Re: Please help upgrading eigensoft
On 18/07/16 22:21, Andreas Tille wrote: > Hi, > > I tried to upgrade eigensoft[1]. The build fails with: > > ... > cc -Wl,-z,relro pca.o eigensrc/eigsubs.o eigx.o nicksrc/libnick.a -lgsl > -lblas -lgfortran -lrt -lm -o pca > eigx.o: In function `eigx_': > /build/eigensoft-6.1.2+dfsg/src/eigx.c:100: undefined reference to `dspev_' Hi Andreas, just a few thoughts. The symbols you are looking for are in liblapack: $ sudo apt install eigensoft pax-utils $ symtree /usr/bin/pca ... liblapack.so.3 => dgetrf_,dgetri_,dsygv_,dgetrs_,dspev_,dpotrf_ ... If you add -llapack to the list of libraries, it will pass this step. It will fail later, but adding also -lpthread and -llapacke will make it build. That said, it sounds tricky, because there is zero guarantee that these dgetrf_ functions have the prototype that is in src/eigx.c (they don't seem to be public). This looks very error-prone. Cheers, Tomasz signature.asc Description: PGP signature
Re: Your move of mothur to Git
On 06/09/15 15:00, Andreas Tille wrote: > Hi Tomasz, > > On Sun, Sep 06, 2015 at 01:31:39PM +0200, Tomasz Buchert wrote: > > > > actually, I got this svn-upstream branch wrong and now it is completely > > removed. I also merged my work with the old svn packaging. > > :-) > > > > 2. Droping a README.status at the old SVN location to inform > > > users about the move to Git. I'd volunteer to do so once > > > the history in master is OK. > > > > Go ahead :). > > Done. > > Thanks for your work on mothur > > Andreas. Great. Should I upload to unstable? Tomasz > > > -- > http://fam-tille.de > signature.asc Description: Digital signature
Re: Your move of mothur to Git
On 05/09/15 21:45, Andreas Tille wrote: > Hi Tomasz, > > On Sat, Sep 05, 2015 at 08:30:09PM +0200, Tomasz Buchert wrote: > > > > I don't know to throw previous history either. What about this > > repo: https://anonscm.debian.org/cgit/debian-med/mothur.git/ ? > > I keep old history inside svn-debian and svn-upstream branches. > > Ahh, I missed this branches. I'm not interested in svn-upstream, but if > you would merge svn-debian right into master that would be perfect. Hi Andreas, actually, I got this svn-upstream branch wrong and now it is completely removed. I also merged my work with the old svn packaging. > > > > continue with your commits later this would probably a good idea. So if > > > you agree I move your current mothur.git to mothur_new.git and do the > > > conversion first. You could then commit your later changes on top of > > > these. If you have good reasons to follow a different approach that > > > would be fine for me but please let us know these reasons. As I said it > > > would not be a real problem - I just want to make sure you are > > > proceeding intentionally this way. > > > > I did more or less the same thing as the script does (followind Alioth/git > > wiki). > > I imported the repo and git-svn created two branches (with debian directory > > and > > upstream sources). I renamed the tags to "svn/...". Then I pulled my work. > > > > The histories are separate, but I can think of rebasing my work on top > > of these two branches. I even tried, but failed a bit. > > I have no experience with git-svn and I'm not sure how I could help > but it would be good if you would try harder to get svn-debian and > master merged. It looks fine to me now. > > > Please let me know what you think. > > I think there is no point if I would follow my suggestion to convert > svn2git from scratch since you basically did so. There are two things > missing: > > 1. Change Vcs fields (which I just did, please `git pull`) Thanks! > 2. Droping a README.status at the old SVN location to inform > users about the move to Git. I'd volunteer to do so once > the history in master is OK. Go ahead :). > > Kind regards > >Andreas. > > -- > http://fam-tille.de > Cheers, Tomasz signature.asc Description: Digital signature
Re: Your move of mothur to Git
On 05/09/15 20:30, Tomasz Buchert wrote: > On 05/09/15 18:19, Andreas Tille wrote: > > Hi Tomasz, > > > > thanks for your work on mothur which is really appreciated. I noticed > > that you started a new Git repository that is ignoring the previous work > > done in SVN. I admit I'm not very keen on the history in SVN but I > > managed to convert quite some SVN repositories to Git using a helper > > script[1] and I see now reason to throw away the history without good > > reason. So if you want me to do the Git conversion first and you > > Hi Andreas, > I don't know to throw previous history either. What about this I meant WANT here :). Tomasz signature.asc Description: Digital signature
Re: Your move of mothur to Git
On 05/09/15 18:19, Andreas Tille wrote: > Hi Tomasz, > > thanks for your work on mothur which is really appreciated. I noticed > that you started a new Git repository that is ignoring the previous work > done in SVN. I admit I'm not very keen on the history in SVN but I > managed to convert quite some SVN repositories to Git using a helper > script[1] and I see now reason to throw away the history without good > reason. So if you want me to do the Git conversion first and you Hi Andreas, I don't know to throw previous history either. What about this repo: https://anonscm.debian.org/cgit/debian-med/mothur.git/ ? I keep old history inside svn-debian and svn-upstream branches. > continue with your commits later this would probably a good idea. So if > you agree I move your current mothur.git to mothur_new.git and do the > conversion first. You could then commit your later changes on top of > these. If you have good reasons to follow a different approach that > would be fine for me but please let us know these reasons. As I said it > would not be a real problem - I just want to make sure you are > proceeding intentionally this way. I did more or less the same thing as the script does (followind Alioth/git wiki). I imported the repo and git-svn created two branches (with debian directory and upstream sources). I renamed the tags to "svn/...". Then I pulled my work. The histories are separate, but I can think of rebasing my work on top of these two branches. I even tried, but failed a bit. > > Kind regards > >Andreas. > Please let me know what you think. Cheers, Tomasz > [1] > https://anonscm.debian.org/viewvc/debian-med/trunk/helper-scripts/convert_svn_2_git?view=markup > > -- > http://fam-tille.de > signature.asc Description: Digital signature
Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
On 24/08/15 12:03, Fabian Klötzl wrote: > Hi all, > > Would someome be so kind as to sponser another upload for > libdivsufsort? Thanks in advance. > > Fabian > > ps. Thanks to Andreas for the reminder. I can sponsor the upload. In fact, I'm going to do it right away. Tomasz > > > On 23.08.2015 17:48, Tomasz Buchert wrote: > > On 23/08/15 17:11, Fabian Klötzl wrote: > >> Hi, > >> > >> Am 22.08.2015 um 16:44 schrieb Tomasz Buchert: > >>> Wrt the bug: as the dependency is now explicit, you can close > >>> in the next release. More genrally, you need to format the > >>> changelog with a nice summary of all changes. > >> > >> I wrote up a changelog entry for the next version. If everyone > >> is satisfied with that, I guess we could try another upload. > >> > >> Fabian > >> > > > > The current state looks good to me. > > > > Tomasz > > > signature.asc Description: Digital signature
Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
On 23/08/15 17:11, Fabian Klötzl wrote: > Hi, > > Am 22.08.2015 um 16:44 schrieb Tomasz Buchert: > > Wrt the bug: as the dependency is now explicit, you can close in > > the next release. More genrally, you need to format the changelog > > with a nice summary of all changes. > > I wrote up a changelog entry for the next version. If everyone is > satisfied with that, I guess we could try another upload. > > Fabian > The current state looks good to me. Tomasz signature.asc Description: Digital signature
Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
On 22/08/15 13:25, Fabian Klötzl wrote: > Hi, > > Am 22.08.2015 um 12:28 schrieb Tomasz Buchert: > > I've pushed another change to libdivsufsort which, to my knowledge, > > is "The Right Thing To Do". I still needed to apply a custom patch > > for "include" directory because header files are generated > > on-the-fly, but other than that it seems fine. > > Patch looks ok to me, but I am not an expert on these things. Hi, I did it according to the bug I mentioned. It is supposed to work even when cross-compiling, but I didn't check it. > > > I propose to ask upstream to use them. > > Definitely, once we have the patches ready, they should be bundled in > a pull request. Then we should notify upstream via mail, because they > don't seem to be an active GitHub user. > > With respect to bug #794729. I guess that is fixed now and can be > closed. But since libdivsufsort-dev now depends on libdivsufsort3 > should we also add the 3 to the -dev package: libdivsufsort3-dev? What > is the usual debian way to handle that? The usual way is to have libdivsufsort-dev. Wrt the bug: as the dependency is now explicit, you can close in the next release. More genrally, you need to format the changelog with a nice summary of all changes. > > Best, > Fabian > Cheers, Tomasz signature.asc Description: Digital signature
Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
On 07/08/15 10:24, Fabian Klötzl wrote: > Hi, > > I will be on a week-long vacation, starting tomorrow. Please, feel > free to continue committing so we can release an improved package, soon. > > On 06.08.2015 20:01, Andreas Tille wrote: > > On Thu, Aug 06, 2015 at 05:43:47PM +0200, Tomasz Buchert wrote: > >> I'll also mention that theere are actually 2 different tarballs > >> with 2.0.1: the one the package is based on (from googlecode) and > >> the one that I used in my parallel packaging (from github). The > >> latter has autoconf files removed for example and so is much > >> smaller. > >> > >> I permitted myself to update debian/watch file, with > >> filenamemangle option which renames the file to something with > >> "libdivsufsort" prefix. > > > > In any case pleas point d/watch to github! Googlecode is dead and > > no watch file should point to this. > > d/watch looks correct now. > > Cheers, > Fabian > Hi Fabian, I hope you had great vacations. I've pushed another change to libdivsufsort which, to my knowledge, is "The Right Thing To Do". I still needed to apply a custom patch for "include" directory because header files are generated on-the-fly, but other than that it seems fine. I propose to ask upstream to use them. Please review, Tomasz signature.asc Description: Digital signature
Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
On 06/08/15 10:09, Andreas Tille wrote: > On Thu, Aug 06, 2015 at 09:46:51AM +0200, Tomasz Buchert wrote: > > > > git://anonscm.debian.org/debian-med/libmems.git > > > > > > Ok, I will have a look at it. > > > > Hi, > > I didn't know about d-shlibs! Nice. In my packaging branch [1] I > > attack multi-arch by patching upstream. I don't know yet which > > solution I like the most. I'll leave it to Fabian. > > > > (wrt libmems => shouldn't you declare Multi-Arch: same + Pre-Depends?) > > I have not heard about misc:Pre-Depends admittedly but about Multi-Arch: > same you are probably right. May be this is not an up to date example > ... Hi Andreas, (I don't subscribe to this list, so I almost missed it) I'm referring here to: https://wiki.debian.org/Multiarch/Implementation (dh(1) and autotools). > > > > Also, I included Thomasz in the conversation, as he is also interested > > > in packaging libdivsufsort and has already committed some patches > > > (which may or may not already fix the issue). > > > > My packaging branch has also this bug + section problem (but my > > parallel collab-maint repo is ok :D ). I've pushed two more commits to > > "packaging-merge". > > Feel free to merge your changes into master and create a new changelog > entry. I do not insist in d-shlibs if the problem is fixed otherwise > but it just helps. You could also add yourself to Uploaders if you > want to maintain this package cooperatively. No need to, I need libdivsufsort as a prerequisite for libsdsl. > > Kind regards > >Andreas. > > > [1] > > http://anonscm.debian.org/cgit/debian-med/libdivsufsort.git/log/?h=packaging-merge > > > > -- > http://fam-tille.de > Cheers, Tomasz -- 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/20150806155525.ga12...@buchert.pl
Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
On 06/08/15 16:31, Fabian Klötzl wrote: > Hi, > > On 06.08.2015 10:09, Andreas Tille wrote: > > On Thu, Aug 06, 2015 at 09:46:51AM +0200, Tomasz Buchert wrote: > >> My packaging branch has also this bug + section problem (but my > >> parallel collab-maint repo is ok :D ). I've pushed two more > >> commits to "packaging-merge". > > > > Feel free to merge your changes into master and create a new > > changelog entry. I do not insist in d-shlibs if the problem is > > fixed otherwise but it just helps. You could also add yourself to > > Uploaders if you want to maintain this package cooperatively. > > I merged the `packaging-merge` branch and updated the watch URLs. > Didn't yet manage to properly test with cowbuilder. New machine, new > errors. I'll also mention that theere are actually 2 different tarballs with 2.0.1: the one the package is based on (from googlecode) and the one that I used in my parallel packaging (from github). The latter has autoconf files removed for example and so is much smaller. I permitted myself to update debian/watch file, with filenamemangle option which renames the file to something with "libdivsufsort" prefix. > > Best, > Fabian > Cheers, Tomasz signature.asc Description: Digital signature
Re: [u...@debian.org: Bug#794729: libdivsufsort-dev: missing dependency on libdivsufsort3]
On 06/08/15 09:20, Fabian Klötzl wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Hi, > > On 06.08.2015 08:32, Andreas Tille wrote: > > Hi Fabian, > > > > I hope you read the mailing list > > debian-med-packag...@lists.alioth.debian.org or at least have > > subscribed this package in the Debian Package Tracker. If not > > please do either of one to receive the bug reports of your > > package. > > Done. > > > BTW, using d-shlibs would prevent such kind of problems. You can > > find an example usage for instance here: > > > > git://anonscm.debian.org/debian-med/libmems.git > > Ok, I will have a look at it. Hi, I didn't know about d-shlibs! Nice. In my packaging branch [1] I attack multi-arch by patching upstream. I don't know yet which solution I like the most. I'll leave it to Fabian. (wrt libmems => shouldn't you declare Multi-Arch: same + Pre-Depends?) > > Also, I included Thomasz in the conversation, as he is also interested > in packaging libdivsufsort and has already committed some patches > (which may or may not already fix the issue). My packaging branch has also this bug + section problem (but my parallel collab-maint repo is ok :D ). I've pushed two more commits to "packaging-merge". > > Fabian > Cheers, Tomasz [1] http://anonscm.debian.org/cgit/debian-med/libdivsufsort.git/log/?h=packaging-merge signature.asc Description: Digital signature
