[From nobody Tue Apr 21 23:21:07 2026 Received: (at maintonly) by bugs.debian.org; 13 Apr 2026 13:04:18 +0000 X-Spam-Checker-Version: SpamAssassin 4.0.1-bugs.debian.org_2005_01_02 (2024-03-25) on buxtehude.debian.org X-Spam-Level: X-Spam-Status: No, score=-116.7 required=4.0 tests=BAYES_00, BODY_INCLUDES_PACKAGE,DKIMWL_WL_HIGH,DKIM_SIGNED,DKIM_VALID, DKIM_VALID_AU,DKIM_VALID_EF,FROMDEVELOPER,FVGT_m_MULTI_ODD,HAS_PACKAGE, SPF_HELO_NONE,SPF_NONE,UNPARSEABLE_RELAY,USER_IN_DKIM_WELCOMELIST autolearn=ham autolearn_force=no version=4.0.1-bugs.debian.org_2005_01_02 X-Spam-Bayes: score:0.0000 Tokens: new, 160; hammy, 150; neutral, 164; spammy, 0. spammytokens: hammytokens:0.000-+--Hx-spam-relays-external:sk:stravin, 0.000-+--H*RT:sk:stravin, 0.000-+--Hx-spam-relays-external:311, 0.000-+--H*RT:311, 0.000-+--H*RT:108 Return-path: <ema@debian.org> Received: from stravinsky.debian.org ([2001:41b8:202:deb::311:108]:40998) by buxtehude.debian.org with esmtps (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <ema@debian.org>) id 1wCGxe-002l6q-1k for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:04:18 +0000 DKIM-Signature: v=1; a=rsa-sha256; q=dns/txt; c=relaxed/relaxed; d=debian.org; s=smtpauto.stravinsky; h=X-Debian-User:Content-Transfer-Encoding:Content-Type :MIME-Version:Message-ID:Subject:To:From:Date:Reply-To:Cc:Content-ID: Content-Description:In-Reply-To:References; bh=dHydjkI3sDCQ2jr+iyei9UxseDrV6D3L/8RLvnmAW24=; b=ROiK5GWCdETGmdeXHV9BOurvT4 IgVoM0OVhhqBkEmF1SUtRxDF9XJ3ppUHCS6d6MuYEuzZszBPOo46SdfxRBzaADn/h+CXzByYf0QE4 q6qYlAoSYg/mPAAGbRPcrnIomNd3t2DcoOzK6o+N+2scBenHgSMb/5EODaL1//T4pA4ay7OSz6yRq uD+1d9uwlXBPONO2DPDECuYVttbzZK7DTvHvxzNhwE8rb/zT31eeZSrdDBS0jDSVOBWKb27WLohAd kcmsnDgd/NBaN9JlyEs+j/uWWw4yBi0KEypr5OLkCBGqL0bkU5VUj+c/r+ErAp8LDi+1L+jNj3oPv bUJmgdFg==; Received: from authenticated user by stravinsky.debian.org with esmtpsa (TLS1.3:ECDHE_SECP256R1__RSA_PSS_RSAE_SHA256__AES_256_GCM:256) (Exim 4.96) (envelope-from <ema@debian.org>) id 1wCGxc-00CJMS-2t for maintonly@bugs.debian.org; Mon, 13 Apr 2026 13:04:17 +0000 Date: Mon, 13 Apr 2026 15:04:16 +0200 From: Emanuele Rocca <ema@debian.org> To: maintonly@bugs.debian.org Subject: genomethreader: ftbfs with GCC-16 Message-ID: <adzp0NJKKKWACwkj@ariel.home> MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable X-Debian-User: ema Delivered-To: maintonly@bugs.debian.org Package: src:genomethreader Version: 1.7.3+dfsg-11 Severity: important Tags: sid forky ftbfs User: debian-gcc@lists.debian.org Usertags: ftbfs-gcc-16 Hi, genomethreader fails to build in a test rebuild on at least amd64 and arm64= with gcc-16/g++-16, but builds properly with gcc-15/g++-15. The severity of this report will be raised before the forky release. The full build log can be found at: https://people.debian.org/~ema/gcc-16-rebuilds/output-1/genomethreader_arm6= 4.build.xz The last lines of the build log are at the end of this report. To build with GCC 16, either set CC=3Dgcc-16 CXX=3Dg++-16 explicitly, or install the gcc, g++, gfortran, ... packages from experimental. apt-get -t=3Dexperimental install g++=20 Common build failures include unused (but set) variables, array subscripts partly outside array bounds, and new/dropped symbols in Debian symbols file= s. For other C/C++ related build failures see the porting guide at http://gcc.gnu.org/gcc-16/porting_to.html Please only close this issue after double-checking that the package can be built correctly with GCC 16. Please do not reassign this bug to another package. If a fix in another pac= kage is required, then file a bug for the other package (or clone), and mark this bug as blocked by the bug in the other package. [...] debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+= dfsg' make licensemanager=3Dno opt=3Dyes 64bit=3Dyes make[2]: Entering directory '/build/reproducible-path/genomethreader-1.7.3+= dfsg' [create obj/gth_config.h] [compile findfile.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/findfile.c -o= obj/src/libgenomethreader/findfile.o -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_= LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h= >" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genomet= ools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path= /genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.= 7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1= =2E7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader= -1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=3Dimpli= cit-function-declaration -ffile-prefix-map=3D/build/reproducible-path/genom= ethreader-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-clash-protection = -Wformat -Werror=3Dformat-security -mbranch-protection=3Dstandard -g -Wall = -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-un= known-pragmas -Wno-error=3Dmisleading-indentation -Werror -O3=20 cc -c src/libgenomethreader/findfile.c -o obj/src/libgenomethreader/findfil= e.d -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BI= TS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_V= ERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/= include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/= build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I= /build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I= /build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -D= NOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/findfile.o [compile gt_align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/gt_align_dna.= c -o obj/src/libgenomethreader/gt_align_dna.o -Wdate-time -D_FORTIFY_SOURCE= =3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<= unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include= /genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproduci= ble-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethr= eader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genometh= reader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genometh= reader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror= =3Dimplicit-function-declaration -ffile-prefix-map=3D/build/reproducible-pa= th/genomethreader-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-clash-pro= tection -Wformat -Werror=3Dformat-security -mbranch-protection=3Dstandard -= g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector= -Wno-unknown-pragmas -Wno-error=3Dmisleading-indentation -Werror -O3=20 cc -c src/libgenomethreader/gt_align_dna.c -o obj/src/libgenomethreader/gt_= align_dna.d -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_O= FFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>"= -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch= -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg= /src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_S= OURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/in= clude -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vm= atch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gt_align_dn= a.o [compile gt_gthgetseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/gt_gthgetseq.= c -o obj/src/libgenomethreader/gt_gthgetseq.o -Wdate-time -D_FORTIFY_SOURCE= =3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<= unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include= /genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproduci= ble-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethr= eader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genometh= reader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genometh= reader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror= =3Dimplicit-function-declaration -ffile-prefix-map=3D/build/reproducible-pa= th/genomethreader-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-clash-pro= tection -Wformat -Werror=3Dformat-security -mbranch-protection=3Dstandard -= g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector= -Wno-unknown-pragmas -Wno-error=3Dmisleading-indentation -Werror -O3=20 cc -c src/libgenomethreader/gt_gthgetseq.c -o obj/src/libgenomethreader/gt_= gthgetseq.d -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_O= FFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>"= -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch= -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg= /src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_S= OURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/in= clude -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vm= atch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gt_gthgetse= q.o [compile gthmkvtree.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/gthmkvtree.c = -o obj/src/libgenomethreader/gthmkvtree.o -Wdate-time -D_FORTIFY_SOURCE=3D2= -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unis= td.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/gen= ometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-= path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreade= r-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethread= er-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethread= er-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=3Dimp= licit-function-declaration -ffile-prefix-map=3D/build/reproducible-path/gen= omethreader-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-clash-protectio= n -Wformat -Werror=3Dformat-security -mbranch-protection=3Dstandard -g -Wal= l -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-= unknown-pragmas -Wno-error=3Dmisleading-indentation -Werror -O3=20 cc -c src/libgenomethreader/gthmkvtree.c -o obj/src/libgenomethreader/gthmk= vtree.d -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSE= T_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DR= NV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/= usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src= -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURC= E -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/includ= e -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch= -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthmkvtree.o [compile gthpolyafunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/gthpolyafunc.= c -o obj/src/libgenomethreader/gthpolyafunc.o -Wdate-time -D_FORTIFY_SOURCE= =3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<= unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include= /genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproduci= ble-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethr= eader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genometh= reader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genometh= reader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror= =3Dimplicit-function-declaration -ffile-prefix-map=3D/build/reproducible-pa= th/genomethreader-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-clash-pro= tection -Wformat -Werror=3Dformat-security -mbranch-protection=3Dstandard -= g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector= -Wno-unknown-pragmas -Wno-error=3Dmisleading-indentation -Werror -O3=20 cc -c src/libgenomethreader/gthpolyafunc.c -o obj/src/libgenomethreader/gth= polyafunc.d -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_O= FFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>"= -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch= -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg= /src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_S= OURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/in= clude -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vm= atch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthpolyafun= c.o [compile gthpre.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/gthpre.c -o o= bj/src/libgenomethreader/gthpre.o -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARG= EFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -= DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools= -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/gen= omethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+= dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3= +dfsg/../vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3= +dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=3Dimplicit-fu= nction-declaration -ffile-prefix-map=3D/build/reproducible-path/genomethrea= der-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-clash-protection -Wform= at -Werror=3Dformat-security -mbranch-protection=3Dstandard -g -Wall -Wunus= ed-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-= pragmas -Wno-error=3Dmisleading-indentation -Werror -O3=20 cc -c src/libgenomethreader/gthpre.c -o obj/src/libgenomethreader/gthpre.d = -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS= =3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VER= SION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/in= clude/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/bu= ild/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/b= uild/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/b= uild/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNO= LICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthpre.o [compile gthversionfunc.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/gthversionfun= c.c -o obj/src/libgenomethreader/gthversionfunc.o -Wdate-time -D_FORTIFY_SO= URCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H= =3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/in= clude/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/repr= oducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/geno= methreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/gen= omethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/gen= omethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Wer= ror=3Dimplicit-function-declaration -ffile-prefix-map=3D/build/reproducible= -path/genomethreader-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-clash-= protection -Wformat -Werror=3Dformat-security -mbranch-protection=3Dstandar= d -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protec= tor -Wno-unknown-pragmas -Wno-error=3Dmisleading-indentation -Werror -O3=20 cc -c src/libgenomethreader/gthversionfunc.c -o obj/src/libgenomethreader/g= thversionfunc.d -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FI= LE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat= =2Eh>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/= vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.= 3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FOR= TIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/= src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/= src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthve= rsionfunc.o [compile gthvmatch.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/gthvmatch.c -= o obj/src/libgenomethreader/gthvmatch.o -Wdate-time -D_FORTIFY_SOURCE=3D2 -= D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd= =2Eh>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/gen= ometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-= path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreade= r-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethread= er-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethread= er-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=3Dimp= licit-function-declaration -ffile-prefix-map=3D/build/reproducible-path/gen= omethreader-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-clash-protectio= n -Wformat -Werror=3Dformat-security -mbranch-protection=3Dstandard -g -Wal= l -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-= unknown-pragmas -Wno-error=3Dmisleading-indentation -Werror -O3=20 cc -c src/libgenomethreader/gthvmatch.c -o obj/src/libgenomethreader/gthvma= tch.d -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_= BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV= _VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/us= r/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -= I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE = -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include = -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch = -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/gthvmatch.o [compile jt.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/jt.c -o obj/s= rc/libgenomethreader/jt.o -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SO= URCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H= =3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/= include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethrea= der-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj= -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/..= /vstree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/..= /vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=3Dimplicit-function-d= eclaration -ffile-prefix-map=3D/build/reproducible-path/genomethreader-1.7.= 3+dfsg=3D. -fstack-protector-strong -fstack-clash-protection -Wformat -Werr= or=3Dformat-security -mbranch-protection=3Dstandard -g -Wall -Wunused-param= eter -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas = -Wno-error=3Dmisleading-indentation -Werror -O3=20 cc -c src/libgenomethreader/jt.c -o obj/src/libgenomethreader/jt.d -Wdate-t= ime -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWI= THLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1= =2E7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lu= a5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/repr= oducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/rep= roducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/rep= roducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEM= ANAGER -MM -MP -MT obj/src/libgenomethreader/jt.o [compile jt_align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/jt_align_dna.= c -o obj/src/libgenomethreader/jt_align_dna.o -Wdate-time -D_FORTIFY_SOURCE= =3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<= unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include= /genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproduci= ble-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethr= eader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genometh= reader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genometh= reader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror= =3Dimplicit-function-declaration -ffile-prefix-map=3D/build/reproducible-pa= th/genomethreader-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-clash-pro= tection -Wformat -Werror=3Dformat-security -mbranch-protection=3Dstandard -= g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-protector= -Wno-unknown-pragmas -Wno-error=3Dmisleading-indentation -Werror -O3=20 cc -c src/libgenomethreader/jt_align_dna.c -o obj/src/libgenomethreader/jt_= align_dna.d -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_O= FFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>"= -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch= -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg= /src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_S= OURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/in= clude -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vm= atch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt_align_dn= a.o [compile jt_align_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/jt_align_prot= ein.c -o obj/src/libgenomethreader/jt_align_protein.o -Wdate-time -D_FORTIF= Y_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNIST= D_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr= /include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/r= eproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/g= enomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/= genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/= genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -= Werror=3Dimplicit-function-declaration -ffile-prefix-map=3D/build/reproduci= ble-path/genomethreader-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-cla= sh-protection -Wformat -Werror=3Dformat-security -mbranch-protection=3Dstan= dard -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-pro= tector -Wno-unknown-pragmas -Wno-error=3Dmisleading-indentation -Werror -O3= =20 cc -c src/libgenomethreader/jt_align_protein.c -o obj/src/libgenomethreader= /jt_align_protein.d -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -= D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<e= xpat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/includ= e/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.= 7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_F= ORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstre= e/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstre= e/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/jt_= align_protein.o [compile seq_con_multiseq.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/libgenomethreader/seq_con_multi= seq.c -o obj/src/libgenomethreader/seq_con_multiseq.o -Wdate-time -D_FORTIF= Y_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNIST= D_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr= /include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/r= eproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/g= enomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/= genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/= genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -= Werror=3Dimplicit-function-declaration -ffile-prefix-map=3D/build/reproduci= ble-path/genomethreader-1.7.3+dfsg=3D. -fstack-protector-strong -fstack-cla= sh-protection -Wformat -Werror=3Dformat-security -mbranch-protection=3Dstan= dard -g -Wall -Wunused-parameter -pipe -fPIC -Wpointer-arith -fno-stack-pro= tector -Wno-unknown-pragmas -Wno-error=3Dmisleading-indentation -Werror -O3= =20 cc -c src/libgenomethreader/seq_con_multiseq.c -o obj/src/libgenomethreader= /seq_con_multiseq.d -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -= D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<e= xpat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/includ= e/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.= 7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_F= ORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstre= e/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstre= e/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/libgenomethreader/seq= _con_multiseq.o [compile ags.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/gth/ags.c -o obj/src/gth/ags.o = -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS= =3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VER= SION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch -I/usr/in= clude/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/bu= ild/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/b= uild/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/b= uild/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNO= LICENSEMANAGER -g -O2 -Werror=3Dimplicit-function-declaration -ffile-prefix= -map=3D/build/reproducible-path/genomethreader-1.7.3+dfsg=3D. -fstack-prote= ctor-strong -fstack-clash-protection -Wformat -Werror=3Dformat-security -mb= ranch-protection=3Dstandard -g -Wall -Wunused-parameter -pipe -fPIC -Wpoint= er-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=3Dmisleading-= indentation -Werror -O3=20 cc -c src/gth/ags.c -o obj/src/gth/ags.d -Wdate-time -D_FORTIFY_SOURCE=3D2 = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unist= d.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/geno= metools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/reproducible-p= ath/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/genomethreader= -1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/genomethreade= r-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/genomethreade= r-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP -MT obj/src/= gth/ags.o [compile ags_build.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/gth/ags_build.c -o obj/src/gth/= ags_build.o -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_O= FFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>"= -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch= -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg= /src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_S= OURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/in= clude -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vm= atch -DNOLICENSEMANAGER -g -O2 -Werror=3Dimplicit-function-declaration -ff= ile-prefix-map=3D/build/reproducible-path/genomethreader-1.7.3+dfsg=3D. -fs= tack-protector-strong -fstack-clash-protection -Wformat -Werror=3Dformat-se= curity -mbranch-protection=3Dstandard -g -Wall -Wunused-parameter -pipe -fP= IC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=3Dm= isleading-indentation -Werror -O3=20 cc -c src/gth/ags_build.c -o obj/src/gth/ags_build.d -Wdate-time -D_FORTIFY= _SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD= _H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/= include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/re= producible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/ge= nomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/g= enomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/g= enomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP = -MT obj/src/gth/ags_build.o [compile align_dna.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/gth/align_dna.c -o obj/src/gth/= align_dna.o -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_O= FFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>"= -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/include/vmatch= -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.7.3+dfsg= /src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_S= OURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/in= clude -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstree/src/Vm= atch -DNOLICENSEMANAGER -g -O2 -Werror=3Dimplicit-function-declaration -ff= ile-prefix-map=3D/build/reproducible-path/genomethreader-1.7.3+dfsg=3D. -fs= tack-protector-strong -fstack-clash-protection -Wformat -Werror=3Dformat-se= curity -mbranch-protection=3Dstandard -g -Wall -Wunused-parameter -pipe -fP= IC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-error=3Dm= isleading-indentation -Werror -O3=20 cc -c src/gth/align_dna.c -o obj/src/gth/align_dna.d -Wdate-time -D_FORTIFY= _SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD= _H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/= include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/build/re= producible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible-path/ge= nomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducible-path/g= enomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducible-path/g= enomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER -MM -MP = -MT obj/src/gth/align_dna.o [compile align_protein.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/gth/align_protein.c -o obj/src/= gth/align_protein.o -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -= D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<e= xpat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/includ= e/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-1.= 7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U_F= ORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstre= e/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vstre= e/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=3Dimplicit-function-declara= tion -ffile-prefix-map=3D/build/reproducible-path/genomethreader-1.7.3+dfsg= =3D. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=3Df= ormat-security -mbranch-protection=3Dstandard -g -Wall -Wunused-parameter -= pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -Wno-e= rror=3Dmisleading-indentation -Werror -O3=20 cc -c src/gth/align_protein.c -o obj/src/gth/align_protein.d -Wdate-time -D= _FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=3D64 -DWITHLCP = -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"<expat.h>" -DRNV_VERSION=3D\"1.7.8\"= -I/usr/include/genometools -I/usr/include/vmatch -I/usr/include/lua5.1 -I/= build/reproducible-path/genomethreader-1.7.3+dfsg/src -I/build/reproducible= -path/genomethreader-1.7.3+dfsg/obj -U_FORTIFY_SOURCE -I/build/reproducibl= e-path/genomethreader-1.7.3+dfsg/../vstree/src/include -I/build/reproducibl= e-path/genomethreader-1.7.3+dfsg/../vstree/src/Vmatch -DNOLICENSEMANAGER = -MM -MP -MT obj/src/gth/align_protein.o [compile backtrace_path.o] cc -Wdate-time -D_FORTIFY_SOURCE=3D2 -c src/gth/backtrace_path.c -o obj/src= /gth/backtrace_path.o -Wdate-time -D_FORTIFY_SOURCE=3D2 -D_LARGEFILE_SOURCE= -D_FILE_OFFSET_BITS=3D64 -DWITHLCP -DUNISTD_H=3D"<unistd.h>" -DEXPAT_H=3D"= <expat.h>" -DRNV_VERSION=3D\"1.7.8\" -I/usr/include/genometools -I/usr/incl= ude/vmatch -I/usr/include/lua5.1 -I/build/reproducible-path/genomethreader-= 1.7.3+dfsg/src -I/build/reproducible-path/genomethreader-1.7.3+dfsg/obj -U= _FORTIFY_SOURCE -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vst= ree/src/include -I/build/reproducible-path/genomethreader-1.7.3+dfsg/../vst= ree/src/Vmatch -DNOLICENSEMANAGER -g -O2 -Werror=3Dimplicit-function-decla= ration -ffile-prefix-map=3D/build/reproducible-path/genomethreader-1.7.3+df= sg=3D. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror= =3Dformat-security -mbranch-protection=3Dstandard -g -Wall -Wunused-paramet= er -pipe -fPIC -Wpointer-arith -fno-stack-protector -Wno-unknown-pragmas -W= no-error=3Dmisleading-indentation -Werror -O3=20 src/gth/backtrace_path.c: In function =E2=80=98gth_backtrace_path_reverse= =E2=80=99: src/gth/backtrace_path.c:766:11: error: variable =E2=80=98i=E2=80=99 set bu= t not used [-Werror=3Dunused-but-set-variable=3D] 766 | GtUword i =3D 0; | ^ cc1: all warnings being treated as errors make[2]: *** [Makefile:324: obj/src/gth/backtrace_path.o] Error 1 make[2]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+d= fsg' make[1]: *** [debian/rules:36: override_dh_auto_build] Error 2 make[1]: Leaving directory '/build/reproducible-path/genomethreader-1.7.3+d= fsg' make: *** [debian/rules:26: binary] Error 2 dpkg-buildpackage: error: debian/rules binary subprocess failed with exit s= tatus 2 ]