproducible science on the Debian Med mailing list). These could be run at package build time and also later using autopkgtest in an automated process. So if you could provide such tests this would be really great (independently from the Debian packaging for sure to let others profit from it as well) 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/20140321074810.gc18...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hopefully, yes! I have tracked down as best I can, all the authors of the original JEBL and the LGPL version that it was under. These have been added to the copyright. The removal of the dep of jebl2 was pushed and the adding of the bug number was done. So, I think that is it? Let me know if there are additional things that need to be done or other testing that I should do. Take care, Stephen On Thu, Mar 20, 2014 at 08:28:35PM +0100, Andreas Tille wrote: > Hi Stephen, > > ans news from phyutility packaging? > > Kind regards > > Andreas. > > On Mon, Mar 17, 2014 at 09:04:32AM +0100, Andreas Tille wrote: > > Hi Stephen, > > > > On Sun, Mar 16, 2014 at 10:49:40PM -0400, Stephen Smith wrote: > > > OK, I got the smtp worked out and the bug report got filed. Hopefully > > > things look ok. > > > > That's fine. Just a hint for the future: I usually use the > > short description (in this case > > > > simple analyses or modifications on both phylogenetic trees and data > > matrices > > > > in the initial menu (before the editor pops up) and at the end a verbose > > copy of the long description as it is in debian/control. This needs > > less typing and expresses more exactly what you intent to upload. > > > > BTW, If you as upstream think the description could be enhanced - may be > > you like to fiddle around with what I previously did. The short > > description (the line behind the keyword "Description: ") could be made > > a bit shorter but definitely not longer. > > > > > There was also the query about the copyright. Wondering > > > what I need to do there but happy to do what I need. > > > > I hope this was answered in my other mail. > > > > BTW, you can now replace the Xes in "Closes: #XX" by the actual > > bug number which will solve the lintian issue. Please try this and > > push the change to Git. > > > > 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/20140317080432.ge10...@an3as.eu > > > > > > -- > 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/20140320192835.gp14...@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/20140321020515.GB3837@localhost.localdomain
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, ans news from phyutility packaging? Kind regards Andreas. On Mon, Mar 17, 2014 at 09:04:32AM +0100, Andreas Tille wrote: > Hi Stephen, > > On Sun, Mar 16, 2014 at 10:49:40PM -0400, Stephen Smith wrote: > > OK, I got the smtp worked out and the bug report got filed. Hopefully > > things look ok. > > That's fine. Just a hint for the future: I usually use the > short description (in this case > > simple analyses or modifications on both phylogenetic trees and data > matrices > > in the initial menu (before the editor pops up) and at the end a verbose > copy of the long description as it is in debian/control. This needs > less typing and expresses more exactly what you intent to upload. > > BTW, If you as upstream think the description could be enhanced - may be > you like to fiddle around with what I previously did. The short > description (the line behind the keyword "Description: ") could be made > a bit shorter but definitely not longer. > > > There was also the query about the copyright. Wondering > > what I need to do there but happy to do what I need. > > I hope this was answered in my other mail. > > BTW, you can now replace the Xes in "Closes: #XX" by the actual > bug number which will solve the lintian issue. Please try this and > push the change to Git. > > 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/20140317080432.ge10...@an3as.eu > > -- 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/20140320192835.gp14...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Thorsten, On Mon, Mar 17, 2014 at 11:37:38AM +0100, Thorsten Alteholz wrote: > > >As for jebl being a separate package, it is a bit complicated. The original > >one is no longer maintained (http://sourceforge.net/projects/jebl/) though > >this older one is the one that is included in phyutility. Seems like those > >sources aren't even available anymore. There is an updated > >(https://code.google.com/p/jebl2/) one, but this is not the one used by > >phyutility. > > Oh, thats the answer I didn't expect. As there is a dependency on > libjebl2-java in debian/control I thought that your version of jebl > is just unused and could be removed from the source tarball (not the > original one but the one included in Debian). I guess the Build-Dependency of libjebl2-java was injected by me years ago and probably based on the wrong assumption that jebl2 would be a plug-in replacement for jebl. I do not remember really but I think when doing so I was trying to replace a prebuilded jebl.jar binary. 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/20140317111838.gg10...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Sun, 16 Mar 2014, Stephen Smith wrote: I would be happy to take a look at the copyright contents. However, I am a bit new to this so not exactly sure which bits are missing. In debian/copyright the maintainer must document the copyright holder and license of all files in the source tarball (wildcards are allowed). In your case I found files with license LGPL in the header, so those need to be added. On your website you say something about GPL2+ as license for phyutility, but in debian/copyright it is GPL3+. (http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/) to be dense, just not sure. Maybe Andreas or you could point me in the right direction and I can fix things. Aha, the copyright needs the jebl authors as well I am guessing? Yes, the authors and more important the license of their files. As for jebl being a separate package, it is a bit complicated. The original one is no longer maintained (http://sourceforge.net/projects/jebl/) though this older one is the one that is included in phyutility. Seems like those sources aren't even available anymore. There is an updated (https://code.google.com/p/jebl2/) one, but this is not the one used by phyutility. Oh, thats the answer I didn't expect. As there is a dependency on libjebl2-java in debian/control I thought that your version of jebl is just unused and could be removed from the source tarball (not the original one but the one included in Debian). So from phyutility's perspective, I am not sure it would be helpful to have jebl2 as a package. Again, new to this, so happy to do whatever is best. jebl2 is already available in Debian, so the question is whether you could use it in phyutility. If yes, you could repackage the sources and remove your copy of jebl. If not, you might create a libjebl1 package which might be useful for others (as there are no others sources available, you might create this from your package). Thorsten -- 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/pine.lnx.4.64.1403170931090.16...@tor.gallien.in-chemnitz.de
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Sun, Mar 16, 2014 at 10:49:40PM -0400, Stephen Smith wrote: > OK, I got the smtp worked out and the bug report got filed. Hopefully > things look ok. That's fine. Just a hint for the future: I usually use the short description (in this case simple analyses or modifications on both phylogenetic trees and data matrices in the initial menu (before the editor pops up) and at the end a verbose copy of the long description as it is in debian/control. This needs less typing and expresses more exactly what you intent to upload. BTW, If you as upstream think the description could be enhanced - may be you like to fiddle around with what I previously did. The short description (the line behind the keyword "Description: ") could be made a bit shorter but definitely not longer. > There was also the query about the copyright. Wondering > what I need to do there but happy to do what I need. I hope this was answered in my other mail. BTW, you can now replace the Xes in "Closes: #XX" by the actual bug number which will solve the lintian issue. Please try this and push the change to Git. 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/20140317080432.ge10...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Sun, Mar 16, 2014 at 10:38:44PM -0400, Stephen Smith wrote: > I would be happy to take a look at the copyright contents. However, I am > a bit new to this so not exactly sure which bits are missing. Not trying > to be dense, just not sure. The fact that Thorsten was talking about jebl might give (also me ... I overlooked this as well) a hint: You should mention third party software with their copyright as well. It seems Thorsten had a section Files: src/jebl/* in mind. > Maybe Andreas or you could point me in the > right direction and I can fix things. Aha, the copyright needs the jebl > authors as well I am guessing? Yes. May be there is other third party code included? > As for jebl being a separate package, it is a bit complicated. The original > one is no longer maintained (http://sourceforge.net/projects/jebl/) though > this older one is the one that is included in phyutility. Seems like those > sources aren't even available anymore. There is an updated > (https://code.google.com/p/jebl2/) one, but this is not the one used by > phyutility. Perhaps you might be able to shed some light into something which is also unclear to me (as the Uploader of jebl2). The jebl* library is used in some phylogeny related projects and I have picked the last maintained version. I hope(!) that it is this version which is used by all its rdependant packages: $ apt-cache rdepends libjebl2-java | grep -v med-bio libjebl2-java Reverse Depends: beast-mcmc spread-phy figtree I think I talked to the authors of these packages before to be sure but I do not exactly remember. At least the packages are building without problems against this library and from a quick look are working (and no bug reports so far but this is not a sure sign for low popcon software). > So from phyutility's perspective, I am not sure it would be > helpful to have jebl2 as a package. Again, new to this, so happy to do > whatever is best. Again repearing that I have no idea about jebl / jebl2: Could you imagine using jebl2 because this *is* maintained? Or are you continue maintaining this jebl code in phyutility. I'm just a bit suspicious since I personally would try to follow the maintained code (if possible) rather than conserving old code. It would be great if you would share your reasons. 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/20140317075245.gc10...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Andreas OK, I got the smtp worked out and the bug report got filed. Hopefully things look ok. There was also the query about the copyright. Wondering what I need to do there but happy to do what I need. Take care, Stephen On Sun, Mar 16, 2014 at 11:32:19AM +0100, Andreas Tille wrote: > Hi Stephen, > > On Sat, Mar 15, 2014 at 04:48:00PM -0400, Stephen Smith wrote: > > > Yup. Please note that I pushed another change to point to Git i nthe > > > Vcs URLs (I simply forgot this after the move from SVN to Git). > > > > Great! Got it. > > > > > Hmmm, I need to check why it is not yet rendered at the tasks page (but > > > should!). > > > > Hm, wondering if I did something wrong here. Obviously created the bug > > report but perhaps it didn't send? > > This was my suspicion as well since the usual delay between sending a > bug report and showing up in the BTS is less than 15min. > > > Do you think it best that I try again > > , making sure that it sends (I can modify smtp settings)? > > Probably your SMTP is broken. You might like to verify whether there > are files > > /tmp/reportbug.* > > remaining to save you from typing the stuff again. > > You can also send the mail using your usual mail program to > cont...@bugs.debian.org. However, it might make sense to fix your SMTP > since you most probably want to be able to use reportbug in your day to > day work (not only for ITPs). May be you also check your logfiles from > exim or whatever mail daemon you are using. > > 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/20140316103219.gc15...@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/20140317024939.GD3808@localhost.localdomain
Re: [MoM] incorporating phyutility into the packages
Hi Thorsten I would be happy to take a look at the copyright contents. However, I am a bit new to this so not exactly sure which bits are missing. Not trying to be dense, just not sure. Maybe Andreas or you could point me in the right direction and I can fix things. Aha, the copyright needs the jebl authors as well I am guessing? As for jebl being a separate package, it is a bit complicated. The original one is no longer maintained (http://sourceforge.net/projects/jebl/) though this older one is the one that is included in phyutility. Seems like those sources aren't even available anymore. There is an updated (https://code.google.com/p/jebl2/) one, but this is not the one used by phyutility. So from phyutility's perspective, I am not sure it would be helpful to have jebl2 as a package. Again, new to this, so happy to do whatever is best. Take care, Stephen On Sun, Mar 16, 2014 at 10:17:18PM +0100, Thorsten Alteholz wrote: > Hi Stephen, > > thanks to Andreas I learned today that I need to write more emails and that > phyutility is going to be uploaded soon. > Before this upload, can you please have a closer look at the (yet) > incomplete contents of debian/copyright. > Would it make sense to create a separate package from the included jebl > library? > > Thorsten > > > -- > 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/pine.lnx.4.64.1403162158340.12...@tor.gallien.in-chemnitz.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/20140317023842.GC3808@localhost.localdomain
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, thanks to Andreas I learned today that I need to write more emails and that phyutility is going to be uploaded soon. Before this upload, can you please have a closer look at the (yet) incomplete contents of debian/copyright. Would it make sense to create a separate package from the included jebl library? Thorsten -- 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/pine.lnx.4.64.1403162158340.12...@tor.gallien.in-chemnitz.de
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Sat, Mar 15, 2014 at 04:48:00PM -0400, Stephen Smith wrote: > > Yup. Please note that I pushed another change to point to Git i nthe > > Vcs URLs (I simply forgot this after the move from SVN to Git). > > Great! Got it. > > > Hmmm, I need to check why it is not yet rendered at the tasks page (but > > should!). > > Hm, wondering if I did something wrong here. Obviously created the bug > report but perhaps it didn't send? This was my suspicion as well since the usual delay between sending a bug report and showing up in the BTS is less than 15min. > Do you think it best that I try again > , making sure that it sends (I can modify smtp settings)? Probably your SMTP is broken. You might like to verify whether there are files /tmp/reportbug.* remaining to save you from typing the stuff again. You can also send the mail using your usual mail program to cont...@bugs.debian.org. However, it might make sense to fix your SMTP since you most probably want to be able to use reportbug in your day to day work (not only for ITPs). May be you also check your logfiles from exim or whatever mail daemon you are using. 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/20140316103219.gc15...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
> Yup. Please note that I pushed another change to point to Git i nthe > Vcs URLs (I simply forgot this after the move from SVN to Git). > Great! Got it. > > Hmmm, I need to check why it is not yet rendered at the tasks page (but > should!). Hm, wondering if I did something wrong here. Obviously created the bug report but perhaps it didn't send? Do you think it best that I try again , making sure that it sends (I can modify smtp settings)? 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/20140315204759.GA4217@localhost.localdomain
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Sat, Mar 15, 2014 at 07:28:01AM -0400, Stephen Smith wrote: > > > By take over do you mean just rerun dch --create -v 2.7.3 --package > > > phyutility? Or dch -i ? > > This one is done. Just did the --create. The result is exactly what I mean. > Waiting for the number and then will update the file. Yup. Please note that I pushed another change to point to Git i nthe Vcs URLs (I simply forgot this after the move from SVN to Git). > > to understand how to specify citations which is IMHO a nice service to > > upstream developers and scientists. > > Thanks for doing this! Hmmm, I need to check why it is not yet rendered at the tasks page (but should!). 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/20140315141711.ga15...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Wed, Mar 12, 2014 at 09:19:10PM -0400, Stephen Smith wrote: > > any news from your side? > > yeah, sorry about the bit of silence there. I got bogged down in some > work things. Anyway, back on track. :-) > > I noticed you have changed debian/compat but you will definitely get > > a lintian warning about the fact that debian/control remained at > > > > debhelper (>= 8) > > > > Can you confirm this? > > Aha, I missed that one. Fixed and committed. No problem, fix is OK. > > I noticed that you added your name to Uploaders. As I said please feel > > free to take over also the changelog - as said above the most easy way > > is to use `dch` (see manpage). > > By take over do you mean just rerun dch --create -v 2.7.3 --package > phyutility? Or dch -i ? Well, the result is that your ID is the changelog entry owner (instead of mine) and the time stamp is updated. There are a lot of options to dch and I do not know them all. The most important thing is the result once you are leaving the editor which is fired up by dch after some changes (in principle you can totally ignore dch and fire up the editor directly ... but for instance to get a proper time stamp dch does a nice job). I personally take over packages with dch -i and I also make sure that I reset the increases Debian version (which is another effect of `dch -i` back to the old version. When you do this you will see that also a new paragraph in this changelog section is created which represents the changes of "Andreas Tille". Feel free to delete this since the changelog of a new package should only read "Initial release" and nothing else and finally you want to do this initial release. > > > cme fix dpkg-copyright > > > > > > is your friend! > > > > What about this? > > I believe we are good here now. Committed. Basically. I made some nitpicking change in the copyright of the Files: debian/* section. I worked on these in 2012 and you in 2014 (even if you worked on the upstream code since 2007) > > Any question how to issue an ITP bug? > > > > Just let me know if something remains unclear. I could easily give > > more verboes hints if they are needed. > > I think the ITP bug is one that is getting me a little stuck. I > understand it is the Intent to Package bug, but can't seem to find how > to close it. If you could point me in the right direction, I think I > could get it. Well, you are opening it by reportbug --no-query-bts wnpp (the --no-query-bts option saves you some time if you know for certain that there is no such bug.) Than you are guided by some text based menu framework. Please do not forget to add the Debian Med team address (as in the debian/control file set as Maintainer) once you are asked whether this bug report should be sended to additional e-mail addresses. Once you sended this bug report you get a bug number. This is the number you should fill in where we currently have ? in the debian/changelog file. If you would have called lintian (did you do so actually??) it would have told you about a missing bug number which is exactly the ITP number (new-package-should-close-itp-bug). > > > Ahh, if there are any publications for phyutility available these > > > should be mentioned in debian/upstream/metadata. > > > > Feel free to just point me to a publication if existing and I provide a > > working metadata file. > > > > The publication is this: > Smith, S. A. and C. Dunn. 2008. Phyutility: a phyloinformatics utility > for trees, alignments, and molecular data. Bioinformatics. 24: 715-716. > pdf: http://blackrim.org/files/smithdunn2008.pdf OK, I added a debian/upstream/metadata file. One effect of injecting this will be that on the taskspage section for phyutility[1] the sitation will be added after the next regeneration cycle of the tasks pages (at latest in 24 hours). Please have a look at the file debian/upstream/metadata to understand how to specify citations which is IMHO a nice service to upstream developers and scientists. > I am also working on the manpage. I think I know what to do there, just > getting it together. I think everything should be set then. Fine. I think once the ITP bug is filed the package is ready for upload ... and this only after half of the MoM period! Thanks for your work on this Andreas. [1] http://blends.debian.org/med/tasks/bio#phyutility -- 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/20140313080141.gc...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Andreas Responses inline below > any news from your side? yeah, sorry about the bit of silence there. I got bogged down in some work things. Anyway, back on track. > On Thu, Mar 06, 2014 at 08:57:13AM +0100, Andreas Tille wrote: > > Further needed changes: > > > > - When I created the packaging debhelper compatibility level was 8 > > Please increade debian/compat to 9 (and adjust the debhelper version > > in debian/control) > > I noticed you have changed debian/compat but you will definitely get > a lintian warning about the fact that debian/control remained at > > debhelper (>= 8) > > Can you confirm this? Aha, I missed that one. Fixed and committed. > > - Please add yourself in debian/changelog and add your ID (same > > Name and e-mail as in debian/changelog) to Uploaders in d/control. > > The easiest way would be to use > > > > dch > > > > (see `man dch`) Feel free to drop my name from d/changelog it > > is fine if the entry is kept short and it remains in d/copyright. > > I noticed that you added your name to Uploaders. As I said please feel > free to take over also the changelog - as said above the most easy way > is to use `dch` (see manpage). By take over do you mean just rerun dch --create -v 2.7.3 --package phyutility? Or dch -i ? > > - Please update debian/copyright by adding your name to the > > debian/* section. You should also update the Format. Hint: > > > > cme fix dpkg-copyright > > > > is your friend! > > What about this? I believe we are good here now. Committed. > > - Finally you should write an ITP bug > > Any question how to issue an ITP bug? > > Just let me know if something remains unclear. I could easily give > more verboes hints if they are needed. I think the ITP bug is one that is getting me a little stuck. I understand it is the Intent to Package bug, but can't seem to find how to close it. If you could point me in the right direction, I think I could get it. > > Ahh, if there are any publications for phyutility available these > > should be mentioned in debian/upstream/metadata. > > Feel free to just point me to a publication if existing and I provide a > working metadata file. > The publication is this: Smith, S. A. and C. Dunn. 2008. Phyutility: a phyloinformatics utility for trees, alignments, and molecular data. Bioinformatics. 24: 715-716. pdf: http://blackrim.org/files/smithdunn2008.pdf I am also working on the manpage. I think I know what to do there, just getting it together. I think everything should be set then. Take care and thanks for the patience, 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/20140313011909.GA4269@localhost.localdomain
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, any news from your side? On Thu, Mar 06, 2014 at 08:57:13AM +0100, Andreas Tille wrote: > Further needed changes: > > - When I created the packaging debhelper compatibility level was 8 > Please increade debian/compat to 9 (and adjust the debhelper version > in debian/control) I noticed you have changed debian/compat but you will definitely get a lintian warning about the fact that debian/control remained at debhelper (>= 8) Can you confirm this? > - Please add yourself in debian/changelog and add your ID (same > Name and e-mail as in debian/changelog) to Uploaders in d/control. > The easiest way would be to use > > dch > > (see `man dch`) Feel free to drop my name from d/changelog it > is fine if the entry is kept short and it remains in d/copyright. I noticed that you added your name to Uploaders. As I said please feel free to take over also the changelog - as said above the most easy way is to use `dch` (see manpage). > - Please update debian/copyright by adding your name to the > debian/* section. You should also update the Format. Hint: > > cme fix dpkg-copyright > > is your friend! What about this? > - Finally you should write an ITP bug Any question how to issue an ITP bug? Just let me know if something remains unclear. I could easily give more verboes hints if they are needed. > Ahh, if there are any publications for phyutility available these > should be mentioned in debian/upstream/metadata. Feel free to just point me to a publication if existing and I provide a working metadata file. 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/20140312100703.gf12...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Good Evening Andreas: For this debian-med project, is it important where a git repository is kept for a particular package ? I would guess that as long as it is a public git resource it can be anywhere ? --Hiram -- 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/531830e1.2010...@soe.ucsc.edu
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Wed, Mar 05, 2014 at 09:28:39PM -0500, Stephen Smith wrote: > Hi Andreas, > Been playing around a lot more with pbuilder and the like and I believe I > have it right. For some reason my lintian call wasn't calling the location > of the changes files. Everything is getting put > in /var/cache/pbuilder/result/ but I do have a deb As I said I get the BUILDRESULT=../build-area and if you might prefer this it is probably easy to find the documentation how to do this (if not - as always - please do not hesitate to ask). > and things seem ok other > than a few things from lintian: > W: phyutility: new-package-should-close-itp-bug > W: phyutility: binary-without-manpage usr/bin/phyutility > Also, I should add a rule to put a simple shell file that installs with the > deb that calls to jar for easier use (like java -jar phyutility.jar). > Do you have a suggestion of what would be the best way to do that? :-) Since this *is* done you get the warning about binary-without-manpage. The script is originated from my first attempt to package and is (hidden) in debian/rules/bin. Please verify that it is carrying the best set of options you want your users to use. Moreover you might like to create a simple manpage which gives a short explanation. Usually help2man gives some reasonable skeleton for this. Further needed changes: - When I created the packaging debhelper compatibility level was 8 Please increade debian/compat to 9 (and adjust the debhelper version in debian/control) - Please add yourself in debian/changelog and add your ID (same Name and e-mail as in debian/changelog) to Uploaders in d/control. The easiest way would be to use dch (see `man dch`) Feel free to drop my name from d/changelog it is fine if the entry is kept short and it remains in d/copyright. - Please update debian/copyright by adding your name to the debian/* section. You should also update the Format. Hint: cme fix dpkg-copyright is your friend! - Finally you should write an ITP bug Ahh, if there are any publications for phyutility available these should be mentioned in debian/upstream/metadata. 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/20140306075713.gn...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Wed, Mar 05, 2014 at 04:53:33PM -0500, Stephen Smith wrote: > Thanks for all that info. I had definitely missed some of those. If you think something is missing in the policy document or should be enhanced to better fit a newcomers need any patch would be more than welcome. > I can definitely remove the jar from the package. I will just move to > taking the tag from uscan which doesn't have the jar. That has been updated > and pushed. Cool. I admit it is real fun to work together with an interested upstream developer since all those change requests are running really smoothly. > I have updated the watch, updated phyutility which now compiles just fine. I can confirm that it also builds for me now - that's great! > I: unmounting run/shm filesystem > I: unmounting proc filesystem > I: Current time: Wed Mar 5 16:51:18 EST 2014 > I: pbuilder-time-stamp: 1394056278 > -> Cleaning COW directory > forking: rm -rf /var/cache/pbuilder/build//cow.13278 > warning: "../phyutility_2.7.3-1_*.changes" cannot be processed. > warning: It is not a valid lab query and it is not an existing file. > gbp:error: Couldn't run '~/bin/git-pbuilder': ~/bin/git-pbuilder returned 2 > > I am going to investigate now (using basically your same setup that you > sent along last time but clearly something is up there). I will let you > know what I find. In your other mail you wrote that you solved this. It might be that I configured my setup to create the package in ../build-area and I do not even remember where to configure this but I'm sure it is easy to find in the docs. May be my script relies a bit on this location. 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/20140306073642.gm...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Andreas,
Been playing around a lot more with pbuilder and the like and I believe I
have it right. For some reason my lintian call wasn't calling the location
of the changes files. Everything is getting put
in /var/cache/pbuilder/result/ but I do have a deb and things seem ok other
than a few things from lintian:
W: phyutility: new-package-should-close-itp-bug
W: phyutility: binary-without-manpage usr/bin/phyutility
Also, I should add a rule to put a simple shell file that installs with the
deb that calls to jar for easier use (like java -jar phyutility.jar).
Do you have a suggestion of what would be the best way to do that?
Take care,
Stephen
On Wed, Mar 5, 2014 at 4:53 PM, Stephen Smith wrote:
> Hi Andreas,
> Thanks for all that info. I had definitely missed some of those.
>
> I can definitely remove the jar from the package. I will just move to
> taking the tag from uscan which doesn't have the jar. That has been updated
> and pushed.
>
> I have updated the watch, updated phyutility which now compiles just fine.
> Getting an error at the end of my git-buildpackage
> that looks like
>
> dpkg-gencontrol: warning: Depends field of package phyutility: unknown
> substitution variable ${shlibs:Depends}
> dpkg-gencontrol: warning: File::FcntlLock not available; using flock which
> is not NFS-safe
>dh_md5sums
>dh_builddeb
> dpkg-deb: building package `phyutility' in
> `../phyutility_2.7.3-1_amd64.deb'.
> dpkg-genchanges >../phyutility_2.7.3-1_amd64.changes
> dpkg-genchanges: including full source code in upload
> dpkg-source -i.git -I.git -i.git -I.git --after-build phyutility-2.7.3
> dpkg-buildpackage: full upload (original source is included)
> I: Copying back the cached apt archive contents
> I: unmounting dev/pts filesystem
> I: unmounting run/shm filesystem
> I: unmounting proc filesystem
> I: Current time: Wed Mar 5 16:51:18 EST 2014
> I: pbuilder-time-stamp: 1394056278
> -> Cleaning COW directory
> forking: rm -rf /var/cache/pbuilder/build//cow.13278
> warning: "../phyutility_2.7.3-1_*.changes" cannot be processed.
> warning: It is not a valid lab query and it is not an existing file.
> gbp:error: Couldn't run '~/bin/git-pbuilder': ~/bin/git-pbuilder returned 2
>
> I am going to investigate now (using basically your same setup that you
> sent along last time but clearly something is up there). I will let you
> know what I find.
>
> Take care,
> Stephen
>
>
> On Wed, Mar 5, 2014 at 3:53 PM, Andreas Tille wrote:
>
>> Hi Stephen,
>>
>> On Wed, Mar 05, 2014 at 03:39:44PM -0500, Stephen Smith wrote:
>> > Hi Andreas,
>> > I updated the changelog and committed and pushed after
>> > git import-orig --pristine-tar phyutility_2_7_1.tar.gz
>> >
>> > I haven't updated for uscan yet, but will do that in a bit. However,
>> > on git-buildpackage, I am still getting the old tar although it is
>> saying
>> > it is getting the newer one. If I actually grab
>> > the phyutility_2.7.1.orig.tar.gz, untar, and ant compile it is the
>> correct
>> > version (no bug in compilation). So I am sure I am still missing
>> something
>> > here. Any idea?
>>
>> Hmmm, as you might guess from my previous mail I simply pulled your last
>> changes and tried to build before reading this. Since I have no trouble
>> at all I can only wild-guess that you might not have followed the Debian
>> policy step by step regarding your setup for git-buildpackage. Just for
>> your comparison:
>>
>> $ cat ~/.gbp.conf
>> [DEFAULT]
>> builder = ~/bin/git-pbuilder
>>
>> # Might lead to problems because it tries to use non-patched makefiles
>> # cleaner = fakeroot debian/rules clean
>> cleaner = /bin/true
>> pristine-tar = True
>> export=WC
>>
>> [git-buildpackage]
>> # use this for more svn-buildpackage like behaviour:
>> export-dir = ../build-area/
>> tarball-dir = ../tarballs/
>>
>>
>>
>> my ~/bin/git-pbuilder looks basically like
>>
>>
>> /usr/bin/pdebuild --pbuilder cowbuilder --debbuildopts "-i\.git -I.git
>> $*" --debsign-k "Andreas Tille "
>> rm -f ../*_source.changes
>> lintian -i ../`dpkg-parsechangelog | awk '/^Source:/ {print
>> $2}'`_`dpkg-parsechangelog | awk '/^Version:/ {print $2}'`_*.changes
>>
>>
>> so you see I'm using cowbuilder which you need to prepare first via
>>
>>
>>sudo cowbuilder --create
>>
>>
>> May be these hints are helpful. Otherwise you need to provide more
>> information with complete copy-n-paste of the output you get.
>>
>> 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/20140305205311.gh16...@an3as.eu
>>
>>
>
Re: [MoM] incorporating phyutility into the packages
Hi Andreas,
Thanks for all that info. I had definitely missed some of those.
I can definitely remove the jar from the package. I will just move to
taking the tag from uscan which doesn't have the jar. That has been updated
and pushed.
I have updated the watch, updated phyutility which now compiles just fine.
Getting an error at the end of my git-buildpackage
that looks like
dpkg-gencontrol: warning: Depends field of package phyutility: unknown
substitution variable ${shlibs:Depends}
dpkg-gencontrol: warning: File::FcntlLock not available; using flock which
is not NFS-safe
dh_md5sums
dh_builddeb
dpkg-deb: building package `phyutility' in
`../phyutility_2.7.3-1_amd64.deb'.
dpkg-genchanges >../phyutility_2.7.3-1_amd64.changes
dpkg-genchanges: including full source code in upload
dpkg-source -i.git -I.git -i.git -I.git --after-build phyutility-2.7.3
dpkg-buildpackage: full upload (original source is included)
I: Copying back the cached apt archive contents
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: Current time: Wed Mar 5 16:51:18 EST 2014
I: pbuilder-time-stamp: 1394056278
-> Cleaning COW directory
forking: rm -rf /var/cache/pbuilder/build//cow.13278
warning: "../phyutility_2.7.3-1_*.changes" cannot be processed.
warning: It is not a valid lab query and it is not an existing file.
gbp:error: Couldn't run '~/bin/git-pbuilder': ~/bin/git-pbuilder returned 2
I am going to investigate now (using basically your same setup that you
sent along last time but clearly something is up there). I will let you
know what I find.
Take care,
Stephen
On Wed, Mar 5, 2014 at 3:53 PM, Andreas Tille wrote:
> Hi Stephen,
>
> On Wed, Mar 05, 2014 at 03:39:44PM -0500, Stephen Smith wrote:
> > Hi Andreas,
> > I updated the changelog and committed and pushed after
> > git import-orig --pristine-tar phyutility_2_7_1.tar.gz
> >
> > I haven't updated for uscan yet, but will do that in a bit. However,
> > on git-buildpackage, I am still getting the old tar although it is saying
> > it is getting the newer one. If I actually grab
> > the phyutility_2.7.1.orig.tar.gz, untar, and ant compile it is the
> correct
> > version (no bug in compilation). So I am sure I am still missing
> something
> > here. Any idea?
>
> Hmmm, as you might guess from my previous mail I simply pulled your last
> changes and tried to build before reading this. Since I have no trouble
> at all I can only wild-guess that you might not have followed the Debian
> policy step by step regarding your setup for git-buildpackage. Just for
> your comparison:
>
> $ cat ~/.gbp.conf
> [DEFAULT]
> builder = ~/bin/git-pbuilder
>
> # Might lead to problems because it tries to use non-patched makefiles
> # cleaner = fakeroot debian/rules clean
> cleaner = /bin/true
> pristine-tar = True
> export=WC
>
> [git-buildpackage]
> # use this for more svn-buildpackage like behaviour:
> export-dir = ../build-area/
> tarball-dir = ../tarballs/
>
>
>
> my ~/bin/git-pbuilder looks basically like
>
>
> /usr/bin/pdebuild --pbuilder cowbuilder --debbuildopts "-i\.git -I.git $*"
> --debsign-k "Andreas Tille "
> rm -f ../*_source.changes
> lintian -i ../`dpkg-parsechangelog | awk '/^Source:/ {print
> $2}'`_`dpkg-parsechangelog | awk '/^Version:/ {print $2}'`_*.changes
>
>
> so you see I'm using cowbuilder which you need to prepare first via
>
>
>sudo cowbuilder --create
>
>
> May be these hints are helpful. Otherwise you need to provide more
> information with complete copy-n-paste of the output you get.
>
> 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/20140305205311.gh16...@an3as.eu
>
>
Re: [MoM] incorporating phyutility into the packages
Hi Stephen,
On Wed, Mar 05, 2014 at 03:39:44PM -0500, Stephen Smith wrote:
> Hi Andreas,
> I updated the changelog and committed and pushed after
> git import-orig --pristine-tar phyutility_2_7_1.tar.gz
>
> I haven't updated for uscan yet, but will do that in a bit. However,
> on git-buildpackage, I am still getting the old tar although it is saying
> it is getting the newer one. If I actually grab
> the phyutility_2.7.1.orig.tar.gz, untar, and ant compile it is the correct
> version (no bug in compilation). So I am sure I am still missing something
> here. Any idea?
Hmmm, as you might guess from my previous mail I simply pulled your last
changes and tried to build before reading this. Since I have no trouble
at all I can only wild-guess that you might not have followed the Debian
policy step by step regarding your setup for git-buildpackage. Just for
your comparison:
$ cat ~/.gbp.conf
[DEFAULT]
builder = ~/bin/git-pbuilder
# Might lead to problems because it tries to use non-patched makefiles
# cleaner = fakeroot debian/rules clean
cleaner = /bin/true
pristine-tar = True
export=WC
[git-buildpackage]
# use this for more svn-buildpackage like behaviour:
export-dir = ../build-area/
tarball-dir = ../tarballs/
my ~/bin/git-pbuilder looks basically like
/usr/bin/pdebuild --pbuilder cowbuilder --debbuildopts "-i\.git -I.git $*"
--debsign-k "Andreas Tille "
rm -f ../*_source.changes
lintian -i ../`dpkg-parsechangelog | awk '/^Source:/ {print
$2}'`_`dpkg-parsechangelog | awk '/^Version:/ {print $2}'`_*.changes
so you see I'm using cowbuilder which you need to prepare first via
sudo cowbuilder --create
May be these hints are helpful. Otherwise you need to provide more
information with complete copy-n-paste of the output you get.
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/20140305205311.gh16...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Stephen,
On Tue, Mar 04, 2014 at 10:54:49PM -0500, Stephen Smith wrote:
> Hi again,
> OK, I believe I have fixed the code in phyutility (in the source repo not
> the debian repo). Also, in noticing that code.google doesn't allow
> downloads anymore, I moved it to github and added the new release. Now, it
> seems I need to update the package but having some difficulty in the steps
> for this. I have tried git-import-orig with the new tar as well as
> git-import-orig --pristine-tar as well as pristine tar alone and it still
> seems to grab the older tar when doing git-buildpackage. What am I missing?
I have checked your last commits and it seems to become better but not
finished yet:
compile:
[mkdir] Created dir: /tmp/buildd/phyutility-2.7.1/build/classes
[javac] /tmp/buildd/phyutility-2.7.1/build.xml:7: warning:
'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to
false for repeatable builds
[javac] Compiling 520 source files to
/tmp/buildd/phyutility-2.7.1/build/classes
[javac]
/tmp/buildd/phyutility-2.7.1/src/jebl/gui/trees/treeviewer_dev/TreePane.java:495:
error: reference to Painter is ambiguous, both interface javax.swing.Painter
in javax.swing and interface jebl.gui.trees.treeviewer_dev.painters.Painter in
jebl.gui.trees.treeviewer_dev.painters match
[javac] public void setScaleBarPainter(Painter
scaleBarPainter) {
[javac]^
[javac]
/tmp/buildd/phyutility-2.7.1/src/jebl/gui/trees/treeviewer_dev/TreePane.java:508:
error: reference to Painter is ambiguous, both interface javax.swing.Painter
in javax.swing and interface jebl.gui.trees.treeviewer_dev.painters.Painter in
jebl.gui.trees.treeviewer_dev.painters match
[javac] public Painter getScaleBarPainter() {
[javac]^
...
Any idea what might be missing here?
Moreover, I wonder whether you as upstream maintainer could not simply
drop the *.jar file from the source archive. We need to rebuild it
anyway and it simply bloats the archive.
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/20140305204109.gg16...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Andreas, I updated the changelog and committed and pushed after git import-orig --pristine-tar phyutility_2_7_1.tar.gz I haven't updated for uscan yet, but will do that in a bit. However, on git-buildpackage, I am still getting the old tar although it is saying it is getting the newer one. If I actually grab the phyutility_2.7.1.orig.tar.gz, untar, and ant compile it is the correct version (no bug in compilation). So I am sure I am still missing something here. Any idea? Take care, Stephen On Wed, Mar 5, 2014 at 1:57 AM, Andreas Tille wrote: > Hi Stephen, > > On Tue, Mar 04, 2014 at 10:54:49PM -0500, Stephen Smith wrote: > > Hi again, > > great to see your progress while I was sleeping. ;-) > > > OK, I believe I have fixed the code in phyutility (in the source repo not > > the debian repo). Also, in noticing that code.google doesn't allow > > downloads anymore, I moved it to github and added the new release. > > Could you please adapt the debian/watch file to reflect the new location? > > > Now, it > > seems I need to update the package but having some difficulty in the > steps > > for this. I have tried git-import-orig with the new tar as well as > > git-import-orig --pristine-tar as well as pristine tar alone and it still > > seems to grab the older tar when doing git-buildpackage. What am I > missing? > > Did you adjusted the version in d/changelog (as I also did in > > commit 9040368bb9374142c884bc1ba72b6d53c07fb4e5 > > )? If this is not the problem please send a full log and as always do > not hesitate to push your changes. > > Kind regards > > Andreas. > > PS: The policy on Debian lists is to not CC the poster of a mail - just > use the mailing list as To (except if the poster explicitly asks for > beeing CCed since he is not subscribed. It is no real problem for > me personally but MoM includes teaching how to behave correctly in > the Debian universe and you might get unfriendly answers if you do > not respect this somewhere else on one hand and on the other hand you > might miss answers if you are posting to a list where you are not > subscribed if you are not aware that you will not be CCed. > > -- > 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/20140305065716.ga...@an3as.eu > >
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Tue, Mar 04, 2014 at 10:54:49PM -0500, Stephen Smith wrote: > Hi again, great to see your progress while I was sleeping. ;-) > OK, I believe I have fixed the code in phyutility (in the source repo not > the debian repo). Also, in noticing that code.google doesn't allow > downloads anymore, I moved it to github and added the new release. Could you please adapt the debian/watch file to reflect the new location? > Now, it > seems I need to update the package but having some difficulty in the steps > for this. I have tried git-import-orig with the new tar as well as > git-import-orig --pristine-tar as well as pristine tar alone and it still > seems to grab the older tar when doing git-buildpackage. What am I missing? Did you adjusted the version in d/changelog (as I also did in commit 9040368bb9374142c884bc1ba72b6d53c07fb4e5 )? If this is not the problem please send a full log and as always do not hesitate to push your changes. Kind regards Andreas. PS: The policy on Debian lists is to not CC the poster of a mail - just use the mailing list as To (except if the poster explicitly asks for beeing CCed since he is not subscribed. It is no real problem for me personally but MoM includes teaching how to behave correctly in the Debian universe and you might get unfriendly answers if you do not respect this somewhere else on one hand and on the other hand you might miss answers if you are posting to a list where you are not subscribed if you are not aware that you will not be CCed. -- 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/20140305065716.ga...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi again, OK, I believe I have fixed the code in phyutility (in the source repo not the debian repo). Also, in noticing that code.google doesn't allow downloads anymore, I moved it to github and added the new release. Now, it seems I need to update the package but having some difficulty in the steps for this. I have tried git-import-orig with the new tar as well as git-import-orig --pristine-tar as well as pristine tar alone and it still seems to grab the older tar when doing git-buildpackage. What am I missing? Thanks Stephen On Tue, Mar 4, 2014 at 7:46 PM, Stephen Smith wrote: > Sorry, spoke too soon. I noted the missing dependencies there. Once > installed, it gets further and then fails at compile with > [javac] > phyutility/src/jebl/gui/trees/treeviewer_dev/TreePane.java:495: error: > reference to Painter is ambiguous, both interface javax.swing.Painter in > javax.swing and interface jebl.gui.trees.treeviewer_dev.painters.Painter in > jebl.gui.trees.treeviewer_dev.painters match > > BUNCH OF STUFF AND THEN > > BUILD FAILED > phyutility/build.xml:7: Compile failed; see the compiler error output for > details. > > Total time: 8 seconds > make[1]: *** [override_dh_auto_build] Error 1 > make[1]: Leaving directory `phyutility' > make: *** [build] Error 2 > dpkg-buildpackage: error: debian/rules build gave error exit status 2 > debuild: fatal error at line 1364: > dpkg-buildpackage -rfakeroot -D -us -uc -i -I failed > gbp:error: Couldn't run 'debuild -i -I': debuild -i -I returned 29 > > Does that look more like it? If so, seems like the solution is me fixing > the phyutility code and then bringing it back in, correct? (At least since > I am the developer of phyutility this seems like the easiest thing). > > Take care, > Stephen > > > On Tue, Mar 4, 2014 at 7:42 PM, Stephen Smith wrote: > >> Hi Andreas >> >> OK. When I do git-buildpackage (no arguments) in the directory I have >> been working in, I get >> dpkg-buildpackage -rfakeroot -D -us -uc -i -I >> dpkg-buildpackage: source package phyutility >> dpkg-buildpackage: source version 2.6-1 >> dpkg-buildpackage: source distribution UNRELEASED >> dpkg-buildpackage: source changed by Andreas Tille >> dpkg-source -i -I --before-build phyutility >> dpkg-buildpackage: host architecture amd64 >> dpkg-checkbuilddeps: Unmet build dependencies: javahelper default-jdk >> libjebl2-java >> dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; >> aborting >> dpkg-buildpackage: warning: (Use -d flag to override.) >> debuild: fatal error at line 1364: >> dpkg-buildpackage -rfakeroot -D -us -uc -i -I failed >> gbp:error: Couldn't run 'debuild -i -I': debuild -i -I returned 29 >> >> Is this the error you were getting? I am looking at the git-buildpackage >> documentation but am having a little difficulty determining when the >> arguments are necessary (despite the fact that I understand arguments). >> >> Take care, >> Stephen >> >> >> On Tue, Mar 4, 2014 at 1:57 PM, Andreas Tille wrote: >> >>> Hi Stephen, >>> >>> On Tue, Mar 04, 2014 at 01:17:17PM -0500, Stephen Smith wrote: >>> > All sounds good. OK, I have done an initial commit so you can check out >>> > where I am at. >>> >>> I was really curious where you are at and thus I took the freedom to do >>> two commits: >>> >>> 1. Adapt changelog version to the injected upstream version >>> (otherwise git-buildpackage would not have worked). >>> 2. Use default-jdk (instead of an outdated JDK) >>> >>> So the build at least starts but runs into an error you most probably >>> will be able to reproduce (hopefully). >>> >>> Please confirm thyt you can run git-buildpackage and the build problem >>> can be reproduced at your side. >>> >>> 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/20140304185716.gc16...@an3as.eu >>> >>> >> >
Re: [MoM] incorporating phyutility into the packages
Sorry, spoke too soon. I noted the missing dependencies there. Once installed, it gets further and then fails at compile with [javac] phyutility/src/jebl/gui/trees/treeviewer_dev/TreePane.java:495: error: reference to Painter is ambiguous, both interface javax.swing.Painter in javax.swing and interface jebl.gui.trees.treeviewer_dev.painters.Painter in jebl.gui.trees.treeviewer_dev.painters match BUNCH OF STUFF AND THEN BUILD FAILED phyutility/build.xml:7: Compile failed; see the compiler error output for details. Total time: 8 seconds make[1]: *** [override_dh_auto_build] Error 1 make[1]: Leaving directory `phyutility' make: *** [build] Error 2 dpkg-buildpackage: error: debian/rules build gave error exit status 2 debuild: fatal error at line 1364: dpkg-buildpackage -rfakeroot -D -us -uc -i -I failed gbp:error: Couldn't run 'debuild -i -I': debuild -i -I returned 29 Does that look more like it? If so, seems like the solution is me fixing the phyutility code and then bringing it back in, correct? (At least since I am the developer of phyutility this seems like the easiest thing). Take care, Stephen On Tue, Mar 4, 2014 at 7:42 PM, Stephen Smith wrote: > Hi Andreas > > OK. When I do git-buildpackage (no arguments) in the directory I have been > working in, I get > dpkg-buildpackage -rfakeroot -D -us -uc -i -I > dpkg-buildpackage: source package phyutility > dpkg-buildpackage: source version 2.6-1 > dpkg-buildpackage: source distribution UNRELEASED > dpkg-buildpackage: source changed by Andreas Tille > dpkg-source -i -I --before-build phyutility > dpkg-buildpackage: host architecture amd64 > dpkg-checkbuilddeps: Unmet build dependencies: javahelper default-jdk > libjebl2-java > dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; > aborting > dpkg-buildpackage: warning: (Use -d flag to override.) > debuild: fatal error at line 1364: > dpkg-buildpackage -rfakeroot -D -us -uc -i -I failed > gbp:error: Couldn't run 'debuild -i -I': debuild -i -I returned 29 > > Is this the error you were getting? I am looking at the git-buildpackage > documentation but am having a little difficulty determining when the > arguments are necessary (despite the fact that I understand arguments). > > Take care, > Stephen > > > On Tue, Mar 4, 2014 at 1:57 PM, Andreas Tille wrote: > >> Hi Stephen, >> >> On Tue, Mar 04, 2014 at 01:17:17PM -0500, Stephen Smith wrote: >> > All sounds good. OK, I have done an initial commit so you can check out >> > where I am at. >> >> I was really curious where you are at and thus I took the freedom to do >> two commits: >> >> 1. Adapt changelog version to the injected upstream version >> (otherwise git-buildpackage would not have worked). >> 2. Use default-jdk (instead of an outdated JDK) >> >> So the build at least starts but runs into an error you most probably >> will be able to reproduce (hopefully). >> >> Please confirm thyt you can run git-buildpackage and the build problem >> can be reproduced at your side. >> >> 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/20140304185716.gc16...@an3as.eu >> >> >
Re: [MoM] incorporating phyutility into the packages
Hi Andreas OK. When I do git-buildpackage (no arguments) in the directory I have been working in, I get dpkg-buildpackage -rfakeroot -D -us -uc -i -I dpkg-buildpackage: source package phyutility dpkg-buildpackage: source version 2.6-1 dpkg-buildpackage: source distribution UNRELEASED dpkg-buildpackage: source changed by Andreas Tille dpkg-source -i -I --before-build phyutility dpkg-buildpackage: host architecture amd64 dpkg-checkbuilddeps: Unmet build dependencies: javahelper default-jdk libjebl2-java dpkg-buildpackage: warning: build dependencies/conflicts unsatisfied; aborting dpkg-buildpackage: warning: (Use -d flag to override.) debuild: fatal error at line 1364: dpkg-buildpackage -rfakeroot -D -us -uc -i -I failed gbp:error: Couldn't run 'debuild -i -I': debuild -i -I returned 29 Is this the error you were getting? I am looking at the git-buildpackage documentation but am having a little difficulty determining when the arguments are necessary (despite the fact that I understand arguments). Take care, Stephen On Tue, Mar 4, 2014 at 1:57 PM, Andreas Tille wrote: > Hi Stephen, > > On Tue, Mar 04, 2014 at 01:17:17PM -0500, Stephen Smith wrote: > > All sounds good. OK, I have done an initial commit so you can check out > > where I am at. > > I was really curious where you are at and thus I took the freedom to do > two commits: > > 1. Adapt changelog version to the injected upstream version > (otherwise git-buildpackage would not have worked). > 2. Use default-jdk (instead of an outdated JDK) > > So the build at least starts but runs into an error you most probably > will be able to reproduce (hopefully). > > Please confirm thyt you can run git-buildpackage and the build problem > can be reproduced at your side. > > 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/20140304185716.gc16...@an3as.eu > >
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Tue, Mar 04, 2014 at 01:17:17PM -0500, Stephen Smith wrote: > All sounds good. OK, I have done an initial commit so you can check out > where I am at. I was really curious where you are at and thus I took the freedom to do two commits: 1. Adapt changelog version to the injected upstream version (otherwise git-buildpackage would not have worked). 2. Use default-jdk (instead of an outdated JDK) So the build at least starts but runs into an error you most probably will be able to reproduce (hopefully). Please confirm thyt you can run git-buildpackage and the build problem can be reproduced at your side. 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/20140304185716.gc16...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
All sounds good. OK, I have done an initial commit so you can check out where I am at. Take care, Stephen On Tue, Mar 4, 2014 at 2:12 AM, Andreas Tille wrote: > Hi Stephen, > > On Mon, Mar 03, 2014 at 09:14:55PM -0500, Stephen Smith wrote: > > No problem. I am sure I added to the confusion there. I have added the > bare > > repo on Alitoh from "Pushing to git.debian.org, creating a new bare > > repository on Alitoh." but haven't pushed yet. I have my local git repo > > with the debian folder from the svn. > > Sounds good. > > > For this part, "git import-orig > > --pristine-tar /path/to/package_version.orig.tar.gz", I did git > > import-orig --pristine-tar phyutility_2_2_6.tar.gz using the package from > > the release. I have branches master, pristine-tar and upstream. > > Seems you are on track now. :-) > > > There are > > edits that will presumably need to be made (following the instructions > from > > https://www.debian.org/doc/manuals/maint-guide/ presumably) before it is > > ready to go, so should I wait to push until that is all ready or go ahead > > and git add all and push? > > Please push early. Then I could inspect and remove my old stuff in SVN. > > > Sorry for all the questions, but I am getting > > there. > > No need to sorry. MoM is exactly invented to encourage people to ask > questions which is way better than if newcomers would sit at home > desperately seeking for a solution and are to shy to ask. Please push > and keep on asking if something might remain unclear. > > 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/20140304071210.ga...@an3as.eu > >
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Mon, Mar 03, 2014 at 09:14:55PM -0500, Stephen Smith wrote: > No problem. I am sure I added to the confusion there. I have added the bare > repo on Alitoh from "Pushing to git.debian.org, creating a new bare > repository on Alitoh." but haven't pushed yet. I have my local git repo > with the debian folder from the svn. Sounds good. > For this part, "git import-orig > --pristine-tar /path/to/package_version.orig.tar.gz", I did git > import-orig --pristine-tar phyutility_2_2_6.tar.gz using the package from > the release. I have branches master, pristine-tar and upstream. Seems you are on track now. :-) > There are > edits that will presumably need to be made (following the instructions from > https://www.debian.org/doc/manuals/maint-guide/ presumably) before it is > ready to go, so should I wait to push until that is all ready or go ahead > and git add all and push? Please push early. Then I could inspect and remove my old stuff in SVN. > Sorry for all the questions, but I am getting > there. No need to sorry. MoM is exactly invented to encourage people to ask questions which is way better than if newcomers would sit at home desperately seeking for a solution and are to shy to ask. Please push and keep on asking if something might remain unclear. 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/20140304071210.ga...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Andreas, No problem. I am sure I added to the confusion there. I have added the bare repo on Alitoh from "Pushing to git.debian.org, creating a new bare repository on Alitoh." but haven't pushed yet. I have my local git repo with the debian folder from the svn. For this part, "git import-orig --pristine-tar /path/to/package_version.orig.tar.gz", I did git import-orig --pristine-tar phyutility_2_2_6.tar.gz using the package from the release. I have branches master, pristine-tar and upstream. There are edits that will presumably need to be made (following the instructions from https://www.debian.org/doc/manuals/maint-guide/ presumably) before it is ready to go, so should I wait to push until that is all ready or go ahead and git add all and push? Sorry for all the questions, but I am getting there. Take care, Stephen On Mon, Mar 3, 2014 at 5:16 PM, Andreas Tille wrote: > > Hi Stephen, > > On Mon, Mar 03, 2014 at 04:47:46PM -0500, Stephen Smith wrote: > > Hi Andreas > > I seem to be having a bit of a problem in converting this from subversion > > to git. Checking out from svn seems fine > > This command: > > debcheckout --user blackrim-guest svn:// > > svn.debian.org/debian-med/trunk/packages/phyutility/trunk phyutility > > Gets this result: > > declared svn repository at svn+ssh:// > > blackrim-gu...@svn.debian.org/svn/debian-med/trunk/packages/phyutility/trunk > > svn co svn+ssh:// > > blackrim-gu...@svn.debian.org/svn/debian-med/trunk/packages/phyutility/trunkphyutility > > ... > > Ahhh, sorry - I was not precise enough. I was considering to create a > Git repository *from* *scratch*! There is no point in keeping the > history! I'd (strongly) recommend to create a new Git repository, > inject the upstream source (as described in the policy) and copy over > the debian/ dir from SVN. That should perfectly do the trick! > > > Feeling like I am missing something obvious. Any suggestion? Thanks > > Just take the easy short-cut by ignoring irrelevant history. > > Sorry for missleading you. > > 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/20140303221643.gk7...@an3as.eu >
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Mon, Mar 03, 2014 at 04:47:46PM -0500, Stephen Smith wrote: > Hi Andreas > I seem to be having a bit of a problem in converting this from subversion > to git. Checking out from svn seems fine > This command: > debcheckout --user blackrim-guest svn:// > svn.debian.org/debian-med/trunk/packages/phyutility/trunk phyutility > Gets this result: > declared svn repository at svn+ssh:// > blackrim-gu...@svn.debian.org/svn/debian-med/trunk/packages/phyutility/trunk > svn co svn+ssh:// > blackrim-gu...@svn.debian.org/svn/debian-med/trunk/packages/phyutility/trunkphyutility > ... Ahhh, sorry - I was not precise enough. I was considering to create a Git repository *from* *scratch*! There is no point in keeping the history! I'd (strongly) recommend to create a new Git repository, inject the upstream source (as described in the policy) and copy over the debian/ dir from SVN. That should perfectly do the trick! > Feeling like I am missing something obvious. Any suggestion? Thanks Just take the easy short-cut by ignoring irrelevant history. Sorry for missleading you. 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/20140303221643.gk7...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Andreas I seem to be having a bit of a problem in converting this from subversion to git. Checking out from svn seems fine This command: debcheckout --user blackrim-guest svn:// svn.debian.org/debian-med/trunk/packages/phyutility/trunk phyutility Gets this result: declared svn repository at svn+ssh:// blackrim-gu...@svn.debian.org/svn/debian-med/trunk/packages/phyutility/trunk svn co svn+ssh:// blackrim-gu...@svn.debian.org/svn/debian-med/trunk/packages/phyutility/trunkphyutility ... and so on However, following the instructions here http://debian-med.alioth.debian.org/docs/policy.html#subversion-to-git and getting the to git-svn step here https://wiki.debian.org/Alioth/Git#Convert_a_SVN_Alioth_repository_to_Git I try git svn clone svn+ssh:// blackrim-gu...@svn.debian.org/debian-med/trunk/packages/phyutility/trunk --prefix=svn-import/ --stdlayout --authors-file=../community/infrastructure/comitters --no-metadata phyutility-git And get this result Couldn't find a repository: Unable to connect to a repository at URL 'svn+ssh:// blackrim-gu...@svn.debian.org/debian-med/trunk/packages/phyutility/trunk': No repository found in 'svn+ssh:// blackrim-gu...@svn.debian.org/debian-med/trunk/packages/phyutility/trunk' at /usr/share/perl5/Git/SVN.pm line 310. Feeling like I am missing something obvious. Any suggestion? Thanks Take care, Stephen On Mon, Mar 3, 2014 at 1:49 PM, Andreas Tille wrote: > Hi Stephen, > > On Mon, Mar 03, 2014 at 01:25:15PM -0500, Stephen Smith wrote: > > I definitely use git more than svn. I would prefer to move it to git and > > have been looking at the docs for doing that correctly. > > Seeking > >http://debian-med.alioth.debian.org/docs/policy.html > > for the keyword 'git' should give you all answers how to do so. Please > let me know (via the list) if it leaves open questions and you might > have trouble. > > Good luck > > 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/20140303184936.gh7...@an3as.eu > >
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Mon, Mar 03, 2014 at 01:25:15PM -0500, Stephen Smith wrote: > I definitely use git more than svn. I would prefer to move it to git and > have been looking at the docs for doing that correctly. Seeking http://debian-med.alioth.debian.org/docs/policy.html for the keyword 'git' should give you all answers how to do so. Please let me know (via the list) if it leaves open questions and you might have trouble. Good luck 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/20140303184936.gh7...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi Andreas I definitely use git more than svn. I would prefer to move it to git and have been looking at the docs for doing that correctly. Take care, Stephen On Mon, Mar 3, 2014 at 1:17 PM, Andreas Tille wrote: > Hi Stephen, > > any opinion about SVN versus Git for phyutility packaging? > > Kind regards > >Andreas. > > On Sat, Mar 01, 2014 at 05:56:58PM +0100, Andreas Tille wrote: > > Hi, > > > > On Sat, Mar 01, 2014 at 09:31:12AM -0500, Stephen Smith wrote: > > > Great! Going through the process now. > > > > Just accepted for the Debian Med team. Please confirm that you can ssh > > into ssh by passwordless login into alioth. > > > > BTW, since I previously used SVN for the packaging and people are now > > moving to Git: If you might prefer Git as well you can for sure move > > this to Git (by follosing the procedure explained in the policy > > document). > > > > 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/20140301165658.ge28...@an3as.eu > > > > > > -- > 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/20140303181734.gf7...@an3as.eu > >
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, any opinion about SVN versus Git for phyutility packaging? Kind regards Andreas. On Sat, Mar 01, 2014 at 05:56:58PM +0100, Andreas Tille wrote: > Hi, > > On Sat, Mar 01, 2014 at 09:31:12AM -0500, Stephen Smith wrote: > > Great! Going through the process now. > > Just accepted for the Debian Med team. Please confirm that you can ssh > into ssh by passwordless login into alioth. > > BTW, since I previously used SVN for the packaging and people are now > moving to Git: If you might prefer Git as well you can for sure move > this to Git (by follosing the procedure explained in the policy > document). > > 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/20140301165658.ge28...@an3as.eu > > -- 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/20140303181734.gf7...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Hi, On Sat, Mar 01, 2014 at 09:31:12AM -0500, Stephen Smith wrote: > Great! Going through the process now. Just accepted for the Debian Med team. Please confirm that you can ssh into ssh by passwordless login into alioth. BTW, since I previously used SVN for the packaging and people are now moving to Git: If you might prefer Git as well you can for sure move this to Git (by follosing the procedure explained in the policy document). 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/20140301165658.ge28...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Great! Going through the process now. Take care, Stephen On Sat, Mar 1, 2014 at 3:46 AM, Andreas Tille wrote: > Hi Stephen, > > On Fri, Feb 28, 2014 at 10:35:36PM -0500, Stephen Smith wrote: > > I wanted to express my interest in getting more involved in debian and > > possibly doing this with Andreas Tille through the MoM program. > > That's great. I have added an entry for March 2014. :-) > > > The package > > I would like to start helping get into the system is phyutility - a > program > > that is useful for formatting and postprocessing of sequence data and > > phylogenetic trees. For some background, I am a biologist and develop a > > number of programs for analysis of biological data and long time debian > > user (and lurker) but wanting to get more involved. Thanks for the > > consideration. > > As you might know I have previously injected some packaging code where > you can start from the status that is just in SVN[1]. I realised that I > forgot to add the package to our tasks page[2] and for some very boring > reason the system to rebuild this page is currently broken > (svn://anonscm.debian.org does not seem to work since yesterday - so you > might be affected as well - but you should checkout via svn+ssh anyway > so you can safely circumvent this problem). > > I think to start working you should simply follow the Debian Med policy > document, register on alioth.debian.org and ask for beeing added to the > Debian Med project. Please do not hesitate to ask here when facing any > trouble in doing so. > > Kind regards > >Andreas. > > [1] > http://anonscm.debian.org/viewvc/debian-med/trunk/packages/phyutility/trunk/ > [2] http://blends.debian.org/med/tasks/bio > > -- > 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/20140301084633.gd28...@an3as.eu > >
Re: [MoM] incorporating phyutility into the packages
Hi Stephen, On Fri, Feb 28, 2014 at 10:35:36PM -0500, Stephen Smith wrote: > I wanted to express my interest in getting more involved in debian and > possibly doing this with Andreas Tille through the MoM program. That's great. I have added an entry for March 2014. :-) > The package > I would like to start helping get into the system is phyutility - a program > that is useful for formatting and postprocessing of sequence data and > phylogenetic trees. For some background, I am a biologist and develop a > number of programs for analysis of biological data and long time debian > user (and lurker) but wanting to get more involved. Thanks for the > consideration. As you might know I have previously injected some packaging code where you can start from the status that is just in SVN[1]. I realised that I forgot to add the package to our tasks page[2] and for some very boring reason the system to rebuild this page is currently broken (svn://anonscm.debian.org does not seem to work since yesterday - so you might be affected as well - but you should checkout via svn+ssh anyway so you can safely circumvent this problem). I think to start working you should simply follow the Debian Med policy document, register on alioth.debian.org and ask for beeing added to the Debian Med project. Please do not hesitate to ask here when facing any trouble in doing so. Kind regards Andreas. [1] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/phyutility/trunk/ [2] http://blends.debian.org/med/tasks/bio -- 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/20140301084633.gd28...@an3as.eu
Re: [MoM] incorporating phyutility into the packages
Welcome to the team. +Emilien Le 1 mars 2014 04:35, "Stephen Smith" a écrit : > Hi, > I wanted to express my interest in getting more involved in debian and > possibly doing this with Andreas Tille through the MoM program. The package > I would like to start helping get into the system is phyutility - a program > that is useful for formatting and postprocessing of sequence data and > phylogenetic trees. For some background, I am a biologist and develop a > number of programs for analysis of biological data and long time debian > user (and lurker) but wanting to get more involved. Thanks for the > consideration. > Take care, > Stephen >
[MoM] incorporating phyutility into the packages
Hi, I wanted to express my interest in getting more involved in debian and possibly doing this with Andreas Tille through the MoM program. The package I would like to start helping get into the system is phyutility - a program that is useful for formatting and postprocessing of sequence data and phylogenetic trees. For some background, I am a biologist and develop a number of programs for analysis of biological data and long time debian user (and lurker) but wanting to get more involved. Thanks for the consideration. Take care, Stephen
