IGV (Was: Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest)
On Mon, Dec 17, 2018 at 05:29:28PM +0100, Olivier Sallou wrote: > > Thanks a lot. Could you please also have a look at igv in Git? > > What is the issue? I only see bug to switch to mariadb in debian tracker https://lists.debian.org/debian-med/2018/12/msg00026.html As always feel free to upload right after you found a fix. There is no point to run extra build cycles on my local hardware. ;-) Kind regards Andreas. -- http://fam-tille.de
Re: cyvcf2 issue with htslib
Hi Liubov, On Mon, Dec 17, 2018 at 06:00:59PM +0100, Liubov Chuprikova wrote: > > Could someone please have a look? > > I have started to investigate this: the fail is related to recent upstream > changes [1] and [2]. I have no time to look deeper into this right now, > maybe at the end of the week, That's perfect. > if nobody resolve it earlier. I admit I'm afraid the "competition" to solve this kind of issues is not that hard. ;-) > > PS: I've just closed #904836. I'd like to repeat my plea that people > > join our Advent calendar bug squashing. This was the easiest bug so > > far since it was closed with a previous upload but forgotten in > > d/changelog. > > oh, I had not noticed this bug then. No problem - nobody else has noticed until now as well. I was just using this as proof that extremely easy bugs exist in our long list of bugs and was hoping that this might be motivating for other readers of this list that it is really worth spending some time. I need to admit that I'm not very happy about this years bug fixing advent calendar. It would help a lot if everybody who considers beeing an active team member to fix one bug per week. But maybe that's just wishful thinking. :-( > > It would really help if others could check for those > > easy ones in our list of bugs. Thank you. > > Sorry, but I am participating in another squashing, trying to finish all > the assignments I had to do for my university :-P I do not expect that single readers send personal excuses why not taking part in the bug squashing. It would be even better if those bugs would be fixed by Uploaders once filed. Kind regards Andreas. > [1] https://github.com/brentp/cyvcf2/pull/93 > [2] > https://github.com/brentp/cyvcf2/commit/14d7443cba5234fd95b59760f834e8eb283bd8d2 -- http://fam-tille.de
Re: cyvcf2 issue with htslib
Hi Andreas, On Sat, 15 Dec 2018 at 08:51, Andreas Tille wrote: > > upstream has closed issue #91[1] and it should work with Debian > packaged htslib. Thus I've added libhts-dev to Build-Depends but the build finally fails with > > ... > I: pybuild base:217: cd > /build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build; python2.7 -m nose > -v. > Failure: ImportError > (/build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so: > undefined symbol: bcf_float_missing) ... ERROR > > == > ERROR: Failure: ImportError > (/build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so: > undefined symbol: bcf_float_missing) > -- > Traceback (most recent call last): > File "/usr/lib/python2.7/dist-packages/nose/loader.py", line 418, in > loadTestsFromName > addr.filename, addr.module) > File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 47, in > importFromPath > return self.importFromDir(dir_path, fqname) > File "/usr/lib/python2.7/dist-packages/nose/importer.py", line 94, in > importFromDir > mod = load_module(part_fqname, fh, filename, desc) > File > "/build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/__init__.py", > line 1, in > from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, > par_relatedness, > ImportError: > /build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build/cyvcf2/cyvcf2.so: > undefined symbol: bcf_float_missing > > -- > Ran 1 test in 0.006s > > FAILED (errors=1) > E: pybuild pybuild:338: test: plugin distutils failed with: exit code=1: > cd /build/cyvcf2-0.10.2/.pybuild/cpython2_2.7_cyvcf2/build; python2.7 -m > nose -v. > ... > > > Could someone please have a look? > I have started to investigate this: the fail is related to recent upstream changes [1] and [2]. I have no time to look deeper into this right now, maybe at the end of the week, if nobody resolve it earlier. PS: I've just closed #904836. I'd like to repeat my plea that people > join our Advent calendar bug squashing. This was the easiest bug so > far since it was closed with a previous upload but forgotten in > d/changelog. oh, I had not noticed this bug then. > It would really help if others could check for those > easy ones in our list of bugs. Thank you. > Sorry, but I am participating in another squashing, trying to finish all the assignments I had to do for my university :-P Kind regards, Liubov [1] https://github.com/brentp/cyvcf2/pull/93 [2] https://github.com/brentp/cyvcf2/commit/14d7443cba5234fd95b59760f834e8eb283bd8d2
Re: Bug#906371: Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest (Was: Bug#906371: jmodeltest: FTBFS in buster/sid)
- Andreas Tille a écrit : > Hi Olivier, > > On Mon, Dec 17, 2018 at 03:40:30PM +0100, Olivier Sallou wrote: > > > > I fixed the issue and pushed to git my patch d/patches/fix_alter-lib.patch > > > > The lib was used but the package name in alter-lib.jar is different. > > ModelTestService is patched to use correct package name > > Thanks a lot. Could you please also have a look at igv in Git? What is the issue? I only see bug to switch to mariadb in debian tracker If > it builds for you in pbuilder feel free to upload. > > Kind regards > >Andreas. > > -- > http://fam-tille.de >
Re: Bug#906371: Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest (Was: Bug#906371: jmodeltest: FTBFS in buster/sid)
Hi Olivier, On Mon, Dec 17, 2018 at 03:40:30PM +0100, Olivier Sallou wrote: > > I fixed the issue and pushed to git my patch d/patches/fix_alter-lib.patch > > The lib was used but the package name in alter-lib.jar is different. > ModelTestService is patched to use correct package name Thanks a lot. Could you please also have a look at igv in Git? If it builds for you in pbuilder feel free to upload. Kind regards Andreas. -- http://fam-tille.de
Re: [Debian-med-packaging] Bug#906371: Changes in alter-sequence-alignment break build of jmodeltest (Was: Bug#906371: jmodeltest: FTBFS in buster/sid)
On 12/17/18 11:07 AM, Andreas Tille wrote: > Hi, > > after I tried to follow the initial hint of Emmanuel I admit I was not > successful to finally build the package: > > On Wed, Oct 17, 2018 at 10:32:58AM +0200, Andreas Tille wrote: >>> Good catch. The latest upstream version of alter-sequence-alignment has >>> split these to an additional alter-lib.jar and the time of the build >>> failure of jmodeltest correlates with the upload of >>> alter-sequence-alignment 1.3.4-1. But now the question is: How to >>> teach the jmodeltest build system to use alter-lib.jar. I think adding >>> it to debian/manifest[1] is needed to *run* jmodeltest but it surely >>> does not help at build time. I have not found any place where the >>> build system specifies the needed jars. :-( >> I tried to add alter-lib.jar to build.xml[1]. Unfortunately this does >> not help to fix the issue >> >> [javac] >> /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:28: >> error: package parser does not exist >> [javac] import parser.ParseException; >> [javac] ^ >> [javac] >> /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:29: >> error: package converter does not exist >> [javac] import converter.Converter; >> [javac] ^ >> [javac] >> /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:30: >> error: package converter does not exist >> [javac] import converter.DefaultFactory; >> [javac] ^ >> [javac] >> /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/ModelTestService.java:31: >> error: package converter does not exist >> [javac] import converter.Factory; >> >> Any hint how to get the classes in alter-lib.jar found? I fixed the issue and pushed to git my patch d/patches/fix_alter-lib.patch The lib was used but the package name in alter-lib.jar is different. ModelTestService is patched to use correct package name >> Moreover I get lots of >> >> [javac] >> /build/jmodeltest-2.1.10+dfsg/src/main/java/es/uvigo/darwin/jmodeltest/exe/Distributor.java:23: >> warning: [deprecation] Observable in java.util has been deprecated >> [javac] import java.util.Observable; >> [javac] ^ > Any more hints? > > Kind regards > >Andreas. > -- Olivier Sallou Univ Rennes, Inria, CNRS, IRISA Irisa, Campus de Beaulieu F-35042 RENNES - FRANCE Tel: 02.99.84.71.95 gpg key id: 4096R/326D8438 (keyring.debian.org) Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
