[02:28] <TheLordOfTime> are Precise's repos still frozen?
[06:55] <dholbach> good morning
[06:56] <TheDrums> micahg: You happen to be about?
[09:31] <gch-scilifelab> hello everybody
[09:31] <gch-scilifelab> I'm doing my master thesis in the scilifelab (scilifelab.se) in Stockholm, we are currently working in a nexgen-data processing pipeline and I'm packagin all its dependencies 11:24:57 AM
[09:31] <gch-scilifelab> i've already packaged some of them, but I'm having problems when packaging gatk 11:25:21 AM
[09:31] <gch-scilifelab> it looks like it's failing to download some data, and this is what I don't understand, locally, I can build the package without problems, but when submitting to launchpad I get this error 11:26:35 AM
[09:31] <gch-scilifelab> https://launchpadlibrarian.net/113060176/buildlog_ubuntu-precise-amd64.gatk_1.6-0ubuntu1_FAILEDTOBUILD.txt.gz 11:26:42 AM
[09:31] <gch-scilifelab> can anybody give me a clue of what is happening please?
[09:32] <tumbleweed> the buildds don't have internet access
[09:32] <gch-scilifelab> (sorry for the time stamps, I asked before in the wrong channel)
[09:32] <Zhenech> gch-scilifelab, you should not download when building
[09:32] <directhex> gch-scilifelab, build daemons don't have internet access
[09:32] <tumbleweed> everything that you need for the build should be included in the source package
[09:32] <tumbleweed> (or its dependencies)
[09:32] <gch-scilifelab> hm.. oks
[09:32] <directhex> gch-scilifelab, this is a design choice, otherwise it would penalise people who have no internet access but do want to develop free software
[09:33] <gch-scilifelab> fast answer :-)
[09:33] <gch-scilifelab> thank you very much
[09:33] <gch-scilifelab> I'll try to fix it
[09:33] <Zhenech> gch-scilifelab, I think you are looking for the "ivy" package into your build-depends
[09:33] <tumbleweed> err, it's more of a design choice for reproducability and licence compliance
[09:33] <directhex> that too
[09:34] <directhex> it's especially annoying when a build system uses a CURRENT file to download the latest version of some non-bundled component, but doesn't actually work with the latest version
[09:34] <directhex> or if the latest version is missing
[09:34] <directhex> e.g. cgit was unbuildable for a while due to kernel.org being down due to hacks
[09:37] <gch-scilifelab> but, they don't have an internet connection? or they cannot download stuff?
[09:37] <tumbleweed> what's the difference?
[09:38] <Zhenech> for you, they have no internet connection
[09:38] <gch-scilifelab> well just because I thought that the other software I packaged also checked for some dependencies
[09:38] <tumbleweed> they have access to a mirror. nothing else
[09:38] <gch-scilifelab> obciously I'm wrong if there is no internet connection for the builder machines
[09:38] <gch-scilifelab> ok
[09:39] <gch-scilifelab> thanks
[09:45] <gch-scilifelab> in fact, the other packages I have built doesn't require internet connection. So I'll try to solve this
[09:45] <gch-scilifelab> thank you for your help, very kind you all :-)
[09:51] <xnox> i see that lintian is in sync now, what's the best place / way to propose changes to the ubuntu profile?
[09:51] <xnox> via bts or lp?
[10:24] <tumbleweed> xnox: bts / #debian-qa
[10:24] <tumbleweed> assuming you don't need to discuss this with ubuntu people
[10:25] <xnox> tumbleweed: no need to discuss, "I am always right" (tm).
[10:25] <xnox> tumbleweed: it affects both debian/ubuntu so it should be ok =)
[10:25] <xnox> tumbleweed: filed a bug report.
[10:36] <ESphynx> xnox: Many thanks for the review/upload =)
[10:37] <xnox> ESphynx: no-problem. now you need to wait for it to go through new queue. if it gets accepted you have plenty of work to do on that package still ;-)
[10:37] <ESphynx> xnox: plenty of work eh?
[10:38]  * ESphynx is waiting :P
[10:39] <ESphynx> xnox: Anything in particular that will require more work?
[10:39] <xnox> ESphynx: many compiler warnings to begin with.
[10:40] <xnox> it spits out many int != char
[10:40] <xnox> which will help with porting to 64bit later on upstream.
[10:40] <ESphynx> hmm I think those might be from the lexers & parsers generated by bison/gnu
[10:41] <ESphynx> which unfortunately I can’t do much about... but they’re harmless though ( don’t think they’d affect the 64 bit warnings either )
[10:42] <ESphynx> other than that I know there’s the pthread_mutex_setkind_np warning... which I have yet to decide what to do with... I think now the more portable function is available on Linux, but before it was not ...
[10:42] <ESphynx> There’s also the warnings spit out by GCC from eC generated C code... Which you probably did not see because I hide them :P
[10:42] <ESphynx> that however is a big deal :P
[10:43] <ESphynx> bison/flex*
[10:54] <ESphynx> I’m fixing warning: pthread_mutexattr_setkind_np undefined, cause it was breaking on Android anyways :P
[10:55] <ESphynx> xnox: Are these ( http://pastebin.ca/2197021 ) the other warnings you were referring to?
[10:55] <xnox> yeah.
[10:55] <xnox> some of.
[10:56] <ESphynx> I never got the last one! MAX_INCLUDE_DEPTH is defined to be 10
[10:56] <ESphynx> as in #define
[10:56] <ESphynx> and the others are all from code generated by flex, which unfortunately I can’t fix :S
[10:58] <ESphynx> oh look at that.
[10:58] <ESphynx> all of those are warnings generated by the eC compiler :P
[10:58] <ESphynx> Guess I could fix/tweak the eC compiler :P
[11:00] <ESphynx> xnox: some of? you had a lot more? :P
[11:01] <xnox> ESphynx: busy... =) can't be asked to find the build log again....
[11:01] <ESphynx> Those are the only ones I get apart from warning: pthread_mutexattr_setkind_np undefined; assuming extern
[11:01] <ESphynx> xnox: np. thanks for pointing this out, i’ll make it a point to not output these anymore.
[11:02] <xnox> ESphynx: rather than "not outputing them" they should be fixed.
[11:02] <xnox> either in code, or the parser / code-generator.
[11:02] <ESphynx> xnox: they’re warnings from the eC compiler
[11:02] <xnox> since they are real warnings.
[11:02] <ESphynx> xnox: and they are not valid
[11:03] <ESphynx> (well flex could be modified, but since GCC does not complain about them, they likely won’t fix flex)
[11:03] <ESphynx> and the MAX_INCLUDE_DEPTH thing is a bug in my compiler, it should realize MAX_INCLUDE_DEPTH is 10
[13:39] <micahg> TheDrums: very sporadically this week, how can I help you
[15:46] <gch-scilifelab> hi, I have a problem when updating a re-packaged software. I packaged a software a few days ago, but I did it wrong (I didn't want to include the source code, just the resulting jar files). Today I have repackaged the software properly but when I do a "dput ppa: etc" i receive a mail rejecting the upload with the message:
[15:46] <gch-scilifelab> Rejected:
[15:46] <gch-scilifelab> File gatk_1.6.orig.tar.gz already exists in Bio-tools, but uploaded version has different contents. See more information about this error in https://help.launchpad.net/Packaging/UploadErrors.
[15:46] <gch-scilifelab> File gatk_1.6-0ubuntu0.diff.gz already exists in Bio-tools, but uploaded version has different contents. See more information about this error in https://help.launchpad.net/Packaging/UploadErrors.
[15:46] <gch-scilifelab> Files specified in DSC are broken or missing, skipping package unpack verification.
[15:47] <gch-scilifelab> looking into my ppa I don't see this files, but if I filter by "supress", there they are..
[15:47] <gch-scilifelab> https://launchpad.net/~gch/+archive/utils/+packages?field.name_filter=&field.status_filter=superseded&field.series_filter=
[15:48] <gch-scilifelab> is there any way to supress them definitely? If not, what should I do?
[15:48] <Lasall> gch-scilifelab: increase version
[15:49] <gch-scilifelab> hi lasall, I've tried repackaging with the version name gatk-1.6-0ubuntu1 but doesn't works
[15:49] <Lasall> you have to increase version of orig tarball
[15:50] <gch-scilifelab> aha, ok, but if the program version is 1.6... I cannot put another version
[15:50] <gch-scilifelab> maybe 1.6.0?
[15:50] <gch-scilifelab> do you mean?
[15:52] <Lasall> if it were an official package, this would introduce an epoch imho
[15:52] <Lasall> but for a ppa i would use 1.6.0
[15:52] <tumbleweed> 1.6+source ?
[15:52] <Laney> call it 1.6.0+repack-0ubuntu1 or something
[15:52] <Lasall> ok
[15:52] <Laney> it's a good lesson about messing with orig tarballs
[15:53] <gch-scilifelab> ok then, I'll rename it
[15:53] <gch-scilifelab> thanks
[15:53] <gch-scilifelab> and do you know for how long the orig tarball will be there with the "supressed" or "deleted" state?
[15:54] <tumbleweed> forever
[15:54] <Laney> once a file is there it is there
[15:54] <Laney> and anyway, you'll have to go forward in version number
[15:55] <gch-scilifelab> I mean, they are occupying disk space, don't would it be worth to delete them if the developer wants to?
[15:55] <gch-scilifelab> aha
[15:55] <tumbleweed> it's not a matter of the file taking disk space, but of ensuring that you don't replace it with something different
[15:55] <tumbleweed> once it's been published
[15:57] <gch-scilifelab> ok
[15:57] <gch-scilifelab> thank you very much :-)
[15:57] <gch-scilifelab> It's a good thing to know... :-)
[15:58] <tumbleweed> personally, I think that restriction is unecessarily harsh for PPAs, but it's good training for the archive
[17:44] <jtaylor> ups I uploaded something as mergomatic ._.
[17:45] <jtaylor> well at least I only broke a 5 month streak of that not happing
[17:46] <jtaylor> aren'T there debian like autorejects to prevent such things?
[17:52] <tumbleweed> launchpad tries hard to avoid ubuntu-specific policy
[18:22] <TheDrums> micahg: Sorry, I don't exactly know what I should be doing with that, never done it before and it ran into an error number I can't exactly remember, maybe 19?
[18:33] <arand> gcc-4.4 is the latest available in 10.04 Lucid?
[18:34] <Lasall> yes
[18:34] <TheLordOfTime> yup
[21:03] <verwilst> anyone here with the power to change a bugreport from fix released to confirmed? I messed up but can't correct it myself
[21:07] <tumbleweed> in general, #ubuntu-bugs is the place to ask for that. but I've done it
[21:09] <ESphynx> hey tumbleweed :) xnox uploaded Ecere to Debian Experimental =) \o/
[21:10]  * tumbleweed saw :)
[21:10] <ESphynx> hehe
[21:10]  * ESphynx has a Quetzal (the bird) picture on his desktop :P
[21:10] <Laney> true Nice Guy
[23:26] <a7x> i actually own a Quetzal ESphynx
[23:26] <ESphynx> a7x you do? :) awesome :)
[23:27] <a7x> well, maybe you don't know that i'm not talking about the bird
[23:27] <ESphynx> oh you’re not?
[23:27] <ESphynx> what do you own then :P
[23:27] <a7x> http://en.m.18dao.net/images/0/04/P-99_Guatemala_1998_One_Quetzal.jpg
[23:27] <a7x> :)
[23:27] <ESphynx> lolz
[23:27] <ESphynx> didn’t know that! http://en.wikipedia.org/wiki/Guatemalan_quetzal
[23:28] <a7x> and about the bird, i think it's a protected specie
[23:28] <ESphynx> probably is!
[23:33] <a7x> looks like there is no way to buy the bird ESphynx
[23:33] <a7x> even if it's not really in danger
[23:33] <ESphynx> ah
[23:34] <ESphynx> you just gotta go in the South and catch one yourself
[23:34] <a7x> looks like it's illegal
[23:34] <a7x> but you can't really trust yahoo answers
[23:34] <ESphynx> hehe
[23:35] <ESphynx> well I’ll settle for Quantal Quetzal being able to compile and run eC code :P