Hi Andreas,
On 6/13/19 1:03 AM, Andreas Tille wrote:
What directory has to be built and what files need to be installed?
Run:
make bin/arb_pt_server
and
make lib/arb_tcp.dat
That should do it. I think you have all files required.
I'd make it a sepearate package, something like arb-pt-server, with
arb-pt-server.install:
bin/arb_pt_server usr/bin
lib/arb_tcp.dat /etc/arb
arb-pt-server.links:
etc/arb/arb_tcp.dat usr/lib/${DEB_HOST_MULTIARCH}/arb
For the moment for me the take away message from the paragraph above
is that we need arb_tcp.dat from the original arb tarball. Anything
else?
For backround: the "pt server" is a sequence search engine. It's very
fast, but a memory hog. It was implemented as a daemon so that multiple
users can share the index (which used to take hours to load). Not really
common any more, but back in the day when 32MB was a ton of memory that
was different.
If you can package the arb_pt_server binary as above, the tests for SINA
should run fine.
If you cannot, you could just delete the file
"SINA/tests/accuracy.tests" and then run "make check-filtered P=^tests"
instead of "make check".
The accuracy.tests file contains integration tests checking overall
accuracy with the PT server. There is a second file that does the same
tests with the internal engine. So not running it is fine. The
check-filtered call avoids running the unit tests, calling only the
integration tests on the fully built binary. That should be fine for
packaging - you don't need to have 100% code coverage, you need to know
that the build isn't broken.
I would prefer the solution with tested arb_pt_server support. If I was
to add a "no pt server support" flag to SINA it would have to disable
the support as well, not just the tests. I can do that, it's going to be
quite a bit of work though.
This is perfectly understood and to prove this I have updated
Apologies, I was just trying to make sure no time got wasted on it.
Supporting old versions is a luxury I have to keep minimized.
Thanks a lot for your contribution which is very motivating
Thanks! :) I'm sorry that help from "upstream" is required. For good
software, that should not be necessary.
W.r.t. the build log - this is where it failed first:
configure:14608: checking arbdb.h usability
configure:14608: g++ -c -g -O2
-fdebug-prefix-map=/build/sina-1.6.0+dfsg=. -fstack-protector-strong
-Wformat -Werror=format-security -g -O2
-fdebug-prefix-map=/build/sina-1.6.0+dfsg=. -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2
-DNDEBUG -I/usr/lib/x86_64-linux-gnu/arb/INCLUDE
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
conftest.cpp >&5
conftest.cpp:63:10: fatal error: arbdb.h: No such file or directory
#include <arbdb.h>
^~~~~~~~~
Check that /usr/lib/x86_64-linux-gnu/arb/INCLUDE/arbdb.h exists. Perhaps
I messed up the patch for libarb-dev. INCLUDE should point to
/usr/include/arb.
Elmar
