Re: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye)

2019-12-13 Thread Andrey Rahmatullin
On Fri, Dec 13, 2019 at 10:10:03PM +0100, Andreas Tille wrote: > i$ pdb2pqr > Traceback (most recent call last): > File "/usr/bin/pdb2pqr", line 52, in > from main import mainCommand > File "/usr/share/pdb2pqr/main.py", line 77, in > import extensions > File

Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye)

2019-12-13 Thread Andreas Tille
On Fri, Dec 13, 2019 at 10:49:45PM +0500, Andrey Rahmatullin wrote: > > I think at least this is solved now: > > > > > > https://salsa.debian.org/med-team/pdb2pqr/commit/1f4ee901456641140ef18ca8e91e4701e1175410 > > Nice catch, "env.Append(LIBS=[python_lib])" where "python_lib = 'python' + >

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andrey Rahmatullin
On Fri, Dec 13, 2019 at 03:49:22PM +0100, Andreas Tille wrote: > > g++ -o pdb2pka/substruct/Algorithms.cpython-37m-x86_64-linux-gnu.so > > -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib > > -lpython3.7m -lpython3.7 > > /usr/bin/ld: cannot find -lpython3.7 > >

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andreas Tille
On Fri, Dec 13, 2019 at 03:16:32PM +0100, Andreas Tille wrote: > > ... > g++ -o pdb2pka/substruct/Algorithms.cpython-37m-x86_64-linux-gnu.so > -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib > -lpython3.7m -lpython3.7 > /usr/bin/ld: cannot find -lpython3.7 > collect2:

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andreas Tille
On Fri, Dec 13, 2019 at 05:46:42PM +0500, Andrey Rahmatullin wrote: > > > > Thanks for that additional hint. I can confirm that I checked whether > > pkgconfig can be used before I was asking here. But we seem to agree > > that this is not the case. I admit I have no real clue how to convince

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andrey Rahmatullin
On Fri, Dec 13, 2019 at 01:40:34PM +0100, Andreas Tille wrote: > > > g++ -o pdb2pka/substruct/Algorithms.cpython-37m-x86_64-linux-gnu.so > > > -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os > > > -L/usr/lib -lpython3.7 > > > /usr/bin/ld: cannot find -lpython3.7 > > Actually,

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andreas Tille
Hi Andrey, On Fri, Dec 13, 2019 at 05:18:45PM +0500, Andrey Rahmatullin wrote: > On Fri, Dec 13, 2019 at 09:49:47AM +0100, Andreas Tille wrote: > > g++ -o pdb2pka/substruct/Algorithms.cpython-37m-x86_64-linux-gnu.so > > -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andrey Rahmatullin
On Fri, Dec 13, 2019 at 09:49:47AM +0100, Andreas Tille wrote: > g++ -o pdb2pka/substruct/Algorithms.cpython-37m-x86_64-linux-gnu.so > -Wl,-z,relro -Wl,-z,now -shared pdb2pka/substruct/Algorithms.os -L/usr/lib > -lpython3.7 > /usr/bin/ld: cannot find -lpython3.7 Actually, it's a different

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andreas Tille
On Fri, Dec 13, 2019 at 03:23:19PM +0500, Andrey Rahmatullin wrote: > On Fri, Dec 13, 2019 at 09:49:47AM +0100, Andreas Tille wrote: > > So how can I enable proper linking to -lpython3.7 which is obviously not > > in the library search path (but package libpython3.7 is definitely > > installed in

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andrey Rahmatullin
On Fri, Dec 13, 2019 at 09:49:47AM +0100, Andreas Tille wrote: > So how can I enable proper linking to -lpython3.7 which is obviously not > in the library search path (but package libpython3.7 is definitely > installed in the pbuilder chroot). To link to a library you need to install its -dev

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-13 Thread Andreas Tille
Hi Scott, On Thu, Dec 12, 2019 at 04:34:09PM -0500, Scott Talbert wrote: > On Thu, 12 Dec 2019, Andreas Tille wrote: > > mkdir -p /build/pdb2pqr-2.1.1+dfsg/debian/tmp/usr/share/pdb2pqr > > scons \ > >URL="http://localhost/pdb2pqr/; \ > >

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-12 Thread Scott Talbert
On Thu, 12 Dec 2019, Andreas Tille wrote: That hint was helpful anyway and I get further now. I think now the problem is to convince scons to install in $(CURDIR)/debian/tmp which seems to try rather /usr/share/pdb2pqr directly: Looks like the debian/rules file is specifying

Re: Bug#937262: Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-12 Thread Andreas Tille
On Thu, Dec 12, 2019 at 03:49:13PM -0500, Scott Talbert wrote: > > > > That hint was helpful anyway and I get further now. I think now the > > problem is to convince scons to install in $(CURDIR)/debian/tmp which > > seems to try rather /usr/share/pdb2pqr directly: > > Looks like the

Help with scons needed (Was: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye))

2019-12-12 Thread Andreas Tille
Hi Scott, On Thu, Dec 12, 2019 at 11:31:09AM -0500, Scott Talbert wrote: > On Thu, 12 Dec 2019, Andreas Tille wrote: > > I don't see any Python3 changes in that repository. Did you push your > changes? Argh, its pushed now. > Anyway, the problem is likely in CopySubAction in

Re: Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye)

2019-12-12 Thread Scott Talbert
On Thu, 12 Dec 2019, Andreas Tille wrote: Control: tags -1 help Hi, it seems pdb2pqr is orphaned upstream. However, it seems to be worth keeping inside Debian thus I tried my luck to port it to Python3 in Git[1]. Unfortunately the build runs into scons: Building targets ...

Help needed (Was: pdb2pqr: Python2 removal in sid/bullseye)

2019-12-12 Thread Andreas Tille
Control: tags -1 help Hi, it seems pdb2pqr is orphaned upstream. However, it seems to be worth keeping inside Debian thus I tried my luck to port it to Python3 in Git[1]. Unfortunately the build runs into scons: Building targets ... CopySubAction("pdb2pqr.py", "pdb2pqr.py.in")