Your message dated Wed, 22 Jul 2020 11:48:47 +0000
with message-id <[email protected]>
and subject line Bug#957268: fixed in genometools 1.6.1+ds-3
has caused the Debian Bug report #957268,
regarding genometools: ftbfs with GCC-10
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
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--
957268: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957268
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:genometools
Version: 1.6.1+ds-2
Severity: normal
Tags: sid bullseye
User: [email protected]
Usertags: ftbfs-gcc-10
Please keep this issue open in the bug tracker for the package it
was filed for. If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.
The package fails to build in a test rebuild on at least amd64 with
gcc-10/g++-10, but succeeds to build with gcc-9/g++-9. The
severity of this report will be raised before the bullseye release,
so nothing has to be done for the buster release.
The full build log can be found at:
http://people.debian.org/~doko/logs/gcc10-20200225/genometools_1.6.1+ds-2_unstable_gcc10.log
The last lines of the build log are at the end of this report.
To build with GCC 10, either set CC=gcc-10 CXX=g++-10 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.
apt-get -t=experimental install g++
Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-10/porting_to.html
[...]
test -d obj/src/examples || mkdir -p obj/src/examples
cc -c src/examples/gff3sort.c -o obj/src/examples/gff3sort.o -Wdate-time
-D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/glib-2
.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith
-Wno-unknown-pragmas -O3
cc -c src/tools/gt_wtree.c -o obj/src/tools/gt_wtree.d -Wdate-time
-D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/glib-2.0 -I/
usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -MM -MP -MT obj/src/tools/gt_wtree.o
test -d obj/src/examples || mkdir -p obj/src/examples
cc -c src/examples/gff3validator.c -o obj/src/examples/gff3validator.o
-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN
-DLUA_USE_MKSTEMP -DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2
-I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz
-I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2
-I/usr/include/libpng16 -I/usr/incl
ude/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith
-Wno-unknown-pragmas -O3
cc -c src/examples/custom_stream.c -o obj/src/examples/custom_stream.d
-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN
-DLUA_USE_MKSTEMP -DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2
-I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz
-I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2
-I/usr/include/libpng16 -I/usr/incl
ude/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -MM -MP -MT obj/src/examples/custom_stream.o
cc -c src/examples/gff3sort.c -o obj/src/examples/gff3sort.d -Wdate-time
-D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/glib-2
.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -MM -MP -MT obj/src/examples/gff3sort.o
test -d obj/src/examples || mkdir -p obj/src/examples
cc -c src/examples/noop.c -o obj/src/examples/noop.o -Wdate-time
-D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/glib-2.0 -I/us
r/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith
-Wno-unknown-pragmas -O3
cc -c src/examples/gff3validator.c -o obj/src/examples/gff3validator.d
-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN
-DLUA_USE_MKSTEMP -DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2
-I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz
-I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2
-I/usr/include/libpng16 -I/usr/incl
ude/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -MM -MP -MT obj/src/examples/gff3validator.o
cc -c src/tools/gt_wtree_bench.c -o obj/src/tools/gt_wtree_bench.d -Wdate-time
-D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/
glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -MM -MP -MT obj/src/tools/gt_wtree_bench.o
test -d obj/src/examples || mkdir -p obj/src/examples
cc -c src/examples/sketch_constructed.c -o
obj/src/examples/sketch_constructed.o -Wdate-time -D_FORTIFY_SOURCE=2
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -
I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith
-Wno-unknown-pragmas -O3
test -d obj/src/examples || mkdir -p obj/src/examples
cc -c src/examples/sketch_parsed_with_ctrack.c -o
obj/src/examples/sketch_parsed_with_ctrack.o -Wdate-time -D_FORTIFY_SOURCE=2
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/incl
ude/libpng16 -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith
-Wno-unknown-pragmas -O3
test -d obj/src/examples || mkdir -p obj/src/examples
cc -c src/examples/sketch_parsed_with_ordering.c -o
obj/src/examples/sketch_parsed_with_ordering.o -Wdate-time -D_FORTIFY_SOURCE=2
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/
include/libpng16 -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith
-Wno-unknown-pragmas -O3
cc -c src/examples/noop.c -o obj/src/examples/noop.d -Wdate-time
-D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/glib-2.0 -I/us
r/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -MM -MP -MT obj/src/examples/noop.o
test -d obj/src/examples || mkdir -p obj/src/examples
cc -c src/examples/sketch_parsed.c -o obj/src/examples/sketch_parsed.o
-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN
-DLUA_USE_MKSTEMP -DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2
-I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz
-I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2
-I/usr/include/libpng16 -I/usr/incl
ude/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith
-Wno-unknown-pragmas -O3
cc -c src/examples/sketch_constructed.c -o
obj/src/examples/sketch_constructed.d -Wdate-time -D_FORTIFY_SOURCE=2
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16 -
I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -MM -MP -MT obj/src/examples/sketch_constructed.o
test -d lib || mkdir -p lib
cc -c src/examples/sketch_parsed_with_ctrack.c -o
obj/src/examples/sketch_parsed_with_ctrack.d -Wdate-time -D_FORTIFY_SOURCE=2
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/incl
ude/libpng16 -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -MM -MP -MT
obj/src/examples/sketch_parsed_with_ctrack.o
ar r lib/libgenometools.a obj/src/core/alphabet.o obj/src/core/array.o
obj/src/core/array2dim.o obj/src/core/array2dim_sparse.o
obj/src/core/array3dim.o obj/src/core/basename.o obj/src/core/bioseq.o
obj/src/core/bioseq_col.o obj/src/core/bioseq_iterator.o
obj/src/core/bitbuffer.o obj/src/core/bitpackstringop.o
obj/src/core/bitpackstringop16.o obj/src/core/bitpackstringop32.o
obj/src/core/bitpackstringop64.o obj/src/core/bitpackstringop8.o
obj/src/core/bittab.o obj/src/core/bool_matrix.o obj/src/core/bsearch.o
obj/src/core/byte_popcount.o obj/src/core/byte_select.o
obj/src/core/checkbitpackarray.o obj/src/core/checkbitpackstring-int.o
obj/src/core/checkbitpackstring.o obj/src/core/checkbitpackstring16.o
obj/src/core/checkbitpackstring32.o obj/src/core/checkbitpackstring64.o
obj/src/core/checkbitpackstring8.o obj/src/core/class_alloc.o
obj/src/core/class_alloc_lock.o obj/src/core/codon_iterator.o
obj/src/core/codon_iterator_encseq.o obj/src/core/codon_iterator_simple.o
obj/src/core/col
orspace.o obj/src/core/combinatorics.o obj/src/core/compact_ulong_store.o
obj/src/core/compat.o obj/src/core/complement.o obj/src/core/countingsort.o
obj/src/core/cstr.o obj/src/core/cstr_array.o obj/src/core/cstr_table.o
obj/src/core/csvline_reader.o obj/src/core/desc_buffer.o
obj/src/core/disc_distri.o obj/src/core/dlist.o obj/src/core/dual-pivot-qsort.o
obj/src/core/dyn_bittab.o obj/src/core/dynalloc.o obj/src/core/eansi.o
obj/src/core/ebzlib.o obj/src/core/encseq.o obj/src/core/encseq_access_type.o
obj/src/core/encseq_col.o obj/src/core/encseq_metadata.o
obj/src/core/encseq_options.o obj/src/core/encseq_ptr.o
obj/src/core/endianess.o obj/src/core/error.o obj/src/core/example.o
obj/src/core/example_a.o obj/src/core/example_b.o obj/src/core/ezlib.o
obj/src/core/fa.o obj/src/core/fasta.o obj/src/core/fasta_reader.o
obj/src/core/fasta_reader_fsm.o obj/src/core/fasta_reader_rec.o
obj/src/core/fasta_reader_seqit.o obj/src/core/fastq.o obj/src/core/file.o
obj/src/core/fileutils.o obj/s
rc/core/gc_content.o obj/src/core/grep.o obj/src/core/gtdatapath.o
obj/src/core/hashmap.o obj/src/core/hashtable.o obj/src/core/init.o
obj/src/core/interval_tree.o obj/src/core/io.o obj/src/core/log.o
obj/src/core/logger.o obj/src/core/ma.o obj/src/core/mapspec.o
obj/src/core/mathsupport.o obj/src/core/md5_encoder.o
obj/src/core/md5_fingerprint.o obj/src/core/md5_seqid.o obj/src/core/md5_tab.o
obj/src/core/msort.o obj/src/core/multithread.o obj/src/core/option.o
obj/src/core/orf.o obj/src/core/output_file.o obj/src/core/parseutils.o
obj/src/core/password_entry.o obj/src/core/phase.o obj/src/core/process.o
obj/src/core/progressbar.o obj/src/core/qsort-ulong.o obj/src/core/qsort_r.o
obj/src/core/quality.o obj/src/core/queue.o obj/src/core/radix_sort.o
obj/src/core/range.o obj/src/core/readmode.o obj/src/core/safearith.o
obj/src/core/score_function.o obj/src/core/score_matrix.o obj/src/core/seq.o
obj/src/core/seq_col.o obj/src/core/seq_info_cache.o
obj/src/core/seq_iterator.o obj/src/c
ore/seq_iterator_fastq.o obj/src/core/seq_iterator_sequence_buffer.o
obj/src/core/sequence_buffer.o obj/src/core/sequence_buffer_embl.o
obj/src/core/sequence_buffer_fasta.o obj/src/core/sequence_buffer_fastq.o
obj/src/core/sequence_buffer_gb.o obj/src/core/sequence_buffer_plain.o
obj/src/core/showtime.o obj/src/core/sig.o obj/src/core/spacepeak.o
obj/src/core/splitter.o obj/src/core/str.o obj/src/core/str_array.o
obj/src/core/str_cache.o obj/src/core/strand.o obj/src/core/strcmp.o
obj/src/core/string_distri.o obj/src/core/symbol.o obj/src/core/thread.o
obj/src/core/timer.o obj/src/core/tokenizer.o obj/src/core/tool.o
obj/src/core/tool_iterator.o obj/src/core/toolbox.o obj/src/core/tooldriver.o
obj/src/core/trans_table.o obj/src/core/translator.o
obj/src/core/unit_testing.o obj/src/core/version.o obj/src/core/versionfunc.o
obj/src/core/warning.o obj/src/core/xansi.o obj/src/core/xbsd.o
obj/src/core/xbzlib.o obj/src/core/xposix.o obj/src/core/xzlib.o
obj/src/core/yarandom.o obj/src/ex
tended/add_ids_stream.o obj/src/extended/add_ids_visitor.o
obj/src/extended/add_introns_stream.o obj/src/extended/affinealign.o
obj/src/extended/aligned_segment.o obj/src/extended/aligned_segments_pile.o
obj/src/extended/alignment.o obj/src/extended/anno_db_gfflike.o
obj/src/extended/anno_db_schema.o obj/src/extended/array_in_stream.o
obj/src/extended/array_out_stream.o
obj/src/extended/assembly_stats_calculator.o obj/src/extended/bed_in_stream.o
obj/src/extended/bed_parser.o obj/src/extended/bitinstream.o
obj/src/extended/bitoutstream.o obj/src/extended/blast_process_call.o
obj/src/extended/buffer_stream.o obj/src/extended/cds_check_stream.o
obj/src/extended/cds_check_visitor.o obj/src/extended/cds_stream.o
obj/src/extended/cds_visitor.o obj/src/extended/chain.o
obj/src/extended/check_boundaries_visitor.o obj/src/extended/chseqids_stream.o
obj/src/extended/clustered_set.o obj/src/extended/clustered_set_uf.o
obj/src/extended/coin_hmm.o obj/src/extended/collect_ids_visitor.o obj/src/
extended/comment_node.o obj/src/extended/compressed_bitsequence.o
obj/src/extended/condenseq.o obj/src/extended/condenseq_creator.o
obj/src/extended/condenseq_search_arguments.o obj/src/extended/consensus_sa.o
obj/src/extended/csa_gene.o obj/src/extended/csa_splice_form.o
obj/src/extended/csa_stream.o obj/src/extended/csa_variable_strands.o
obj/src/extended/csa_visitor.o obj/src/extended/cstr_iterator.o
obj/src/extended/diagonalbandalign.o
obj/src/extended/diagonalbandalign_affinegapcost.o obj/src/extended/dice_hmm.o
obj/src/extended/dot_out_stream.o obj/src/extended/dot_visitor.o
obj/src/extended/dup_feature_stream.o obj/src/extended/dup_feature_visitor.o
obj/src/extended/editscript.o obj/src/extended/elias_gamma.o
obj/src/extended/encdesc.o obj/src/extended/encdesc_header_io.o
obj/src/extended/eof_node.o obj/src/extended/evaluator.o
obj/src/extended/extract_feature_sequence.o
obj/src/extended/extract_feature_stream.o
obj/src/extended/extract_feature_visitor.o obj/src/extended/fast
a_header_iterator.o obj/src/extended/feature_in_stream.o
obj/src/extended/feature_index.o obj/src/extended/feature_index_memory.o
obj/src/extended/feature_info.o obj/src/extended/feature_node.o
obj/src/extended/feature_node_iterator.o
obj/src/extended/feature_node_observer.o obj/src/extended/feature_out_stream.o
obj/src/extended/feature_stream.o obj/src/extended/feature_visitor.o
obj/src/extended/gap_str.o obj/src/extended/genome_node.o
obj/src/extended/gff3_escaping.o obj/src/extended/gff3_in_stream.o
obj/src/extended/gff3_in_stream_plain.o
obj/src/extended/gff3_linesorted_out_stream.o
obj/src/extended/gff3_numsorted_out_stream.o obj/src/extended/gff3_out_stream.o
obj/src/extended/gff3_output.o obj/src/extended/gff3_parser.o
obj/src/extended/gff3_visitor.o obj/src/extended/globalchaining.o
obj/src/extended/golomb.o obj/src/extended/gtdatahelp.o
obj/src/extended/gtf_in_stream.o obj/src/extended/gtf_out_stream.o
obj/src/extended/gtf_parser.o obj/src/extended/gtf_visitor.o obj/src/ext
ended/hcr.o obj/src/extended/hmm.o obj/src/extended/hpol_processor.o
obj/src/extended/huffcode.o obj/src/extended/id_to_md5_stream.o
obj/src/extended/id_to_md5_visitor.o obj/src/extended/inter_feature_stream.o
obj/src/extended/inter_feature_visitor.o obj/src/extended/intset.o
obj/src/extended/intset_16.o obj/src/extended/intset_32.o
obj/src/extended/intset_8.o obj/src/extended/intset_combined.o
obj/src/extended/io_function_pointers.o obj/src/extended/kmer_database.o
obj/src/extended/linearalign.o obj/src/extended/linearalign_affinegapcost.o
obj/src/extended/linspace_management.o obj/src/extended/load_stream.o
obj/src/extended/luahelper.o obj/src/extended/luaserialize.o
obj/src/extended/mapping.o obj/src/extended/match.o
obj/src/extended/match_blast.o obj/src/extended/match_iterator.o
obj/src/extended/match_iterator_blast.o obj/src/extended/match_iterator_last.o
obj/src/extended/match_iterator_open.o obj/src/extended/match_iterator_sw.o
obj/src/extended/match_last.o obj/src/extended/
match_open.o obj/src/extended/match_sw.o obj/src/extended/match_visitor.o
obj/src/extended/maxcoordvalue.o obj/src/extended/md5_to_id_stream.o
obj/src/extended/md5_to_id_visitor.o obj/src/extended/md5set.o
obj/src/extended/merge_feature_stream.o
obj/src/extended/merge_feature_visitor.o obj/src/extended/merge_stream.o
obj/src/extended/meta_node.o obj/src/extended/multi_sanitizer_visitor.o
obj/src/extended/multieoplist.o obj/src/extended/mutate.o
obj/src/extended/node_stream.o obj/src/extended/node_visitor.o
obj/src/extended/obo_parse_tree.o obj/src/extended/obo_stanza.o
obj/src/extended/orf_finder_stream.o obj/src/extended/orf_finder_visitor.o
obj/src/extended/orf_iterator.o obj/src/extended/orphanage.o
obj/src/extended/permute_words.o obj/src/extended/popcount_tab.o
obj/src/extended/priority_queue.o obj/src/extended/ranked_list.o
obj/src/extended/rbtree.o obj/src/extended/rcr.o obj/src/extended/rdb.o
obj/src/extended/rdb_sqlite.o obj/src/extended/rdb_visitor.o
obj/src/extended/recon
structalignment.o obj/src/extended/region_mapping.o
obj/src/extended/region_node.o obj/src/extended/region_node_builder.o
obj/src/extended/regioncov_visitor.o obj/src/extended/regular_seqid.o
obj/src/extended/reverse.o obj/src/extended/rmq.o obj/src/extended/safe_popen.o
obj/src/extended/sam_alignment.o obj/src/extended/sam_query_name_iterator.o
obj/src/extended/samfile_encseq_mapping.o obj/src/extended/samfile_iterator.o
obj/src/extended/sampling.o obj/src/extended/scorehandler.o
obj/src/extended/script_filter.o obj/src/extended/script_wrapper_stream.o
obj/src/extended/script_wrapper_visitor.o obj/src/extended/select_stream.o
obj/src/extended/select_visitor.o obj/src/extended/seqid2file.o
obj/src/extended/seqid2seqnum_mapping.o obj/src/extended/seqpos_classifier.o
obj/src/extended/sequence_node.o obj/src/extended/sequence_node_add_stream.o
obj/src/extended/sequence_node_out_stream.o
obj/src/extended/sequence_node_out_visitor.o
obj/src/extended/set_source_visitor.o obj/src/extended/
shredder.o obj/src/extended/snp_annotator_stream.o
obj/src/extended/snp_annotator_visitor.o obj/src/extended/sort_stream.o
obj/src/extended/spec_results.o obj/src/extended/spec_visitor.o
obj/src/extended/splice_site_info_stream.o
obj/src/extended/splice_site_info_visitor.o obj/src/extended/splicedseq.o
obj/src/extended/squarealign.o obj/src/extended/sspliced_alignment.o
obj/src/extended/sspliced_alignment_parsing.o obj/src/extended/stat_stream.o
obj/src/extended/stat_visitor.o obj/src/extended/stream_evaluator.o
obj/src/extended/string_matching.o obj/src/extended/swalign.o
obj/src/extended/tag_value_map.o obj/src/extended/targetbest_select_stream.o
obj/src/extended/tidy_region_node_stream.o
obj/src/extended/tidy_region_node_visitor.o obj/src/extended/tir_stream.o
obj/src/extended/transcript_bittabs.o obj/src/extended/transcript_counts.o
obj/src/extended/transcript_evaluators.o obj/src/extended/transcript_exons.o
obj/src/extended/transcript_used_exons.o obj/src/extended/type_checker.
o obj/src/extended/type_checker_builtin.o obj/src/extended/type_checker_obo.o
obj/src/extended/type_graph.o obj/src/extended/type_node.o
obj/src/extended/typecheck_info.o obj/src/extended/uint64hashtable.o
obj/src/extended/union_find.o obj/src/extended/uniq_stream.o
obj/src/extended/visitor_stream.o obj/src/extended/wtree.o
obj/src/extended/wtree_encseq.o obj/src/extended/xrf_abbr_entry.o
obj/src/extended/xrf_abbr_parse_tree.o obj/src/extended/xrf_checker.o
obj/src/extended/xrfcheck_info.o obj/src/gtlua/alphabet_lua.o
obj/src/gtlua/annotationsketch_lua.o obj/src/gtlua/bittab_lua.o
obj/src/gtlua/canvas_lua.o obj/src/gtlua/cds_stream_lua.o
obj/src/gtlua/csa_stream_lua.o obj/src/gtlua/diagram_lua.o
obj/src/gtlua/encseq_lua.o obj/src/gtlua/feature_index_lua.o
obj/src/gtlua/feature_node_iterator_lua.o obj/src/gtlua/feature_stream_lua.o
obj/src/gtlua/feature_visitor_lua.o obj/src/gtlua/genome_node_lua.o
obj/src/gtlua/genome_stream_lua.o obj/src/gtlua/genome_visitor_lua.o
obj/src/gtlua/gt_
lua.o obj/src/gtlua/gtcore_lua.o obj/src/gtlua/gtext_lua.o
obj/src/gtlua/image_info_lua.o obj/src/gtlua/layout_lua.o
obj/src/gtlua/mathsupport_lua.o obj/src/gtlua/range_lua.o
obj/src/gtlua/region_mapping_lua.o obj/src/gtlua/score_matrix_lua.o
obj/src/gtlua/stream_evaluator_lua.o obj/src/gtlua/translate_lua.o
obj/src/match/apmeoveridx.o obj/src/match/asqg_writer.o
obj/src/match/bare-encseq.o obj/src/match/bcktab.o
obj/src/match/cgr_spacedseed.o obj/src/match/chain2dim.o
obj/src/match/chainofin.o obj/src/match/cutendpfx.o
obj/src/match/dbs_spaced_seeds.o obj/src/match/diagband-struct.o
obj/src/match/diagbandseed.o obj/src/match/dist-short.o obj/src/match/echoseq.o
obj/src/match/eis-blockcomp-param.o obj/src/match/eis-blockcomp.o
obj/src/match/eis-bwtseq-construct.o obj/src/match/eis-bwtseq-context-param.o
obj/src/match/eis-bwtseq-context.o obj/src/match/eis-bwtseq-extinfo.o
obj/src/match/eis-bwtseq-param.o obj/src/match/eis-bwtseq-sass.o
obj/src/match/eis-bwtseq.o obj/src/match/eis-en
cidxseq-construct.o obj/src/match/eis-encidxseq-param.o
obj/src/match/eis-encidxseq.o obj/src/match/eis-mrangealphabet.o
obj/src/match/eis-sa-common.o obj/src/match/eis-seqblocktranslate.o
obj/src/match/eis-seqranges.o obj/src/match/eis-sequencemultiread.o
obj/src/match/eis-specialsrank.o obj/src/match/eis-suffixarray-interface.o
obj/src/match/eis-suffixerator-interface.o obj/src/match/eis-voiditf.o
obj/src/match/encseq2offset.o obj/src/match/enum-patt.o
obj/src/match/esa-bottomup.o obj/src/match/esa-dfs.o
obj/src/match/esa-lcpintervals.o obj/src/match/esa-map.o
obj/src/match/esa-maxpairs.o obj/src/match/esa-merge.o
obj/src/match/esa-minunique.o obj/src/match/esa-mmsearch.o
obj/src/match/esa-scanprj.o obj/src/match/esa-seqread.o
obj/src/match/esa-shulen.o obj/src/match/esa-splititv-simple.o
obj/src/match/esa-splititv.o obj/src/match/esa-spmitvs.o
obj/src/match/esa-spmsk.o obj/src/match/esa_lcpintervals_visitor.o
obj/src/match/esa_spmitvs_visitor.o obj/src/match/esa_visitor.o obj/src
/match/firstcodes-accum.o obj/src/match/firstcodes-cache.o
obj/src/match/firstcodes-insert.o obj/src/match/firstcodes-psbuf.o
obj/src/match/firstcodes-scan.o obj/src/match/firstcodes-spacelog.o
obj/src/match/firstcodes-tab.o obj/src/match/firstcodes.o
obj/src/match/fmi-fwduni.o obj/src/match/fmi-keyval.o
obj/src/match/fmi-locate.o obj/src/match/fmi-map.o obj/src/match/fmi-mapspec.o
obj/src/match/fmi-mkindex.o obj/src/match/fmi-save.o
obj/src/match/fmi-sufbwtstream.o obj/src/match/ft-eoplist.o
obj/src/match/ft-front-generation.o obj/src/match/ft-front-prune.o
obj/src/match/ft-polish.o obj/src/match/ft-trimstat.o
obj/src/match/gfa_writer.o obj/src/match/giextract.o
obj/src/match/greedyedist.o obj/src/match/greedyfwdmat.o
obj/src/match/hashfirstcodes.o obj/src/match/hlk-version.o
obj/src/match/hplstore.o obj/src/match/idx-limdfs.o obj/src/match/idxlocali.o
obj/src/match/idxlocalidp.o obj/src/match/idxlocalisw.o
obj/src/match/index_options.o obj/src/match/initbasepower.o obj/src/match/i
niteqsvec.o obj/src/match/iter-window.o obj/src/match/karlin_altschul_stat.o
obj/src/match/kmer2string.o obj/src/match/lua_tools.o
obj/src/match/marksubstring.o obj/src/match/merger-trie.o
obj/src/match/mssufpat.o obj/src/match/myersapm.o obj/src/match/nullcols.o
obj/src/match/optionargmode.o obj/src/match/pck-count-nodes.o
obj/src/match/pckbucket.o obj/src/match/pckdfs.o obj/src/match/prsqualint.o
obj/src/match/pssm.o obj/src/match/querymatch-align.o
obj/src/match/querymatch-display.o obj/src/match/querymatch.o
obj/src/match/radixsort_str.o obj/src/match/randomcodes-correct.o
obj/src/match/randomcodes-find-seldom.o obj/src/match/randomcodes-hpcorrect.o
obj/src/match/randomcodes-insert.o obj/src/match/randomcodes-sfx-partssuf.o
obj/src/match/randomcodes-tab.o obj/src/match/randomcodes.o
obj/src/match/rdj-cntlist.o obj/src/match/rdj-contfind-bottomup.o
obj/src/match/rdj-contfinder.o obj/src/match/rdj-contigpaths.o
obj/src/match/rdj-contigs-graph.o obj/src/match/rdj-contigs-writer.o o
bj/src/match/rdj-errfind.o obj/src/match/rdj-ovlfind-bf.o
obj/src/match/rdj-ovlfind-dp.o obj/src/match/rdj-ovlfind-gusfield.o
obj/src/match/rdj-ovlfind-kmp.o obj/src/match/rdj-pairwise.o
obj/src/match/rdj-spmfind.o obj/src/match/rdj-spmlist.o
obj/src/match/rdj-spmproc.o obj/src/match/rdj-strgraph.o
obj/src/match/rdj-twobitenc-editor.o obj/src/match/rdj-version.o
obj/src/match/reads2twobit.o obj/src/match/reads_libraries_table.o
obj/src/match/rectangle-store.o obj/src/match/revcompl.o
obj/src/match/seed-extend-iter.o obj/src/match/seed-extend.o
obj/src/match/seed_extend_parts.o obj/src/match/seqabstract.o
obj/src/match/seqnumrelpos.o obj/src/match/sfx-apfxlen.o
obj/src/match/sfx-bentsedg.o obj/src/match/sfx-bltrie.o
obj/src/match/sfx-copysort.o obj/src/match/sfx-diffcov.o
obj/src/match/sfx-enumcodes.o obj/src/match/sfx-lcpvalues.o
obj/src/match/sfx-linlcp.o obj/src/match/sfx-lwcheck.o
obj/src/match/sfx-mappedstr.o obj/src/match/sfx-maprange.o
obj/src/match/sfx-opt.o obj/src/match/sfx
-outprj.o obj/src/match/sfx-partssuf.o obj/src/match/sfx-radixsort.o
obj/src/match/sfx-run.o obj/src/match/sfx-sain.o
obj/src/match/sfx-shortreadsort.o obj/src/match/sfx-suffixer.o
obj/src/match/sfx-suffixgetset.o obj/src/match/sfx-suftaborder.o
obj/src/match/shu-dfs.o obj/src/match/shu-divergence.o
obj/src/match/shu-encseq-gc.o obj/src/match/shu-genomediff.o
obj/src/match/shu_unitfile.o obj/src/match/spaced-seeds.o
obj/src/match/specialrank.o obj/src/match/spmsuftab.o
obj/src/match/squarededist.o obj/src/match/substriter.o
obj/src/match/tagerator.o obj/src/match/test-mappedstr.o
obj/src/match/test-maxpairs.o obj/src/match/test-mergeesa.o
obj/src/match/test-mtrieins.o obj/src/match/test-pairwise.o
obj/src/match/turnwheels.o obj/src/match/twobits2kmers.o
obj/src/match/tyr-map.o obj/src/match/tyr-mersplit.o
obj/src/match/tyr-mkindex.o obj/src/match/tyr-occratio.o
obj/src/match/tyr-search.o obj/src/match/xdrop.o obj/src/ltr/gt_ltrclustering.o
obj/src/ltr/gt_ltrdigest.o obj/src/ltr/gt_l
trharvest.o obj/src/ltr/ltr_classify_stream.o
obj/src/ltr/ltr_cluster_prepare_seq_visitor.o obj/src/ltr/ltr_cluster_stream.o
obj/src/ltr/ltr_four_char_motif.o obj/src/ltr/ltr_input_check_visitor.o
obj/src/ltr/ltr_orf_annotator_stream.o obj/src/ltr/ltr_refseq_match_stream.o
obj/src/ltr/ltrdigest_file_out_stream.o obj/src/ltr/ltrdigest_pbs_visitor.o
obj/src/ltr/ltrdigest_pdom_visitor.o obj/src/ltr/ltrdigest_ppt_visitor.o
obj/src/ltr/ltrdigest_strand_assign_visitor.o
obj/src/ltr/ltrharvest_fasta_out_stream.o
obj/src/ltr/ltrharvest_fasta_out_visitor.o obj/src/ltr/ltrharvest_stream.o
obj/src/ltr/ltrharvest_tabout_stream.o obj/src/ltr/ltrharvest_tabout_visitor.o
obj/src/ltr/pdom_model_set.o obj/src/mgth/metagenomethreader.o
obj/src/mgth/mg_codon.o obj/src/mgth/mg_combinedscore.o
obj/src/mgth/mg_compute_gene_prediction.o obj/src/mgth/mg_computepath.o
obj/src/mgth/mg_outputwriter.o obj/src/mgth/mg_reverse.o
obj/src/mgth/mg_xmlparser.o obj/src/annotationsketch/block.o
obj/src/annotationsketc
h/canvas.o obj/src/annotationsketch/canvas_cairo.o
obj/src/annotationsketch/canvas_cairo_context.o
obj/src/annotationsketch/canvas_cairo_file.o obj/src/annotationsketch/color.o
obj/src/annotationsketch/coords.o obj/src/annotationsketch/custom_track.o
obj/src/annotationsketch/custom_track_example.o
obj/src/annotationsketch/custom_track_gc_content.o
obj/src/annotationsketch/custom_track_script_wrapper.o
obj/src/annotationsketch/diagram.o obj/src/annotationsketch/drawing_range.o
obj/src/annotationsketch/element.o obj/src/annotationsketch/graphics.o
obj/src/annotationsketch/graphics_cairo.o obj/src/annotationsketch/gt_sketch.o
obj/src/annotationsketch/gt_sketch_page.o obj/src/annotationsketch/image_info.o
obj/src/annotationsketch/layout.o obj/src/annotationsketch/line.o
obj/src/annotationsketch/line_breaker.o
obj/src/annotationsketch/line_breaker_bases.o
obj/src/annotationsketch/line_breaker_captions.o
obj/src/annotationsketch/luastyle.o obj/src/annotationsketch/rec_map.o
obj/src/annota
tionsketch/style.o obj/src/annotationsketch/text_width_calculator.o
obj/src/annotationsketch/text_width_calculator_cairo.o
obj/src/annotationsketch/track.o
ar: creating lib/libgenometools.a
cc -c src/examples/sketch_parsed_with_ordering.c -o
obj/src/examples/sketch_parsed_with_ordering.d -Wdate-time -D_FORTIFY_SOURCE=2
-D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DHAVE_MEMMOVE
-D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN -DLUA_USE_MKSTEMP
-DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1 -Wdate-time
-D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0 -I/usr/include/fribidi
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/include/libpng16
-I/usr/include/pango-1.0 -I/usr/include/harfbuzz -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/cairo -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/pixman-1
-I/usr/include/uuid -I/usr/include/freetype2 -I/usr/
include/libpng16 -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -MM -MP -MT
obj/src/examples/sketch_parsed_with_ordering.o
test -d lib || mkdir -p lib
cc -Wl,-z,relro -Wl,-z,now -L/usr/local/lib
-Wl,--version-script=obj/public_symbols.lst \
-Llib -shared \
-Wl,-soname,libgenometools.so.0 obj/src/core/alphabet.o
obj/src/core/array.o obj/src/core/array2dim.o obj/src/core/array2dim_sparse.o
obj/src/core/array3dim.o obj/src/core/basename.o obj/src/core/bioseq.o
obj/src/core/bioseq_col.o obj/src/core/bioseq_iterator.o
obj/src/core/bitbuffer.o obj/src/core/bitpackstringop.o
obj/src/core/bitpackstringop16.o obj/src/core/bitpackstringop32.o
obj/src/core/bitpackstringop64.o obj/src/core/bitpackstringop8.o
obj/src/core/bittab.o obj/src/core/bool_matrix.o obj/src/core/bsearch.o
obj/src/core/byte_popcount.o obj/src/core/byte_select.o
obj/src/core/checkbitpackarray.o obj/src/core/checkbitpackstring-int.o
obj/src/core/checkbitpackstring.o obj/src/core/checkbitpackstring16.o
obj/src/core/checkbitpackstring32.o obj/src/core/checkbitpackstring64.o
obj/src/core/checkbitpackstring8.o obj/src/core/class_alloc.o
obj/src/core/class_alloc_lock.o obj/src/core/codon_iterator.o
obj/src/core/codon_iterator_encseq.o obj/src/core/codon_iterator_simple.o
obj/src/c
ore/colorspace.o obj/src/core/combinatorics.o
obj/src/core/compact_ulong_store.o obj/src/core/compat.o
obj/src/core/complement.o obj/src/core/countingsort.o obj/src/core/cstr.o
obj/src/core/cstr_array.o obj/src/core/cstr_table.o
obj/src/core/csvline_reader.o obj/src/core/desc_buffer.o
obj/src/core/disc_distri.o obj/src/core/dlist.o obj/src/core/dual-pivot-qsort.o
obj/src/core/dyn_bittab.o obj/src/core/dynalloc.o obj/src/core/eansi.o
obj/src/core/ebzlib.o obj/src/core/encseq.o obj/src/core/encseq_access_type.o
obj/src/core/encseq_col.o obj/src/core/encseq_metadata.o
obj/src/core/encseq_options.o obj/src/core/encseq_ptr.o
obj/src/core/endianess.o obj/src/core/error.o obj/src/core/example.o
obj/src/core/example_a.o obj/src/core/example_b.o obj/src/core/ezlib.o
obj/src/core/fa.o obj/src/core/fasta.o obj/src/core/fasta_reader.o
obj/src/core/fasta_reader_fsm.o obj/src/core/fasta_reader_rec.o
obj/src/core/fasta_reader_seqit.o obj/src/core/fastq.o obj/src/core/file.o
obj/src/core/fileutils.
o obj/src/core/gc_content.o obj/src/core/grep.o obj/src/core/gtdatapath.o
obj/src/core/hashmap.o obj/src/core/hashtable.o obj/src/core/init.o
obj/src/core/interval_tree.o obj/src/core/io.o obj/src/core/log.o
obj/src/core/logger.o obj/src/core/ma.o obj/src/core/mapspec.o
obj/src/core/mathsupport.o obj/src/core/md5_encoder.o
obj/src/core/md5_fingerprint.o obj/src/core/md5_seqid.o obj/src/core/md5_tab.o
obj/src/core/msort.o obj/src/core/multithread.o obj/src/core/option.o
obj/src/core/orf.o obj/src/core/output_file.o obj/src/core/parseutils.o
obj/src/core/password_entry.o obj/src/core/phase.o obj/src/core/process.o
obj/src/core/progressbar.o obj/src/core/qsort-ulong.o obj/src/core/qsort_r.o
obj/src/core/quality.o obj/src/core/queue.o obj/src/core/radix_sort.o
obj/src/core/range.o obj/src/core/readmode.o obj/src/core/safearith.o
obj/src/core/score_function.o obj/src/core/score_matrix.o obj/src/core/seq.o
obj/src/core/seq_col.o obj/src/core/seq_info_cache.o
obj/src/core/seq_iterator.o ob
j/src/core/seq_iterator_fastq.o obj/src/core/seq_iterator_sequence_buffer.o
obj/src/core/sequence_buffer.o obj/src/core/sequence_buffer_embl.o
obj/src/core/sequence_buffer_fasta.o obj/src/core/sequence_buffer_fastq.o
obj/src/core/sequence_buffer_gb.o obj/src/core/sequence_buffer_plain.o
obj/src/core/showtime.o obj/src/core/sig.o obj/src/core/spacepeak.o
obj/src/core/splitter.o obj/src/core/str.o obj/src/core/str_array.o
obj/src/core/str_cache.o obj/src/core/strand.o obj/src/core/strcmp.o
obj/src/core/string_distri.o obj/src/core/symbol.o obj/src/core/thread.o
obj/src/core/timer.o obj/src/core/tokenizer.o obj/src/core/tool.o
obj/src/core/tool_iterator.o obj/src/core/toolbox.o obj/src/core/tooldriver.o
obj/src/core/trans_table.o obj/src/core/translator.o
obj/src/core/unit_testing.o obj/src/core/version.o obj/src/core/versionfunc.o
obj/src/core/warning.o obj/src/core/xansi.o obj/src/core/xbsd.o
obj/src/core/xbzlib.o obj/src/core/xposix.o obj/src/core/xzlib.o
obj/src/core/yarandom.o obj
/src/extended/add_ids_stream.o obj/src/extended/add_ids_visitor.o
obj/src/extended/add_introns_stream.o obj/src/extended/affinealign.o
obj/src/extended/aligned_segment.o obj/src/extended/aligned_segments_pile.o
obj/src/extended/alignment.o obj/src/extended/anno_db_gfflike.o
obj/src/extended/anno_db_schema.o obj/src/extended/array_in_stream.o
obj/src/extended/array_out_stream.o
obj/src/extended/assembly_stats_calculator.o obj/src/extended/bed_in_stream.o
obj/src/extended/bed_parser.o obj/src/extended/bitinstream.o
obj/src/extended/bitoutstream.o obj/src/extended/blast_process_call.o
obj/src/extended/buffer_stream.o obj/src/extended/cds_check_stream.o
obj/src/extended/cds_check_visitor.o obj/src/extended/cds_stream.o
obj/src/extended/cds_visitor.o obj/src/extended/chain.o
obj/src/extended/check_boundaries_visitor.o obj/src/extended/chseqids_stream.o
obj/src/extended/clustered_set.o obj/src/extended/clustered_set_uf.o
obj/src/extended/coin_hmm.o obj/src/extended/collect_ids_visitor.o o
bj/src/extended/comment_node.o obj/src/extended/compressed_bitsequence.o
obj/src/extended/condenseq.o obj/src/extended/condenseq_creator.o
obj/src/extended/condenseq_search_arguments.o obj/src/extended/consensus_sa.o
obj/src/extended/csa_gene.o obj/src/extended/csa_splice_form.o
obj/src/extended/csa_stream.o obj/src/extended/csa_variable_strands.o
obj/src/extended/csa_visitor.o obj/src/extended/cstr_iterator.o
obj/src/extended/diagonalbandalign.o
obj/src/extended/diagonalbandalign_affinegapcost.o obj/src/extended/dice_hmm.o
obj/src/extended/dot_out_stream.o obj/src/extended/dot_visitor.o
obj/src/extended/dup_feature_stream.o obj/src/extended/dup_feature_visitor.o
obj/src/extended/editscript.o obj/src/extended/elias_gamma.o
obj/src/extended/encdesc.o obj/src/extended/encdesc_header_io.o
obj/src/extended/eof_node.o obj/src/extended/evaluator.o
obj/src/extended/extract_feature_sequence.o
obj/src/extended/extract_feature_stream.o
obj/src/extended/extract_feature_visitor.o obj/src/extend
ed/fasta_header_iterator.o obj/src/extended/feature_in_stream.o
obj/src/extended/feature_index.o obj/src/extended/feature_index_memory.o
obj/src/extended/feature_info.o obj/src/extended/feature_node.o
obj/src/extended/feature_node_iterator.o
obj/src/extended/feature_node_observer.o obj/src/extended/feature_out_stream.o
obj/src/extended/feature_stream.o obj/src/extended/feature_visitor.o
obj/src/extended/gap_str.o obj/src/extended/genome_node.o
obj/src/extended/gff3_escaping.o obj/src/extended/gff3_in_stream.o
obj/src/extended/gff3_in_stream_plain.o
obj/src/extended/gff3_linesorted_out_stream.o
obj/src/extended/gff3_numsorted_out_stream.o obj/src/extended/gff3_out_stream.o
obj/src/extended/gff3_output.o obj/src/extended/gff3_parser.o
obj/src/extended/gff3_visitor.o obj/src/extended/globalchaining.o
obj/src/extended/golomb.o obj/src/extended/gtdatahelp.o
obj/src/extended/gtf_in_stream.o obj/src/extended/gtf_out_stream.o
obj/src/extended/gtf_parser.o obj/src/extended/gtf_visitor.o obj/
src/extended/hcr.o obj/src/extended/hmm.o obj/src/extended/hpol_processor.o
obj/src/extended/huffcode.o obj/src/extended/id_to_md5_stream.o
obj/src/extended/id_to_md5_visitor.o obj/src/extended/inter_feature_stream.o
obj/src/extended/inter_feature_visitor.o obj/src/extended/intset.o
obj/src/extended/intset_16.o obj/src/extended/intset_32.o
obj/src/extended/intset_8.o obj/src/extended/intset_combined.o
obj/src/extended/io_function_pointers.o obj/src/extended/kmer_database.o
obj/src/extended/linearalign.o obj/src/extended/linearalign_affinegapcost.o
obj/src/extended/linspace_management.o obj/src/extended/load_stream.o
obj/src/extended/luahelper.o obj/src/extended/luaserialize.o
obj/src/extended/mapping.o obj/src/extended/match.o
obj/src/extended/match_blast.o obj/src/extended/match_iterator.o
obj/src/extended/match_iterator_blast.o obj/src/extended/match_iterator_last.o
obj/src/extended/match_iterator_open.o obj/src/extended/match_iterator_sw.o
obj/src/extended/match_last.o obj/src/ex
tended/match_open.o obj/src/extended/match_sw.o
obj/src/extended/match_visitor.o obj/src/extended/maxcoordvalue.o
obj/src/extended/md5_to_id_stream.o obj/src/extended/md5_to_id_visitor.o
obj/src/extended/md5set.o obj/src/extended/merge_feature_stream.o
obj/src/extended/merge_feature_visitor.o obj/src/extended/merge_stream.o
obj/src/extended/meta_node.o obj/src/extended/multi_sanitizer_visitor.o
obj/src/extended/multieoplist.o obj/src/extended/mutate.o
obj/src/extended/node_stream.o obj/src/extended/node_visitor.o
obj/src/extended/obo_parse_tree.o obj/src/extended/obo_stanza.o
obj/src/extended/orf_finder_stream.o obj/src/extended/orf_finder_visitor.o
obj/src/extended/orf_iterator.o obj/src/extended/orphanage.o
obj/src/extended/permute_words.o obj/src/extended/popcount_tab.o
obj/src/extended/priority_queue.o obj/src/extended/ranked_list.o
obj/src/extended/rbtree.o obj/src/extended/rcr.o obj/src/extended/rdb.o
obj/src/extended/rdb_sqlite.o obj/src/extended/rdb_visitor.o obj/src/extende
d/reconstructalignment.o obj/src/extended/region_mapping.o
obj/src/extended/region_node.o obj/src/extended/region_node_builder.o
obj/src/extended/regioncov_visitor.o obj/src/extended/regular_seqid.o
obj/src/extended/reverse.o obj/src/extended/rmq.o obj/src/extended/safe_popen.o
obj/src/extended/sam_alignment.o obj/src/extended/sam_query_name_iterator.o
obj/src/extended/samfile_encseq_mapping.o obj/src/extended/samfile_iterator.o
obj/src/extended/sampling.o obj/src/extended/scorehandler.o
obj/src/extended/script_filter.o obj/src/extended/script_wrapper_stream.o
obj/src/extended/script_wrapper_visitor.o obj/src/extended/select_stream.o
obj/src/extended/select_visitor.o obj/src/extended/seqid2file.o
obj/src/extended/seqid2seqnum_mapping.o obj/src/extended/seqpos_classifier.o
obj/src/extended/sequence_node.o obj/src/extended/sequence_node_add_stream.o
obj/src/extended/sequence_node_out_stream.o
obj/src/extended/sequence_node_out_visitor.o
obj/src/extended/set_source_visitor.o obj/src/ex
tended/shredder.o obj/src/extended/snp_annotator_stream.o
obj/src/extended/snp_annotator_visitor.o obj/src/extended/sort_stream.o
obj/src/extended/spec_results.o obj/src/extended/spec_visitor.o
obj/src/extended/splice_site_info_stream.o
obj/src/extended/splice_site_info_visitor.o obj/src/extended/splicedseq.o
obj/src/extended/squarealign.o obj/src/extended/sspliced_alignment.o
obj/src/extended/sspliced_alignment_parsing.o obj/src/extended/stat_stream.o
obj/src/extended/stat_visitor.o obj/src/extended/stream_evaluator.o
obj/src/extended/string_matching.o obj/src/extended/swalign.o
obj/src/extended/tag_value_map.o obj/src/extended/targetbest_select_stream.o
obj/src/extended/tidy_region_node_stream.o
obj/src/extended/tidy_region_node_visitor.o obj/src/extended/tir_stream.o
obj/src/extended/transcript_bittabs.o obj/src/extended/transcript_counts.o
obj/src/extended/transcript_evaluators.o obj/src/extended/transcript_exons.o
obj/src/extended/transcript_used_exons.o obj/src/extended/type_c
hecker.o obj/src/extended/type_checker_builtin.o
obj/src/extended/type_checker_obo.o obj/src/extended/type_graph.o
obj/src/extended/type_node.o obj/src/extended/typecheck_info.o
obj/src/extended/uint64hashtable.o obj/src/extended/union_find.o
obj/src/extended/uniq_stream.o obj/src/extended/visitor_stream.o
obj/src/extended/wtree.o obj/src/extended/wtree_encseq.o
obj/src/extended/xrf_abbr_entry.o obj/src/extended/xrf_abbr_parse_tree.o
obj/src/extended/xrf_checker.o obj/src/extended/xrfcheck_info.o
obj/src/gtlua/alphabet_lua.o obj/src/gtlua/annotationsketch_lua.o
obj/src/gtlua/bittab_lua.o obj/src/gtlua/canvas_lua.o
obj/src/gtlua/cds_stream_lua.o obj/src/gtlua/csa_stream_lua.o
obj/src/gtlua/diagram_lua.o obj/src/gtlua/encseq_lua.o
obj/src/gtlua/feature_index_lua.o obj/src/gtlua/feature_node_iterator_lua.o
obj/src/gtlua/feature_stream_lua.o obj/src/gtlua/feature_visitor_lua.o
obj/src/gtlua/genome_node_lua.o obj/src/gtlua/genome_stream_lua.o
obj/src/gtlua/genome_visitor_lua.o obj/src/gt
lua/gt_lua.o obj/src/gtlua/gtcore_lua.o obj/src/gtlua/gtext_lua.o
obj/src/gtlua/image_info_lua.o obj/src/gtlua/layout_lua.o
obj/src/gtlua/mathsupport_lua.o obj/src/gtlua/range_lua.o
obj/src/gtlua/region_mapping_lua.o obj/src/gtlua/score_matrix_lua.o
obj/src/gtlua/stream_evaluator_lua.o obj/src/gtlua/translate_lua.o
obj/src/match/apmeoveridx.o obj/src/match/asqg_writer.o
obj/src/match/bare-encseq.o obj/src/match/bcktab.o
obj/src/match/cgr_spacedseed.o obj/src/match/chain2dim.o
obj/src/match/chainofin.o obj/src/match/cutendpfx.o
obj/src/match/dbs_spaced_seeds.o obj/src/match/diagband-struct.o
obj/src/match/diagbandseed.o obj/src/match/dist-short.o obj/src/match/echoseq.o
obj/src/match/eis-blockcomp-param.o obj/src/match/eis-blockcomp.o
obj/src/match/eis-bwtseq-construct.o obj/src/match/eis-bwtseq-context-param.o
obj/src/match/eis-bwtseq-context.o obj/src/match/eis-bwtseq-extinfo.o
obj/src/match/eis-bwtseq-param.o obj/src/match/eis-bwtseq-sass.o
obj/src/match/eis-bwtseq.o obj/src/match
/eis-encidxseq-construct.o obj/src/match/eis-encidxseq-param.o
obj/src/match/eis-encidxseq.o obj/src/match/eis-mrangealphabet.o
obj/src/match/eis-sa-common.o obj/src/match/eis-seqblocktranslate.o
obj/src/match/eis-seqranges.o obj/src/match/eis-sequencemultiread.o
obj/src/match/eis-specialsrank.o obj/src/match/eis-suffixarray-interface.o
obj/src/match/eis-suffixerator-interface.o obj/src/match/eis-voiditf.o
obj/src/match/encseq2offset.o obj/src/match/enum-patt.o
obj/src/match/esa-bottomup.o obj/src/match/esa-dfs.o
obj/src/match/esa-lcpintervals.o obj/src/match/esa-map.o
obj/src/match/esa-maxpairs.o obj/src/match/esa-merge.o
obj/src/match/esa-minunique.o obj/src/match/esa-mmsearch.o
obj/src/match/esa-scanprj.o obj/src/match/esa-seqread.o
obj/src/match/esa-shulen.o obj/src/match/esa-splititv-simple.o
obj/src/match/esa-splititv.o obj/src/match/esa-spmitvs.o
obj/src/match/esa-spmsk.o obj/src/match/esa_lcpintervals_visitor.o
obj/src/match/esa_spmitvs_visitor.o obj/src/match/esa_visitor.o
obj/src/match/firstcodes-accum.o obj/src/match/firstcodes-cache.o
obj/src/match/firstcodes-insert.o obj/src/match/firstcodes-psbuf.o
obj/src/match/firstcodes-scan.o obj/src/match/firstcodes-spacelog.o
obj/src/match/firstcodes-tab.o obj/src/match/firstcodes.o
obj/src/match/fmi-fwduni.o obj/src/match/fmi-keyval.o
obj/src/match/fmi-locate.o obj/src/match/fmi-map.o obj/src/match/fmi-mapspec.o
obj/src/match/fmi-mkindex.o obj/src/match/fmi-save.o
obj/src/match/fmi-sufbwtstream.o obj/src/match/ft-eoplist.o
obj/src/match/ft-front-generation.o obj/src/match/ft-front-prune.o
obj/src/match/ft-polish.o obj/src/match/ft-trimstat.o
obj/src/match/gfa_writer.o obj/src/match/giextract.o
obj/src/match/greedyedist.o obj/src/match/greedyfwdmat.o
obj/src/match/hashfirstcodes.o obj/src/match/hlk-version.o
obj/src/match/hplstore.o obj/src/match/idx-limdfs.o obj/src/match/idxlocali.o
obj/src/match/idxlocalidp.o obj/src/match/idxlocalisw.o
obj/src/match/index_options.o obj/src/match/initbasepower.o obj/src/
match/initeqsvec.o obj/src/match/iter-window.o
obj/src/match/karlin_altschul_stat.o obj/src/match/kmer2string.o
obj/src/match/lua_tools.o obj/src/match/marksubstring.o
obj/src/match/merger-trie.o obj/src/match/mssufpat.o obj/src/match/myersapm.o
obj/src/match/nullcols.o obj/src/match/optionargmode.o
obj/src/match/pck-count-nodes.o obj/src/match/pckbucket.o
obj/src/match/pckdfs.o obj/src/match/prsqualint.o obj/src/match/pssm.o
obj/src/match/querymatch-align.o obj/src/match/querymatch-display.o
obj/src/match/querymatch.o obj/src/match/radixsort_str.o
obj/src/match/randomcodes-correct.o obj/src/match/randomcodes-find-seldom.o
obj/src/match/randomcodes-hpcorrect.o obj/src/match/randomcodes-insert.o
obj/src/match/randomcodes-sfx-partssuf.o obj/src/match/randomcodes-tab.o
obj/src/match/randomcodes.o obj/src/match/rdj-cntlist.o
obj/src/match/rdj-contfind-bottomup.o obj/src/match/rdj-contfinder.o
obj/src/match/rdj-contigpaths.o obj/src/match/rdj-contigs-graph.o
obj/src/match/rdj-contigs-wri
ter.o obj/src/match/rdj-errfind.o obj/src/match/rdj-ovlfind-bf.o
obj/src/match/rdj-ovlfind-dp.o obj/src/match/rdj-ovlfind-gusfield.o
obj/src/match/rdj-ovlfind-kmp.o obj/src/match/rdj-pairwise.o
obj/src/match/rdj-spmfind.o obj/src/match/rdj-spmlist.o
obj/src/match/rdj-spmproc.o obj/src/match/rdj-strgraph.o
obj/src/match/rdj-twobitenc-editor.o obj/src/match/rdj-version.o
obj/src/match/reads2twobit.o obj/src/match/reads_libraries_table.o
obj/src/match/rectangle-store.o obj/src/match/revcompl.o
obj/src/match/seed-extend-iter.o obj/src/match/seed-extend.o
obj/src/match/seed_extend_parts.o obj/src/match/seqabstract.o
obj/src/match/seqnumrelpos.o obj/src/match/sfx-apfxlen.o
obj/src/match/sfx-bentsedg.o obj/src/match/sfx-bltrie.o
obj/src/match/sfx-copysort.o obj/src/match/sfx-diffcov.o
obj/src/match/sfx-enumcodes.o obj/src/match/sfx-lcpvalues.o
obj/src/match/sfx-linlcp.o obj/src/match/sfx-lwcheck.o
obj/src/match/sfx-mappedstr.o obj/src/match/sfx-maprange.o
obj/src/match/sfx-opt.o obj/src/ma
tch/sfx-outprj.o obj/src/match/sfx-partssuf.o obj/src/match/sfx-radixsort.o
obj/src/match/sfx-run.o obj/src/match/sfx-sain.o
obj/src/match/sfx-shortreadsort.o obj/src/match/sfx-suffixer.o
obj/src/match/sfx-suffixgetset.o obj/src/match/sfx-suftaborder.o
obj/src/match/shu-dfs.o obj/src/match/shu-divergence.o
obj/src/match/shu-encseq-gc.o obj/src/match/shu-genomediff.o
obj/src/match/shu_unitfile.o obj/src/match/spaced-seeds.o
obj/src/match/specialrank.o obj/src/match/spmsuftab.o
obj/src/match/squarededist.o obj/src/match/substriter.o
obj/src/match/tagerator.o obj/src/match/test-mappedstr.o
obj/src/match/test-maxpairs.o obj/src/match/test-mergeesa.o
obj/src/match/test-mtrieins.o obj/src/match/test-pairwise.o
obj/src/match/turnwheels.o obj/src/match/twobits2kmers.o
obj/src/match/tyr-map.o obj/src/match/tyr-mersplit.o
obj/src/match/tyr-mkindex.o obj/src/match/tyr-occratio.o
obj/src/match/tyr-search.o obj/src/match/xdrop.o obj/src/ltr/gt_ltrclustering.o
obj/src/ltr/gt_ltrdigest.o obj/src/l
tr/gt_ltrharvest.o obj/src/ltr/ltr_classify_stream.o
obj/src/ltr/ltr_cluster_prepare_seq_visitor.o obj/src/ltr/ltr_cluster_stream.o
obj/src/ltr/ltr_four_char_motif.o obj/src/ltr/ltr_input_check_visitor.o
obj/src/ltr/ltr_orf_annotator_stream.o obj/src/ltr/ltr_refseq_match_stream.o
obj/src/ltr/ltrdigest_file_out_stream.o obj/src/ltr/ltrdigest_pbs_visitor.o
obj/src/ltr/ltrdigest_pdom_visitor.o obj/src/ltr/ltrdigest_ppt_visitor.o
obj/src/ltr/ltrdigest_strand_assign_visitor.o
obj/src/ltr/ltrharvest_fasta_out_stream.o
obj/src/ltr/ltrharvest_fasta_out_visitor.o obj/src/ltr/ltrharvest_stream.o
obj/src/ltr/ltrharvest_tabout_stream.o obj/src/ltr/ltrharvest_tabout_visitor.o
obj/src/ltr/pdom_model_set.o obj/src/mgth/metagenomethreader.o
obj/src/mgth/mg_codon.o obj/src/mgth/mg_combinedscore.o
obj/src/mgth/mg_compute_gene_prediction.o obj/src/mgth/mg_computepath.o
obj/src/mgth/mg_outputwriter.o obj/src/mgth/mg_reverse.o
obj/src/mgth/mg_xmlparser.o obj/src/annotationsketch/block.o obj/src/annotati
onsketch/canvas.o obj/src/annotationsketch/canvas_cairo.o
obj/src/annotationsketch/canvas_cairo_context.o
obj/src/annotationsketch/canvas_cairo_file.o obj/src/annotationsketch/color.o
obj/src/annotationsketch/coords.o obj/src/annotationsketch/custom_track.o
obj/src/annotationsketch/custom_track_example.o
obj/src/annotationsketch/custom_track_gc_content.o
obj/src/annotationsketch/custom_track_script_wrapper.o
obj/src/annotationsketch/diagram.o obj/src/annotationsketch/drawing_range.o
obj/src/annotationsketch/element.o obj/src/annotationsketch/graphics.o
obj/src/annotationsketch/graphics_cairo.o obj/src/annotationsketch/gt_sketch.o
obj/src/annotationsketch/gt_sketch_page.o obj/src/annotationsketch/image_info.o
obj/src/annotationsketch/layout.o obj/src/annotationsketch/line.o
obj/src/annotationsketch/line_breaker.o
obj/src/annotationsketch/line_breaker_bases.o
obj/src/annotationsketch/line_breaker_captions.o
obj/src/annotationsketch/luastyle.o obj/src/annotationsketch/rec_map.o obj/src
/annotationsketch/style.o obj/src/annotationsketch/text_width_calculator.o
obj/src/annotationsketch/text_width_calculator_cairo.o
obj/src/annotationsketch/track.o \
-o lib/libgenometools.so.0 -lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg
-llua5.1 -llua5.1-md5 -llua5.1 -llua5.1-filesystem -llua5.1 -llua5.1-des56
-llua5.1 -lbam -ltre -Wl,-z,relro -lm -lpthread -lpango-1.0 -lgobject-2.0
-lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0
-lcairo -lsqlite3 /usr/lib/libbam.a
cc -c src/examples/sketch_parsed.c -o obj/src/examples/sketch_parsed.d
-Wdate-time -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64
-DHAVE_MEMMOVE -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DLUA_DL_DLOPEN
-DLUA_USE_MKSTEMP -DHAVE_SQLITE -I./src -I./obj -I/usr/include/lua5.1
-I/usr/include/lua5.1 -I/usr/include/lua5.1 -I/usr/include/lua5.1
-I/usr/include/lua5.1 -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include/pango-1.0
-I/usr/include/fribidi -I/usr/include/glib-2.0
-I/usr/lib/x86_64-linux-gnu/glib-2.0/include -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2
-I/usr/include/libpng16 -I/usr/include/pango-1.0 -I/usr/include/harfbuzz
-I/usr/include/pango-1.0 -I/usr/include/fribidi -I/usr/include/cairo
-I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include
-I/usr/include/pixman-1 -I/usr/include/uuid -I/usr/include/freetype2
-I/usr/include/libpng16 -I/usr/incl
ude/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -g -O2
-fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
-Werror=format-security -MM -MP -MT obj/src/examples/sketch_parsed.o
/usr/bin/ld:
obj/src/mgth/mg_combinedscore.o:./src/mgth/metagenomethreader.h:224: multiple
definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/mgth/metagenomethreader.o:./src/mgth/metagenomethreader.h:224: first
defined here
/usr/bin/ld:
obj/src/mgth/mg_compute_gene_prediction.o:./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/mgth/metagenomethreader.o:./src/mgth/metagenomethreader.h:224: first
defined here
/usr/bin/ld: obj/src/mgth/mg_computepath.o:./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/mgth/metagenomethreader.o:./src/mgth/metagenomethreader.h:224: first
defined here
/usr/bin/ld:
obj/src/mgth/mg_outputwriter.o:./src/mgth/metagenomethreader.h:224: multiple
definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/mgth/metagenomethreader.o:./src/mgth/metagenomethreader.h:224: first
defined here
/usr/bin/ld: obj/src/mgth/mg_reverse.o:./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/mgth/metagenomethreader.o:./src/mgth/metagenomethreader.h:224: first
defined here
/usr/bin/ld: obj/src/mgth/mg_xmlparser.o:./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/mgth/metagenomethreader.o:./src/mgth/metagenomethreader.h:224: first
defined here
test -d bin || mkdir -p bin
test -d bin/examples || mkdir -p bin/examples
test -d bin/examples || mkdir -p bin/examples
cc -Wl,-z,relro -Wl,-z,now -L/usr/local/lib -Llib obj/src/gt.o obj/src/gtr.o
obj/src/gtt.o obj/src/interactive.o obj/src/tools/gt_bed_to_gff3.o
obj/src/tools/gt_cds.o obj/src/tools/gt_chain2dim.o obj/src/tools/gt_chseqids.o
obj/src/tools/gt_clean.o obj/src/tools/gt_compreads.o
obj/src/tools/gt_compreads_compress.o obj/src/tools/gt_compreads_decompress.o
obj/src/tools/gt_compreads_refcompress.o
obj/src/tools/gt_compreads_refdecompress.o obj/src/tools/gt_compressedbits.o
obj/src/tools/gt_condenseq.o obj/src/tools/gt_condenseq_blast.o
obj/src/tools/gt_condenseq_compress.o obj/src/tools/gt_condenseq_extract.o
obj/src/tools/gt_condenseq_hmmsearch.o obj/src/tools/gt_condenseq_info.o
obj/src/tools/gt_condenseq_search.o obj/src/tools/gt_congruence.o
obj/src/tools/gt_consensus_sa.o obj/src/tools/gt_convertseq.o
obj/src/tools/gt_csa.o obj/src/tools/gt_dev.o obj/src/tools/gt_dot.o
obj/src/tools/gt_dupfeat.o obj/src/tools/gt_encseq.o
obj/src/tools/gt_encseq2spm.o obj/src/tools/gt_encseq_bench.o
obj/src/tools/gt_encseq_bitextract.o obj/src/tools/gt_encseq_check.o
obj/src/tools/gt_encseq_decode.o obj/src/tools/gt_encseq_encode.o
obj/src/tools/gt_encseq_info.o obj/src/tools/gt_encseq_md5.o
obj/src/tools/gt_encseq_sample.o obj/src/tools/gt_eval.o
obj/src/tools/gt_extractfeat.o obj/src/tools/gt_extractseq.o
obj/src/tools/gt_extracttarget.o obj/src/tools/gt_fastq_sample.o
obj/src/tools/gt_featureindex.o obj/src/tools/gt_fingerprint.o
obj/src/tools/gt_gdiffcalc.o obj/src/tools/gt_genomediff.o
obj/src/tools/gt_gff3.o obj/src/tools/gt_gff3_to_gtf.o
obj/src/tools/gt_gff3validator.o obj/src/tools/gt_gtf_to_gff3.o
obj/src/tools/gt_guessprot.o obj/src/tools/gt_hop.o
obj/src/tools/gt_id_to_md5.o obj/src/tools/gt_idxlocali.o
obj/src/tools/gt_inlineseq_add.o obj/src/tools/gt_inlineseq_split.o
obj/src/tools/gt_interfeat.o obj/src/tools/gt_kmer_database.o
obj/src/tools/gt_linspace_align.o obj/src/tools/gt_loccheck.o
obj/src/tools/gt_magicmatch.o obj/src/tools/gt_matchtool.o obj/src/tools/gt
_matstat.o obj/src/tools/gt_md5_to_id.o obj/src/tools/gt_merge.o
obj/src/tools/gt_mergeesa.o obj/src/tools/gt_mergefeat.o
obj/src/tools/gt_mgth.o obj/src/tools/gt_mkfeatureindex.o
obj/src/tools/gt_mkfmindex.o obj/src/tools/gt_mmapandread.o
obj/src/tools/gt_orffinder.o obj/src/tools/gt_packedindex.o
obj/src/tools/gt_packedindex_chk_integrity.o
obj/src/tools/gt_packedindex_chk_search.o
obj/src/tools/gt_packedindex_mkctxmap.o obj/src/tools/gt_packedindex_trsuftab.o
obj/src/tools/gt_paircmp.o obj/src/tools/gt_parsexrf.o
obj/src/tools/gt_patternmatch.o obj/src/tools/gt_prebwt.o
obj/src/tools/gt_readjoiner.o obj/src/tools/gt_readjoiner_asqg.o
obj/src/tools/gt_readjoiner_assembly.o obj/src/tools/gt_readjoiner_cgraph.o
obj/src/tools/gt_readjoiner_cnttest.o obj/src/tools/gt_readjoiner_correct.o
obj/src/tools/gt_readjoiner_gfa.o obj/src/tools/gt_readjoiner_graph.o
obj/src/tools/gt_readjoiner_overlap.o obj/src/tools/gt_readjoiner_prefilter.o
obj/src/tools/gt_readjoiner_spmtest.o obj/src/tools/
gt_readreads.o obj/src/tools/gt_regioncov.o obj/src/tools/gt_repfind.o
obj/src/tools/gt_sain.o obj/src/tools/gt_sam_interface.o
obj/src/tools/gt_script_filter.o obj/src/tools/gt_seed_extend.o
obj/src/tools/gt_select.o obj/src/tools/gt_seq.o obj/src/tools/gt_seqcorrect.o
obj/src/tools/gt_seqfilter.o obj/src/tools/gt_seqids.o
obj/src/tools/gt_seqlensort.o obj/src/tools/gt_seqmutate.o
obj/src/tools/gt_seqorder.o obj/src/tools/gt_seqstat.o
obj/src/tools/gt_seqtransform.o obj/src/tools/gt_seqtranslate.o
obj/src/tools/gt_sequniq.o obj/src/tools/gt_sfxmap.o
obj/src/tools/gt_show_seedext.o obj/src/tools/gt_shredder.o
obj/src/tools/gt_shulen.o obj/src/tools/gt_simreads.o
obj/src/tools/gt_skproto.o obj/src/tools/gt_snpper.o
obj/src/tools/gt_sortbench.o obj/src/tools/gt_speck.o
obj/src/tools/gt_splicesiteinfo.o obj/src/tools/gt_splitfasta.o
obj/src/tools/gt_stat.o obj/src/tools/gt_suffixerator.o
obj/src/tools/gt_tagerator.o obj/src/tools/gt_tallymer.o
obj/src/tools/gt_template.o obj/src/tools/
gt_tir.o obj/src/tools/gt_trieins.o obj/src/tools/gt_uniq.o
obj/src/tools/gt_wtree.o obj/src/tools/gt_wtree_bench.o lib/libgenometools.a
/usr/lib/libbam.a -lm -lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1
-llua5.1-md5 -llua5.1 -llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1
-lbam -ltre -Wl,-z,relro -lm -lpthread -ldl -lpango-1.0 -lgobject-2.0
-lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0
-lcairo -lsqlite3 -lm -lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1
-llua5.1-md5 -llua5.1 -llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1
-lbam -ltre -Wl,-z,relro -lm -lpthread -ldl -lpango-1.0 -lgobject-2.0
-lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0
-lcairo -lsqlite3 -o bin/gt
cc -Wl,-z,relro -Wl,-z,now -L/usr/local/lib -Llib
obj/src/examples/custom_stream.o lib/libgenometools.a /usr/lib/libbam.a -lm
-lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1
-llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1 -lbam -ltre -Wl,-z,relro
-lm -lpthread -ldl -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo
-lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lsqlite3 -lm
-lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1
-llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1 -lbam -ltre -Wl,-z,relro
-lm -lpthread -ldl -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo
-lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lsqlite3 -o
bin/examples/custom_stream
cc -Wl,-z,relro -Wl,-z,now -L/usr/local/lib -Llib obj/src/examples/gff3sort.o
lib/libgenometools.a /usr/lib/libbam.a -lm -lbz2 -lz -lexpat -llua5.1
-llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1 -llua5.1-filesystem -llua5.1
-llua5.1-des56 -llua5.1 -lbam -ltre -Wl,-z,relro -lm -lpthread -ldl -lpango-1.0
-lgobject-2.0 -lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0
-lglib-2.0 -lcairo -lsqlite3 -lm -lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg
-llua5.1 -llua5.1-md5 -llua5.1 -llua5.1-filesystem -llua5.1 -llua5.1-des56
-llua5.1 -lbam -ltre -Wl,-z,relro -lm -lpthread -ldl -lpango-1.0 -lgobject-2.0
-lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0
-lcairo -lsqlite3 -o bin/examples/gff3sort
/usr/bin/ld:
lib/libgenometools.a(metagenomethreader.o):./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/tools/gt_mgth.o:././src/mgth/metagenomethreader.h:224: first defined
here
/usr/bin/ld:
lib/libgenometools.a(mg_outputwriter.o):./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/tools/gt_mgth.o:././src/mgth/metagenomethreader.h:224: first defined
here
/usr/bin/ld:
lib/libgenometools.a(mg_reverse.o):./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/tools/gt_mgth.o:././src/mgth/metagenomethreader.h:224: first defined
here
/usr/bin/ld:
lib/libgenometools.a(mg_xmlparser.o):./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/tools/gt_mgth.o:././src/mgth/metagenomethreader.h:224: first defined
here
/usr/bin/ld:
lib/libgenometools.a(mg_combinedscore.o):./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/tools/gt_mgth.o:././src/mgth/metagenomethreader.h:224: first defined
here
/usr/bin/ld:
lib/libgenometools.a(mg_compute_gene_prediction.o):./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/tools/gt_mgth.o:././src/mgth/metagenomethreader.h:224: first defined
here
/usr/bin/ld:
lib/libgenometools.a(mg_computepath.o):./src/mgth/metagenomethreader.h:224:
multiple definition of `gt_cstr_nofree_ulp_hashtype';
obj/src/tools/gt_mgth.o:././src/mgth/metagenomethreader.h:224: first defined
here
test -d bin/examples || mkdir -p bin/examples
cc -Wl,-z,relro -Wl,-z,now -L/usr/local/lib -Llib
obj/src/examples/gff3validator.o lib/libgenometools.a /usr/lib/libbam.a -lm
-lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1
-llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1 -lbam -ltre -Wl,-z,relro
-lm -lpthread -ldl -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo
-lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lsqlite3 -lm
-lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1
-llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1 -lbam -ltre -Wl,-z,relro
-lm -lpthread -ldl -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo
-lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lsqlite3 -o
bin/examples/gff3validator
test -d bin/examples || mkdir -p bin/examples
cc -Wl,-z,relro -Wl,-z,now -L/usr/local/lib -Llib obj/src/examples/noop.o
lib/libgenometools.a /usr/lib/libbam.a -lm -lbz2 -lz -lexpat -llua5.1
-llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1 -llua5.1-filesystem -llua5.1
-llua5.1-des56 -llua5.1 -lbam -ltre -Wl,-z,relro -lm -lpthread -ldl -lpango-1.0
-lgobject-2.0 -lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0
-lglib-2.0 -lcairo -lsqlite3 -lm -lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg
-llua5.1 -llua5.1-md5 -llua5.1 -llua5.1-filesystem -llua5.1 -llua5.1-des56
-llua5.1 -lbam -ltre -Wl,-z,relro -lm -lpthread -ldl -lpango-1.0 -lgobject-2.0
-lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0
-lcairo -lsqlite3 -o bin/examples/noop
test -d bin/examples || mkdir -p bin/examples
cc -Wl,-z,relro -Wl,-z,now -L/usr/local/lib -Llib
obj/src/examples/sketch_constructed.o lib/libgenometools.a /usr/lib/libbam.a
-lm -lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1
-llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1 -lbam -ltre -Wl,-z,relro
-lm -lpthread -ldl -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo
-lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lsqlite3 -lm
-lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1 -llua5.1-md5 -llua5.1
-llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1 -lbam -ltre -Wl,-z,relro
-lm -lpthread -ldl -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo
-lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0 -lcairo -lsqlite3 -o
bin/examples/sketch_constructed
test -d bin/examples || mkdir -p bin/examples
cc -Wl,-z,relro -Wl,-z,now -L/usr/local/lib -Llib
obj/src/examples/sketch_parsed_with_ctrack.o lib/libgenometools.a
/usr/lib/libbam.a -lm -lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1
-llua5.1-md5 -llua5.1 -llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1
-lbam -ltre -Wl,-z,relro -lm -lpthread -ldl -lpango-1.0 -lgobject-2.0
-lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0
-lcairo -lsqlite3 -lm -lbz2 -lz -lexpat -llua5.1 -llua5.1-lpeg -llua5.1
-llua5.1-md5 -llua5.1 -llua5.1-filesystem -llua5.1 -llua5.1-des56 -llua5.1
-lbam -ltre -Wl,-z,relro -lm -lpthread -ldl -lpango-1.0 -lgobject-2.0
-lglib-2.0 -lcairo -lpangocairo-1.0 -lpango-1.0 -lgobject-2.0 -lglib-2.0
-lcairo -lsqlite3 -o bin/examples/sketch_parsed_with_ctrack
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:622: lib/libgenometools.so] Error 1
make[2]: *** Waiting for unfinished jobs....
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:638: bin/gt] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true"
verbose=yes useshared=yes x32=no 64bit=yes errorcheck=no all docs manuals
returned exit code 2
make[1]: *** [debian/rules:59: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:34: build] Error 2
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
--- End Message ---
--- Begin Message ---
Source: genometools
Source-Version: 1.6.1+ds-3
Done: Sascha Steinbiss <[email protected]>
We believe that the bug you reported is fixed in the latest version of
genometools, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Sascha Steinbiss <[email protected]> (supplier of updated genometools package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 22 Jul 2020 13:00:06 +0200
Source: genometools
Architecture: source
Version: 1.6.1+ds-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Sascha Steinbiss <[email protected]>
Closes: 957268
Changes:
genometools (1.6.1+ds-3) unstable; urgency=medium
.
* Add patch to fix build on GCC 10.
Closes: #957268
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genometools_1.6.1+ds-3.debian.tar.xz
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Files:
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genometools_1.6.1+ds-3.dsc
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genometools_1.6.1+ds-3.debian.tar.xz
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