Re: [dom@earth.li: Bug#899129: prime-phylo: FTBFS: cd obj-x86_64-linux-gnu && make -j8 -Oline returned exit code 2]
Hi Lars and Erik,
On Thu, May 24, 2018 at 12:27:36PM +0000, Lars Arvestad wrote:
> I think Erik is right. I don’t have time to maintain the code and there is better code to use out there.
>
> Thanks a lot for having this code in Debian, but I think it is time to pull the plug.
Thanks for the clarification. From a Debian point of view its probably the
best curse of action to package the replacement first and later remove what
we have.
> But since I have the two of you on the line: what does it take to distribute what essentially is a JAR-file as a Debian package? One would probably want to wrap it with an additional shell-script, but that is all. Any pointers appreciated.
You can not simply wrap a JAR into a DEB package - at least not into an
official Debian package. You need all Java sources and build from
source. That's the very short version. In general we have quite some
record to teach interested people how to package some software. If
you want to speed up jprime integration into Debian that would be really
appreciated.
Kind regards
Andreas.
> On 24 May 2018, at 14:16, Erik Sjölund <erik.sjolund@gmail.com<mailto:erik.sjolund@gmail.com>> wrote:
>
> Hi Andreas,
>
> I think the future for prime-phylo (C++) does not look that good.
> No development has happened for many years as the project was abandoned
> for a Java implementation.
> https://github.com/arvestad/jprime
>
> Although I maintained the web site
> http://prime.sbc.su.se
> before, now the DNS has changed to point to another web server
> where I don't have any log in permission.
>
> I CC Lars Arvestad (the owner of the project), if there is anything he
> wants to add.
>
> Best regards,
> Erik
>
>
>
>
>
>
>
>
> On Sun, May 20, 2018 at 6:31 AM, Andreas Tille <andreas@fam-tille.de> wrote:
> Hi Erik,
>
> besides this issue (and others that where solved inside Debian
> meanwhile) I realised that the download location of PrIME has vanished.
>
> Could you please check this?
>
> Kind regards
>
> Andreas.
>
> ----- Forwarded message from Dominic Hargreaves <dom@earth.li> -----
>
> Date: Sat, 19 May 2018 18:01:53 +0200
> From: Dominic Hargreaves <dom@earth.li>
> To: submit@bugs.debian.org
> Subject: Bug#899129: prime-phylo: FTBFS: cd obj-x86_64-linux-gnu && make -j8 -Oline returned exit code 2
> X-Debian-PR-Message: report 899129
> X-Debian-PR-Package: src:prime-phylo
> X-Debian-PR-Keywords:
> X-Debian-PR-Source: prime-phylo
>
> Source: prime-phylo
> Version: 1.0.11-4
> Severity: serious
> Justification: FTBFS
> User: debian-perl@lists.debian.org
> Usertags: hh2018
>
> When testing packages against the upcoming release of perl, we found
> an unrelated FTBFS on a clean sid chroot:
>
> cd /<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime && /usr/bin/c++ -DONLY_ONE_TIMESAMPLE -DPERTURBED_NODE -Dprime_phylo_EXPORTS -I/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/src/cxx/libraries/prime -I/<<PKGBUILDDIR>>/src/cxx/libraries/prime -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/ompi/mpi/cxx -I/usr/include/libxml2 -I/<<PKGBUILDDIR>>/src/cxx/libraries -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx -I/usr/lib/openmpi/include/openmpi/ompi/mpi/cxx -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wreorder -Wall -fexceptions -g -fPIC -std=gnu++98 -o CMakeFiles/prime-phylo.dir/TreeIO.cc.o -c /<<PKGBUILDDIR>>/src/cxx/libraries/prime/TreeIO.cc
> make[3]: Leaving directory '/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu'
> make[2]: *** [CMakeFiles/Makefile2:137: src/cxx/libraries/prime/CMakeFiles/prime-phylo.dir/all] Error 2
> make[1]: *** [Makefile:155: all] Error 2
> dh_auto_build: cd obj-x86_64-linux-gnu && make -j8 -Oline returned exit code 2
> make: *** [debian/rules:10: build] Error 25
>
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> ----- End forwarded message -----
>
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> http://fam-tille.de
>
>
> --
> Swedish e-Science Research Center
> Science for Life Laboratory
> Dept of Mathematics
> Stockholm University
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