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
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 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 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
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 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
> 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 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 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 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 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
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 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 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 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
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 > >
[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
Re: Source code of phyutility
Hi Andreas, Derby requirement should be gone. Hope that helps and let me know if you run into any other issues. Take care, Stephen On 01/31/2012 10:21 AM, Andreas Tille wrote: Hi Stephen, On Tue, Jan 31, 2012 at 09:52:32AM -0500, Stephen Smith wrote: No problems. How about I just change it from derby to sqlite? I can do that either today or tomorrow but definitely before the end of the week if that would be more helpful. I don't use the derby functionality anymore and sqlite would be easier for users anyway. This would be probably really helpful! I can not promise that I will start with the phyutility packaging right now but this would make things way simpler and will make it pop up on my todo list quite a bit because it becomes more promising to be finished soon than when using Derby. Many thanks for your helpful cooperation, please keep me informed once you have released a new source archive without Derby Andreas. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4f3c2953.10...@gmail.com
Re: Source code of phyutility
No problems. How about I just change it from derby to sqlite? I can do that either today or tomorrow but definitely before the end of the week if that would be more helpful. I don't use the derby functionality anymore and sqlite would be easier for users anyway. I would say you can just ignore the derby bit for now and continue as free and the next iteration will no longer have it. Stephen On 01/31/2012 03:12 AM, Andreas Tille wrote: On Mon, Jan 30, 2012 at 12:31:04PM -0500, Stephen Smith wrote: There is now a basic ant build file included and I released a new version. Thanks a lot, that's very helpful. One question is that typically, so that it can be run like a normal program without the java -jar phyutlity.jar, I encourage using a shell script that just has java -Xmx2g -jar LOCATION/phyutility.jar $* The memory option is something that needs to be available to be changed if need be as well. Anyway, not sure if that is easy to have in the ant build or not, but I am not familiar with a good way. If you know of a good standard way to do that (generate that script and put it somewhere in the PATH), I am happy to include that as part of the build, otherwise, you can do it in the package installation. I do not know whether there is a way to use ant for the script generation and I have to admit that I'm most probably not the correct person to ask such things. I have close to no Java experience and just dived a bit into it because we have a lot pf phylogeny software around which is just written in Java and we simply need it in Debian. So anybody needs to tackle this and it turned out that this anybody is just me. For tricky Java questions I'm consulting the Debian Java team and I observed that they provide such simple scripts just in their package installations which is simple enough. Let me know what else you need. The real problem with phyutility is derby.jar. Debian requires the code for all binary code inside the distribution. So we usually need to do package those JARs from scratch as extra packages and the use the Debian packaged version. While there were some intends to package Derby in the past but with no visible outcome so far. That's a bit unfortunate because I as a beginner do not want to dive into this one. I am an Arch and Ubuntu user so good to see packages being built So it might happen it ends up in Debian non-free section because of the Derby issue - I personally have no idea how this propagates to Ubuntu but using it from the Debian mirror in non-free should be no issue under recent Ubuntu versions. Thanks for your support Andreas. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4f280030.6030...@gmail.com
Re: Source code of phyutility
Hi Andreas, Great! I have the source on http://code.google.com/p/phyutility. I switched to git and it should be relatively easy to see the main branch. I would be very happy to help however I can. And I am currently working on some bug fixes, etc. Please let me know how best to help in terms of helping identify updates and the build.xml configuration. Take care, Stephen On 01/28/2012 07:46 PM, Andreas Tille wrote: Hi, I would like to package phyutility for Debian. At http://code.google.com/p/phyutility/ I found a downloadable ZIP file which contains the resulting JAR. I also was able to check out the according source code from SVN. However, for packaging purposes a downloadable and equally versioned archive (be it tar.gz or zip does not matter) would be really helpful. The thing is that if we would just observe trunk with our automatic tools it is hard to decide whether there might have been a code update or just some changes in the documentation wiki which is in the same place or something like this. In case you would consider to help us with such support in a downloadable source archive it would also very helpful if you would include some build.xml file or something like this which would enable us to make building the project as simple as possible. Kind regards and thanks for providing phyutility as free software Andreas. -- To UNSUBSCRIBE, email to debian-med-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: http://lists.debian.org/4f25d22d.3000...@gmail.com
Re: MUMmer patches and Artistic license.
In <200907281303.42301@iguanasuicide.net>, Boyd Stephen Smith Jr. wrote:
>In <20090728163525.gc31...@an3as.eu>, Andreas Tille wrote:
>>On Sun, Jul 12, 2009 at 10:50:10PM +0900, Charles Plessy wrote:
>>> > This patch is a good idea -- fixed length buffers are rarely
>>> > considered user-friendly. However, it is executed poorly; it's not
>>> > ready for upstream in its current state.
>>>
>>> Hi, thank you for the comment.
>>> I will stop to apply this patch until a better solution is found.
>>
>>Quite late comment after working down my batch of unread mail:
>>The patch was *not* *only* to avoid fixed length buffers - it was
>>invented to stop mummer from *crashing*.
>
>I may be able to reply with a corrected patch later today.
Attached is my new patch that removes the errors I saw in the original
patch. I welcome any comments on the new patch.
I've also attached a interdiff between the old and new patches for
reference.
In case anyone feels this work is copyrightable[1], I license my
contributions under the same license as the original patch.
P.S. Please CC me if you drop debian-mentors, I am not subscribed to
debian-med.
--
Boyd Stephen Smith Jr. ,= ,-_-. =.
b...@iguanasuicide.net ((_/)o o(\_))
ICQ: 514984 YM/AIM: DaTwinkDaddy `-'(. .)`-'
http://iguanasuicide.net/\_/
[1] I don't.
Description: Dynamically allocates space for the strings, instead allocating a predefined size.
Origin: vendor : Debian
Bug: https://sourceforge.net/tracker/?func=detail&aid=1215086&group_id=133157&atid=726404
Index: ./src/tigr/annotate.cc
===
--- ./src/tigr/annotate.cc
+++ ./src/tigr.orig/annotate.cc
@@ -10,6 +10,7 @@
*/
#include "tigrinc.hh"
+#include
#define FIELD_LEN 20
#define MAX_ALIGN 1
@@ -138,19 +139,26 @@ void Show_Alignment (char A [], long in
// Print the alignment between strings A [1 .. M] and B [1 .. N] .
{
- static int D [MAX_ALIGN] [MAX_ALIGN];
- static char Op [MAX_ALIGN] [MAX_ALIGN];
- static char Show_A [2 * MAX_ALIGN];
- static char Show_B [2 * MAX_ALIGN];
+ int **D, *D_buf;
+ char **Op, *Op_buf;
+ char *Show_A;
+ char *Show_B;
int Errors, Tmp;
long int i, j, Ct;
- if (M >= MAX_ALIGN || N >= MAX_ALIGN)
- {
-printf ("\n *** Too long ***\n\n");
-fprintf (Gaps_With_Errors_File, "%s %7s\n", Line, "-");
-return;
- }
+ assert ( SIZE_MAX / (M+1) >= (N+1) ) ;
+ D_buf = (int *) calloc ( (M+1)*(N+1), sizeof(int) ) ;
+ assert ( D_buf ) ;
+ D = &D_buf ;
+ Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ;
+ assert ( Op_buf ) ;
+ Op = &Op_buf ;
+
+ assert ( SIZE_MAX >> 1 >= (M+1) ) ;
+ Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ;
+ assert ( Show_A ) ;
+ Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ;
+ assert ( Show_B ) ;
D [0] [0] = 0;
Op [0] [0] = 'a';
@@ -229,5 +237,10 @@ void Show_Alignment (char A [], long in
putchar ('\n');
Ct -= WIDTH;
} while (Ct > 0);
+
+ free ( D_buf ) ;
+ free ( Op_buf ) ;
+ free ( Show_A ) ;
+ free ( Show_B ) ;
return;
}
diff -u ./src/tigr/annotate.cc ./src/tigr.orig/annotate.cc
--- ./src/tigr/annotate.cc 2007-11-07 21:47:03.0 +0100
+++ ./src/tigr.orig/annotate.cc
@@ -146,12 +146,19 @@
int Errors, Tmp;
long int i, j, Ct;
- assert ( D_buf = (int *) calloc ( (M+1)*(N+1), sizeof(int) ) ) ;
+ assert ( SIZE_MAX / (M+1) >= (N+1) ) ;
+ D_buf = (int *) calloc ( (M+1)*(N+1), sizeof(int) ) ;
+ assert ( D_buf ) ;
D = &D_buf ;
- assert ( Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ) ;
+ Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ;
+ assert ( Op_buf ) ;
Op = &Op_buf ;
- assert ( Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ) ;
- assert ( Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ) ;
+
+ assert ( SIZE_MAX >> 1 >= (M+1) ) ;
+ Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ;
+ assert ( Show_A ) ;
+ Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ;
+ assert ( Show_B ) ;
D [0] [0] = 0;
Op [0] [0] = 'a';
signature.asc
Description: This is a digitally signed message part.
Re: MUMmer patches and Artistic license.
In <20090728163525.gc31...@an3as.eu>, Andreas Tille wrote: >On Sun, Jul 12, 2009 at 10:50:10PM +0900, Charles Plessy wrote: >> > This patch is a good idea -- fixed length buffers are rarely >> > considered user-friendly. However, it is executed poorly; it's not >> > ready for upstream in its current state. >> >> Hi, thank you for the comment. >> I will stop to apply this patch until a better solution is found. > >Quite late comment after working down my batch of unread mail: >The patch was *not* *only* to avoid fixed length buffers - it was >invented to stop mummer from *crashing*. In that case I recommend leaving the patch applied, opening a bug, and assigning it to me. I can re-write the patch to avoid having statements with side-effects inside assert() calls. I may be able to reply with a corrected patch later today. P.S. Please CC me if you drop debian-mentors, I am not subscribed to debian-med. -- Boyd Stephen Smith Jr. ,= ,-_-. =. b...@iguanasuicide.net ((_/)o o(\_)) ICQ: 514984 YM/AIM: DaTwinkDaddy `-'(. .)`-' http://iguanasuicide.net/\_/ signature.asc Description: This is a digitally signed message part.
Re: MUMmer patches and Artistic license.
In <20090704120642.gh6...@kunpuu.plessy.org>, Charles Plessy wrote: >we have a patch in the Debian package mummer for which we lost origin and >detailed description. I would like to forward it upstream, but I would > prefer to know what it does before ;) Would somebody have a few minutes > to throw an eye on it? It is in our SVN, and here is a copy: > >http://svn.debian.org/wsvn/debian-med/trunk/packages/mummer/trunk/debian/p >atches/01sm_src_tigr.diff > >+ assert ( D_buf = (int *) calloc ( (M+1)*(N+1), sizeof(int) ) ) ; >+ D = &D_buf ; >+ assert ( Op_buf = (char *) calloc ( (M+1)*(N+1), sizeof(char) ) ) ; >+ Op = &Op_buf ; >+ assert ( Show_A = (char *) calloc ( 2*(M+1) , sizeof(char) ) ) ; >+ assert ( Show_B = (char *) calloc ( 2*(N+1) , sizeof(char) ) ) ; Four out of these six lines are bugs waiting to happen. If NDEBUG is defined, the calls to calloc will be completely elided. Then you'll have a number of uninitialized pointers that are used here: >D [0] [0] = 0; >Op [0] [0] = 'a'; This patch is a good idea -- fixed length buffers are rarely considered user-friendly. However, it is executed poorly; it's not ready for upstream in its current state. -- Boyd Stephen Smith Jr. ,= ,-_-. =. b...@iguanasuicide.net ((_/)o o(\_)) ICQ: 514984 YM/AIM: DaTwinkDaddy `-'(. .)`-' http://iguanasuicide.net/\_/ signature.asc Description: This is a digitally signed message part.
