Re: Building roadrunner from your salsa branch
Hi,
On Tue, Feb 16, 2021 at 04:46:38PM +0000, B Thomas wrote:
>
> I have no problem. Just that I would have preferred to use a different
> email address for mailing lists to keep the spam bots at check.
Argh, sorry about that.
> > Are you sure about this? I get:
>
> Here is the build error I see (different from yours)
>
> [ 9%] Building CXX object source/CMakeFiles/roadrunner-static.dir/rrRoadRunner.cpp.o
> cd /home/bt/debian/sysbio/roadrunner/git/roadrunner/obj-x86_64-linux-gnu/source && /usr/bin/c++ -DBUILD_LLVM -DLIBLAX_STATIC -DLIBSBML_STATIC -DLIBSBML_USE_CPP_NAMESPACE -DPOCO_NO_AUTOMATIC_LIBS -DPOCO_STATIC -DSTATIC_LIBSTRUCT -DSTATIC_NLEQ1 -DSTATIC_NLEQ2 -DSTATIC_PUGI -DSTATIC_RR -I/home/bt/debian/sysbio/roadrunner/git/roadrunner -I/home/bt/debian/sysbio/roadrunner/git/roadrunner/third_party -I/usr/include/libxml2 -I/usr/lib/llvm-7/include -I/home/bt/debian/sysbio/roadrunner/git/roadrunner/obj-x86_64-linux-gnu/source -I/home/bt/debian/sysbio/roadrunner/git/roadrunner/source/. -I/usr/include/rr-libstruct -I/usr/include/sbml -I/usr/include/cvode -g -O2 -fdebug-prefix-map=/home/bt/debian/sysbio/roadrunner/git/roadrunner=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -o CMakeFiles/roadrunner-static.dir/rrRoadRunner.cpp.o -c /home/bt/debian/sysbio/roadrunner/git/roadrunner/source/rrRoadRunner.cpp
> In file included from /home/bt/debian/sysbio/roadrunner/git/roadrunner/source/rrRoadRunner.cpp:11:
> /home/bt/debian/sysbio/roadrunner/git/roadrunner/source/rrRoadRunner.h:5:10: fatal error: rr-libstruct/lsMatrix.h: No such file or directory
> #include "rr-libstruct/lsMatrix.h"
> ^~~~~~~~~~~~~~~~~~~~~~~~~
OK, thanks to Aaron's hint we are not at same level. I suspect you did
not build against Debian sid and the g++ you were using might not be as
picky as the latest gcc 10.x.
> I was building commit with git sha 183ad2dc76a1a4daa17919f68cdd5c4af64779d8
> CommitDate: Tue May 12 16:53:08 2020 +0200. I was building on
> Debian/Stable and prefer to stay on it till next release.
Sure, that's fine. But new packages always will be built against sid
and thus need to compile there. But as I said that should be settled
now.
> > and since I have no solution for this I stopped working on this issue
> > (and I admit I nearly forgot this project - thanks for bringing it up to
> > my radar again ;-) ).
>
> No problem. Actually I am interested in Debian packages for the
> following Tellurium (http://tellurium.analogmachine.org/) (RoadRunner is
> one of its dependencies). I will be happy to help in packing both, in
> what ever time I can pull out. Let me know how I can help.
>
> > Where did you found that repository?
>
> Here is the where I found the git repo for rr-libstruct
>
> https://github.com/sys-bio/rr-libstruct
>
> rr-libstruct has one problem. It depends on clapack, which as far as I
> understand is deprecated. lapacke is now the standard C interface to
> lapack. I am thinking of investigating how easy it will be to
> migrate it to lapacke (already in debian) and create a pull request
> for upstream.
This would be extremely helpful. BTW, if you might have problems
with this on debian-science@lists.debian.org I once found some help
when I needed to port some other package from clapack to lapacke.
If you might be successfully with your patch I can have a look into
packaging rr-libstruct which looks not like a really big problem
(after a *very* quick look!)
Thanks a lot for your interest
Andreas.
--
http://fam-tille.de
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