[Debian-med-packaging] Just commited new version of vg but its not finding header files provided ba libseqlib-dev

[Étienne Mollier]

Hi there,

Andreas Tille, on 2020-12-13 22:26:14 +0100:
> . ./source_me.sh && g++ -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack  -I/build/vg-1.29.0+ds/include -isystem /build/vg-1.29.0+ds/include -I. -I/build/vg-1.29.0+ds/src -I/build/vg-1.29.0+ds/src/unittest -I/build/vg-1.29.0+ds/src/subcommand -I/build/vg-1.29.0+ds/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/build/vg-1.29.0+ds=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -msse3 -fopenmp -MMD -MP -c -o obj/readfilter.o src/readfilter.cpp 
> In file included from src/readfilter.cpp:1:
> src/readfilter.hpp:14:10: fatal error: IntervalTree.h: No such file or directory
>    14 | #include "IntervalTree.h"
>       |          ^~~~~~~~~~~~~~~~
> compilation terminated.

Apparently the above is due to a refresh needed to the patch
use_packaged_vcflib.  I'm running a build at the moment, will
push when I have something that I can confirm does not ftbfs.
There are probably a few other similar issues because I'm
catching this in my current log:

. ./source_me.sh && g++ -Wl,-z,relro -Wl,-z,now -I/usr/include/fastahack -I/usr/include/smithwaterman -I/usr/include/vcflib -I/usr/include/smithwaterman -I/usr/include/fastahack -I/<<PKGBUILDDIR>>/include -isystem /<<PKGBUILDDIR>>/include -I. -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/unittest -I/<<PKGBUILDDIR>>/src/subcommand -I/<<PKGBUILDDIR>>/include/dynamic -pthread -isystem /usr/include/cairo -isystem /usr/include/glib-2.0 -isystem /usr/lib/x86_64-linux-gnu/glib-2.0/include -isystem /usr/include/pixman-1 -isystem /usr/include/uuid -isystem /usr/include/freetype2 -isystem /usr/include/libpng16 -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -Werror=return-type -std=c++14 -ggdb -g -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -mavx2 -fopenmp -o test/build_graph test/build_graph.cpp -lvg -L/<<PKGBUILDDIR>>/lib /<<PKGBUILDDIR>>/lib/libvgio.a -lz -lvcflib -lgssw -lssw -lsublinearLS -lpthread -lncurses -lgcsa2 -lgbwtgraph -lgbwt -ldivsufsort -ldivsufsort64 -lraptor2 -lpinchesandcacti -l3edgeconnected -lsonlib -lfml -lstructures -lvw -lallreduce -lbdsg -lxg -lsdsl -lhandlegraph -lfastahack -lsmithwaterman -ldisorder -lvcflib -lsmithwaterman -ldisorder -lfastahack -lhts -ltabixpp -lcairo -lz -lgobject-2.0 -lffi -lglib-2.0 -pthread -lpcre -pthread -lpixman-1 -lfontconfig -luuid -lexpat -lfreetype -lbrotlidec -lbrotlicommon -lpng16 -lm -lz -lm -lz -lxcb-shm -lxcb-render -lXrender -lXext -lX11 -lpthread -lxcb -lXau -lXdmcp -ljansson -latomic -rdynamic -ldw -lelf "-lboost_program_options""" -ldl -llzma -lbz2 -lrocksdb -lbz2 -ljemalloc -Wl,-Bstatic /<<PKGBUILDDIR>>/lib/libhts.a /<<PKGBUILDDIR>>/lib/libdeflate.a -lz -lbz2 -llzma -lprotobuf -lz -Wl,-Bdynamic 
g++: error: /<<PKGBUILDDIR>>/lib/libhts.a: No such file or directory
g++: error: /<<PKGBUILDDIR>>/lib/libdeflate.a: No such file or directory
make[2]: *** [Makefile:376: test/build_graph] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j6 "INSTALL=install --strip-program=true" SFX=-avx2 all test/build_graph bin/shuf returned exit code 2

Will continue on that trail...

Kind Regards,
-- 
Étienne Mollier <etienne.mollier at mailoo.org>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/0, please excuse my verbosity.
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