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

[Andreas Tille]

Hi Michael,

I've just commited the new version of vg and adapted the patches.  I
wanted to try the latest upstream version before contacting upstream
about the arm64 issue.  Unfortunately I get

...
. ./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.


I tried the patch


--- a/Makefile
+++ b/Makefile
@@ -50,11 +50,11 @@ DEPGEN_FLAGS := -MMD -MP
 # necessary on all platforms and suppresses warnings.
 # Also, pkg-config flags need to be made -isystem if our dependency install
 # directory is, or they might put a system HTSlib before ours.
-INCLUDE_FLAGS :=$(shell $(PKG_CONFIG) --cflags libfastahack) $(shell $(PKG_CONFIG) --cflags libsmithwaterman) $(shell $(PKG_CONFIG) --cflags libvcflib) -I$(CWD)/$(INC_DIR) -isystem $(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) | sed 's/ -I/ -isystem /g')
+INCLUDE_FLAGS :=$(shell $(PKG_CONFIG) --cflags libfastahack) $(shell $(PKG_CONFIG) --cflags libsmithwaterman) $(shell $(PKG_CONFIG) --cflags libvcflib) $(shell $(PKG_CONFIG) --cflags libseqlib) -I$(CWD)/$(INC_DIR) -isystem $(CWD)/$(INC_DIR) -I. -I$(CWD)/$(SRC_DIR) -I$(CWD)/$(UNITTEST_SRC_DIR) -I$(CWD)/$(SUBCOMMAND_SRC_DIR) -I$(CWD)/$(INC_DIR)/dynamic $(shell $(PKG_CONFIG) --cflags $(PKG_CONFIG_DEPS) $(PKG_CONFIG_STATIC_DEPS) | sed 's/ -I/ -isystem /g')
 
 # Define libraries to link against.
 LD_LIB_DIR_FLAGS := -L$(CWD)/$(LIB_DIR)
-LD_LIB_FLAGS := $(CWD)/$(LIB_DIR)/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 $(shell $(PKG_CONFIG) --libs libfastahack) $(shell $(PKG_CONFIG) --libs libsmithwaterman) $(shell $(PKG_CONFIG) --libs libvcflib) $(shell $(PKG_CONFIG) --libs htslib) -ltabixpp
+LD_LIB_FLAGS := $(CWD)/$(LIB_DIR)/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 $(shell $(PKG_CONFIG) --libs libfastahack) $(shell $(PKG_CONFIG) --libs libsmithwaterman) $(shell $(PKG_CONFIG) --libs libvcflib) $(shell $(PKG_CONFIG) --libs libseqlib) $(shell $(PKG_CONFIG) --libs htslib) -ltabixpp
 # We omit Boost Program Options for now; we find it in a platform-dependent way.
 # By default it has no suffix
 BOOST_SUFFIX=""


but this does not work.  Can you have a look?

Kind regards

      Andreas.




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