DC-Build-Header: hisat2 2.1.0-4 / 2020-02-25 15:04:55 +0000 DC-Task: type:rebuild-binarch-only source:hisat2 version:2.1.0-4 chroot:unstable esttime:262 logfile:/tmp/hisat2_2.1.0-4_unstable_clang8.log modes:clang8:binarch-only DC-Sbuild-call: su user42 -c 'sbuild -n --arch-any --apt-update -d unstable -v --no-run-lintian --chroot-setup-commands=/tmp/clang8 hisat2_2.1.0-4' sbuild (Debian sbuild) 0.78.1 (09 February 2019) on ip-172-31-4-228.eu-central-1.compute.internal +==============================================================================+ | hisat2 2.1.0-4 (amd64) Tue, 25 Feb 2020 15:04:55 +0000 | +==============================================================================+ Package: hisat2 Version: 2.1.0-4 Source Version: 2.1.0-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: amd64 Build Architecture: amd64 Build Type: binary I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-ff8c47ae-80f5-410b-9519-4c7bbb77f230' with '<>' +------------------------------------------------------------------------------+ | Chroot Setup Commands | +------------------------------------------------------------------------------+ /tmp/clang8 ----------- + echo 'Entering customization script...' Entering customization script... + CLANG_VERSION=8 + echo 'Install of clang-8' Install of clang-8 + apt-get update Get:1 http://127.0.0.1:12990/debian sid InRelease [142 kB] Get:2 http://127.0.0.1:12990/debian sid/main Sources.diff/Index [27.9 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-0823.32.pdiff [11.0 kB] Get:5 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-1420.34.pdiff [30.2 kB] Get:6 http://127.0.0.1:12990/debian sid/main Sources 2020-02-24-2014.03.pdiff [16.9 kB] Get:7 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0213.11.pdiff [23.2 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0815.22.pdiff [9222 B] Get:9 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-0823.32.pdiff [15.5 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-1420.34.pdiff [27.5 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-24-2014.03.pdiff [21.6 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0213.11.pdiff [35.0 kB] Get:8 http://127.0.0.1:12990/debian sid/main Sources 2020-02-25-0815.22.pdiff [9222 B] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0815.22.pdiff [20.1 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 Packages 2020-02-25-0815.22.pdiff [20.1 kB] Get:14 http://127.0.0.1:12990/debian sid/main Translation-en [6195 kB] Fetched 6604 kB in 2s (3841 kB/s) Reading package lists... + apt-get install --yes --no-install-recommends --force-yes clang-8 libomp-8-dev libobjc-9-dev Reading package lists... Building dependency tree... The following additional packages will be installed: cpp-9 g++-9 gcc-8-base gcc-9 gcc-9-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libasan5 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libgcc-8-dev libgcc-9-dev libllvm8 libmpx2 libobjc-8-dev libobjc4 libomp5-8 libstdc++-8-dev libstdc++-9-dev Suggested packages: clang-8-doc gcc-9-locales g++-9-multilib gcc-9-doc gcc-9-multilib libomp-8-doc libstdc++-8-doc libstdc++-9-doc Recommended packages: llvm-8-dev python3 The following NEW packages will be installed: clang-8 gcc-8-base lib32gcc-s1 lib32gcc1 lib32stdc++6 libbsd0 libc6-i386 libclang-common-8-dev libclang1-8 libedit2 libgc1c2 libgcc-8-dev libllvm8 libmpx2 libobjc-8-dev libobjc-9-dev libobjc4 libomp-8-dev libomp5-8 libstdc++-8-dev The following packages will be upgraded: cpp-9 g++-9 gcc-9 gcc-9-base libasan5 libgcc-9-dev libstdc++-9-dev 7 upgraded, 20 newly installed, 0 to remove and 2 not upgraded. Need to get 74.9 MB of archives. After this operation, 223 MB of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libasan5 amd64 9.2.1-30 [389 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 g++-9 amd64 9.2.1-30 [10.7 MB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 gcc-9 amd64 9.2.1-30 [10.0 MB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 libstdc++-9-dev amd64 9.2.1-30 [1697 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libgcc-9-dev amd64 9.2.1-30 [2349 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 cpp-9 amd64 9.2.1-30 [9711 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 gcc-9-base amd64 9.2.1-30 [196 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libedit2 amd64 3.1-20191231-1 [95.4 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libllvm8 amd64 1:8.0.1-7 [13.8 MB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 gcc-8-base amd64 8.3.0-29 [194 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 libmpx2 amd64 8.3.0-29 [11.4 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 libgcc-8-dev amd64 8.3.0-29 [2297 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libstdc++-8-dev amd64 8.3.0-29 [1543 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 libgc1c2 amd64 1:7.6.4-0.4 [224 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libobjc4 amd64 10-20200222-1 [41.6 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libobjc-8-dev amd64 8.3.0-29 [227 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libc6-i386 amd64 2.29-10 [2918 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc-s1 amd64 10-20200222-1 [49.4 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 lib32gcc1 amd64 1:10-20200222-1 [1104 B] Get:21 http://127.0.0.1:12990/debian sid/main amd64 lib32stdc++6 amd64 10-20200222-1 [510 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 libclang-common-8-dev amd64 1:8.0.1-7 [2989 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 libclang1-8 amd64 1:8.0.1-7 [6244 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 clang-8 amd64 1:8.0.1-7 [8010 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 libobjc-9-dev amd64 9.2.1-30 [219 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 libomp5-8 amd64 1:8.0.1-7 [331 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libomp-8-dev amd64 1:8.0.1-7 [62.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 74.9 MB in 1s (101 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12119 files and directories currently installed.) Preparing to unpack .../00-libasan5_9.2.1-30_amd64.deb ... Unpacking libasan5:amd64 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../01-g++-9_9.2.1-30_amd64.deb ... Unpacking g++-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../02-gcc-9_9.2.1-30_amd64.deb ... Unpacking gcc-9 (9.2.1-30) over (9.2.1-29) ... Preparing to unpack .../03-libstdc++-9-dev_9.2.1-30_amd64.deb ... 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W: --force-yes is deprecated, use one of the options starting with --allow instead. + echo 'Replace gcc, g++ & cpp by clang' Replace gcc, g++ & cpp by clang + VERSIONS='4.6 4.7 4.8 4.9 5 6 7 8 9 10' + cd /usr/bin + for VERSION in $VERSIONS + rm -f g++-4.6 gcc-4.6 cpp-4.6 gcc + ln -s clang++-8 g++-4.6 + ln -s clang-8 gcc-4.6 + ln -s clang-8 cpp-4.6 + ln -s clang-8 gcc + echo 'gcc-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.7 gcc-4.7 cpp-4.7 gcc + ln -s clang++-8 g++-4.7 + ln -s clang-8 gcc-4.7 + ln -s clang-8 cpp-4.7 + ln -s clang-8 gcc + echo 'gcc-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.8 gcc-4.8 cpp-4.8 gcc + ln -s clang++-8 g++-4.8 + ln -s clang-8 gcc-4.8 + ln -s clang-8 cpp-4.8 + ln -s clang-8 gcc + echo 'gcc-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-4.9 gcc-4.9 cpp-4.9 gcc + ln -s clang++-8 g++-4.9 + ln -s clang-8 gcc-4.9 + ln -s clang-8 cpp-4.9 + ln -s clang-8 gcc + echo 'gcc-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-4.9 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-4.9 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-5 gcc-5 cpp-5 gcc + ln -s clang++-8 g++-5 + ln -s clang-8 gcc-5 + ln -s clang-8 cpp-5 + ln -s clang-8 gcc + echo 'gcc-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-5 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-5 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-6 gcc-6 cpp-6 gcc + ln -s clang++-8 g++-6 + ln -s clang-8 gcc-6 + ln -s clang-8 cpp-6 + ln -s clang-8 gcc + echo 'gcc-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-6 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-6 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-7 gcc-7 cpp-7 gcc + ln -s clang++-8 g++-7 + ln -s clang-8 gcc-7 + ln -s clang-8 cpp-7 + ln -s clang-8 gcc + echo 'gcc-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-7 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-7 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-8 gcc-8 cpp-8 gcc + ln -s clang++-8 g++-8 + ln -s clang-8 gcc-8 + ln -s clang-8 cpp-8 + ln -s clang-8 gcc + echo 'gcc-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-8 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-8 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + for VERSION in $VERSIONS + rm -f g++-9 gcc-9 cpp-9 gcc + ln -s clang++-8 g++-9 + ln -s clang-8 gcc-9 + ln -s clang-8 cpp-9 + ln -s clang-8 gcc + echo 'gcc-9 hold' + dpkg --set-selections + echo 'g++-9 hold' + dpkg --set-selections + for VERSION in $VERSIONS + rm -f g++-10 gcc-10 cpp-10 gcc + ln -s clang++-8 g++-10 + ln -s clang-8 gcc-10 + ln -s clang-8 cpp-10 + ln -s clang-8 gcc + echo 'gcc-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: gcc-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + echo 'g++-10 hold' + dpkg --set-selections dpkg: warning: package not in status nor available database at line 1: g++-10 dpkg: warning: found unknown packages; this might mean the available database is outdated, and needs to be updated through a frontend method; please see the FAQ + cd - /build/hisat2-hWWS09 + echo 'Check if gcc, g++ & cpp are actually clang' Check if gcc, g++ & cpp are actually clang + gcc --version + grep clang + cpp --version + grep clang + g++ --version + grep clang I: Finished running '/tmp/clang8'. Finished processing commands. -------------------------------------------------------------------------------- I: NOTICE: Log filtering will replace 'build/hisat2-hWWS09/resolver-xAdzcT' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Hit:1 http://127.0.0.1:12990/debian sid InRelease Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libgmp10 zlib1g 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 343 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://127.0.0.1:12990/debian sid/main amd64 libgmp10 amd64 2:6.2.0+dfsg-4 [253 kB] Get:2 http://127.0.0.1:12990/debian sid/main amd64 zlib1g amd64 1:1.2.11.dfsg-2 [90.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 343 kB in 0s (6392 kB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13887 files and directories currently installed.) Preparing to unpack .../libgmp10_2%3a6.2.0+dfsg-4_amd64.deb ... Unpacking libgmp10:amd64 (2:6.2.0+dfsg-4) over (2:6.2.0+dfsg-3) ... Setting up libgmp10:amd64 (2:6.2.0+dfsg-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13887 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.11.dfsg-2_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.11.dfsg-2) over (1:1.2.11.dfsg-1.2) ... Setting up zlib1g:amd64 (1:1.2.11.dfsg-2) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Fetch source files | +------------------------------------------------------------------------------+ Check APT --------- Checking available source versions... Download source files with APT ------------------------------ Reading package lists... NOTICE: 'hisat2' packaging is maintained in the 'Git' version control system at: https://salsa.debian.org/med-team/hisat2.git Please use: git clone https://salsa.debian.org/med-team/hisat2.git to retrieve the latest (possibly unreleased) updates to the package. Need to get 2827 kB of source archives. Get:1 http://127.0.0.1:12990/debian sid/main hisat2 2.1.0-4 (dsc) [2105 B] Get:2 http://127.0.0.1:12990/debian sid/main hisat2 2.1.0-4 (tar) [2742 kB] Get:3 http://127.0.0.1:12990/debian sid/main hisat2 2.1.0-4 (diff) [83.0 kB] Fetched 2827 kB in 0s (27.1 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hisat2-hWWS09/hisat2-2.1.0' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-hWWS09' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), help2man, pandoc, python3:any, build-essential, fakeroot Filtered Build-Depends: debhelper-compat (= 12), help2man, pandoc, python3:any, build-essential, fakeroot dpkg-deb: building package 'sbuild-build-depends-main-dummy' in '/<>/apt_archive/sbuild-build-depends-main-dummy.deb'. Ign:1 copy:/<>/apt_archive ./ InRelease Get:2 copy:/<>/apt_archive ./ Release [957 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [400 B] Get:5 copy:/<>/apt_archive ./ Packages [473 B] Fetched 1830 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libreadline8 libsigsegv2 libsqlite3-0 libssl1.1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support pandoc pandoc-data po-debconf python3 python3-minimal python3.7 python3.7-minimal readline-common sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc wamerican | wordlist whois vacation dh-make gettext-doc libasprintf-dev libgettextpo-dev groff libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php python ruby r-base-core libjs-mathjax node-katex libmail-box-perl python3-doc python3-tk python3-venv python3.7-venv python3.7-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev bsdmainutils debhelper dh-autoreconf dh-strip-nondeterminism dwz file gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libcroco3 libdebhelper-perl libelf1 libexpat1 libfile-stripnondeterminism-perl libglib2.0-0 libicu63 liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libreadline8 libsigsegv2 libsqlite3-0 libssl1.1 libsub-override-perl libtool libuchardet0 libxml2 m4 man-db mime-support pandoc pandoc-data po-debconf python3 python3-minimal python3.7 python3.7-minimal readline-common sbuild-build-depends-main-dummy sensible-utils 0 upgraded, 52 newly installed, 0 to remove and 0 not upgraded. Need to get 42.7 MB of archives. After this operation, 226 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [900 B] Get:2 http://127.0.0.1:12990/debian sid/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:3 http://127.0.0.1:12990/debian sid/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:4 http://127.0.0.1:12990/debian sid/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:5 http://127.0.0.1:12990/debian sid/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:6 http://127.0.0.1:12990/debian sid/main amd64 man-db amd64 2.9.0-2 [1307 kB] Get:7 http://127.0.0.1:12990/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:8 http://127.0.0.1:12990/debian sid/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:9 http://127.0.0.1:12990/debian sid/main amd64 libpython3.7-minimal amd64 3.7.6-1+b1 [591 kB] Get:10 http://127.0.0.1:12990/debian sid/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:11 http://127.0.0.1:12990/debian sid/main amd64 python3.7-minimal amd64 3.7.6-1+b1 [1813 kB] Get:12 http://127.0.0.1:12990/debian sid/main amd64 python3-minimal amd64 3.7.5-3 [36.8 kB] Get:13 http://127.0.0.1:12990/debian sid/main amd64 mime-support all 3.64 [37.8 kB] Get:14 http://127.0.0.1:12990/debian sid/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:15 http://127.0.0.1:12990/debian sid/main amd64 readline-common all 8.0-3 [72.5 kB] Get:16 http://127.0.0.1:12990/debian sid/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:17 http://127.0.0.1:12990/debian sid/main amd64 libsqlite3-0 amd64 3.31.1-3 [661 kB] Get:18 http://127.0.0.1:12990/debian sid/main amd64 libpython3.7-stdlib amd64 3.7.6-1+b1 [1735 kB] Get:19 http://127.0.0.1:12990/debian sid/main amd64 python3.7 amd64 3.7.6-1+b1 [351 kB] Get:20 http://127.0.0.1:12990/debian sid/main amd64 libpython3-stdlib amd64 3.7.5-3 [20.2 kB] Get:21 http://127.0.0.1:12990/debian sid/main amd64 python3 amd64 3.7.5-3 [62.1 kB] Get:22 http://127.0.0.1:12990/debian sid/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:23 http://127.0.0.1:12990/debian sid/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:24 http://127.0.0.1:12990/debian sid/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:25 http://127.0.0.1:12990/debian sid/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:26 http://127.0.0.1:12990/debian sid/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:27 http://127.0.0.1:12990/debian sid/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:28 http://127.0.0.1:12990/debian sid/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:29 http://127.0.0.1:12990/debian sid/main amd64 autoconf all 2.69-11.1 [341 kB] Get:30 http://127.0.0.1:12990/debian sid/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:31 http://127.0.0.1:12990/debian sid/main amd64 automake all 1:1.16.1-4 [771 kB] Get:32 http://127.0.0.1:12990/debian sid/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:33 http://127.0.0.1:12990/debian sid/main amd64 libtool all 2.4.6-13 [513 kB] Get:34 http://127.0.0.1:12990/debian sid/main amd64 dh-autoreconf all 19 [16.9 kB] Get:35 http://127.0.0.1:12990/debian sid/main amd64 libdebhelper-perl all 12.9 [183 kB] Get:36 http://127.0.0.1:12990/debian sid/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] Get:37 http://127.0.0.1:12990/debian sid/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:38 http://127.0.0.1:12990/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB] Get:39 http://127.0.0.1:12990/debian sid/main amd64 dh-strip-nondeterminism all 1.6.3-2 [14.7 kB] Get:40 http://127.0.0.1:12990/debian sid/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:41 http://127.0.0.1:12990/debian sid/main amd64 dwz amd64 0.13-5 [151 kB] Get:42 http://127.0.0.1:12990/debian sid/main amd64 libglib2.0-0 amd64 2.62.4-2 [1319 kB] Get:43 http://127.0.0.1:12990/debian sid/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:44 http://127.0.0.1:12990/debian sid/main amd64 libxml2 amd64 2.9.10+dfsg-3 [709 kB] Get:45 http://127.0.0.1:12990/debian sid/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:46 http://127.0.0.1:12990/debian sid/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:47 http://127.0.0.1:12990/debian sid/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:48 http://127.0.0.1:12990/debian sid/main amd64 po-debconf all 1.0.21 [248 kB] Get:49 http://127.0.0.1:12990/debian sid/main amd64 debhelper all 12.9 [994 kB] Get:50 http://127.0.0.1:12990/debian sid/main amd64 help2man amd64 1.47.12 [180 kB] Get:51 http://127.0.0.1:12990/debian sid/main amd64 pandoc-data all 2.5-3 [349 kB] Get:52 http://127.0.0.1:12990/debian sid/main amd64 pandoc amd64 2.5-3+b1 [15.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 42.7 MB in 0s (89.7 MB/s) Selecting previously unselected package bsdmainutils. (Reading database ... 13887 files and directories currently installed.) Preparing to unpack .../0-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../1-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../2-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../3-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../4-man-db_2.9.0-2_amd64.deb ... Unpacking man-db (2.9.0-2) ... Selecting previously unselected package liblocale-gettext-perl. Preparing to unpack .../5-liblocale-gettext-perl_1.07-4_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-4) ... 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Setting up libarchive-zip-perl (1.67-1) ... Setting up libglib2.0-0:amd64 (2.62.4-2) ... No schema files found: doing nothing. Setting up libdebhelper-perl (12.9) ... Setting up libsqlite3-0:amd64 (3.31.1-3) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libicu63:amd64 (63.2-2) ... Setting up autotools-dev (20180224.1) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up autopoint (0.19.8.1-10) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up pandoc-data (2.5-3) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (8.0-3) ... Setting up libxml2:amd64 (2.9.10+dfsg-3) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libtool (2.4.6-13) ... Setting up libreadline8:amd64 (8.0-3) ... Setting up m4 (1.4.18-4) ... Setting up help2man (1.47.12) ... Setting up pandoc (2.5-3+b1) ... Setting up libcroco3:amd64 (0.6.13-1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libpython3.7-stdlib:amd64 (3.7.6-1+b1) ... Setting up gettext (0.19.8.1-10) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libpython3-stdlib:amd64 (3.7.5-3) ... Setting up python3.7 (3.7.6-1+b1) ... Setting up po-debconf (1.0.21) ... Setting up python3 (3.7.5-3) ... Setting up debhelper (12.9) ... Setting up dh-autoreconf (19) ... Setting up sbuild-build-depends-main-dummy (0.invalid.0) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (amd64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.19.0-6-cloud-amd64 #1 SMP Debian 4.19.67-2+deb10u2 (2019-11-11) amd64 (x86_64) Toolchain package versions: binutils_2.34-3 dpkg-dev_1.19.7 g++-9_9.2.1-30 gcc-9_9.2.1-30 libc6-dev_2.29-10 libstdc++-8-dev_8.3.0-29 libstdc++-9-dev_9.2.1-30 libstdc++6_10-20200222-1 linux-libc-dev_5.4.19-1 Package versions: adduser_3.118 apt_1.8.4 autoconf_2.69-11.1 automake_1:1.16.1-4 autopoint_0.19.8.1-10 autotools-dev_20180224.1 base-files_11 base-passwd_3.5.47 bash_5.0-5 binutils_2.34-3 binutils-common_2.34-3 binutils-x86-64-linux-gnu_2.34-3 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 clang-8_1:8.0.1-7 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-9_9.2.1-30 dash_0.5.10.2-6 debconf_1.5.73 debhelper_12.9 debian-archive-keyring_2019.1 debianutils_4.9.1 dh-autoreconf_19 dh-strip-nondeterminism_1.6.3-2 diffutils_1:3.7-3 dpkg_1.19.7 dpkg-dev_1.19.7 dwz_0.13-5 e2fsprogs_1.45.5-2 fakeroot_1.24-1 fdisk_2.34-0.1 file_1:5.38-4 findutils_4.7.0-1 g++_4:9.2.1-3.1 g++-9_9.2.1-30 gcc_4:9.2.1-3.1 gcc-10-base_10-20200222-1 gcc-8-base_8.3.0-29 gcc-9_9.2.1-30 gcc-9-base_9.2.1-30 gettext_0.19.8.1-10 gettext-base_0.19.8.1-10 gpgv_2.2.19-1 grep_3.4-1 groff-base_1.22.4-4 gzip_1.9-3+b1 help2man_1.47.12 hostname_3.23 init-system-helpers_1.57 intltool-debian_0.35.0+20060710.5 lib32gcc-s1_10-20200222-1 lib32gcc1_1:10-20200222-1 lib32stdc++6_10-20200222-1 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-30 libatomic1_10-20200222-1 libattr1_1:2.4.48-5 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libsqlite3-0_3.31.1-3 libss2_1.45.5-2 libssl1.1_1.1.1d-2 libstdc++-8-dev_8.3.0-29 libstdc++-9-dev_9.2.1-30 libstdc++6_10-20200222-1 libsub-override-perl_0.09-2 libsystemd0_244.3-1 libtasn1-6_4.16.0-2 libtinfo6_6.1+20191019-1 libtool_2.4.6-13 libtsan0_10-20200222-1 libubsan1_10-20200222-1 libuchardet0_0.0.6-3 libudev1_244.3-1 libunistring2_0.9.10-2 libuuid1_2.34-0.1 libxml2_2.9.10+dfsg-3 libzstd1_1.4.4+dfsg-3 linux-libc-dev_5.4.19-1 login_1:4.8.1-1 logsave_1.45.5-2 lsb-base_11.1.0 m4_1.4.18-4 make_4.2.1-1.2 man-db_2.9.0-2 mawk_1.3.4.20200120-2 mime-support_3.64 mount_2.34-0.1 ncurses-base_6.1+20191019-1 ncurses-bin_6.1+20191019-1 pandoc_2.5-3+b1 pandoc-data_2.5-3 passwd_1:4.8.1-1 patch_2.7.6-6 perl_5.30.0-9 perl-base_5.30.0-9 perl-modules-5.30_5.30.0-9 po-debconf_1.0.21 python3_3.7.5-3 python3-minimal_3.7.5-3 python3.7_3.7.6-1+b1 python3.7-minimal_3.7.6-1+b1 readline-common_8.0-3 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.12+nmu1 sysvinit-utils_2.96-2.1 tar_1.30+dfsg-6+b1 tzdata_2019c-3 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-2 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hisat2 Binary: hisat2, python3-hisat2 Architecture: any all Version: 2.1.0-4 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://ccb.jhu.edu/software/hisat2/index.shtml Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/hisat2 Vcs-Git: https://salsa.debian.org/med-team/hisat2.git Testsuite: autopkgtest Testsuite-Triggers: bcftools, samtools Build-Depends: debhelper-compat (= 12), help2man , pandoc , python3:any Package-List: hisat2 deb science optional arch=any python3-hisat2 deb python optional arch=all Checksums-Sha1: e428c92bcaf732dd5a0ebab18d2bef6a3bb034dd 2741828 hisat2_2.1.0.orig.tar.xz 64403cf2f599016de6c90b2967dd887cfe713ded 82992 hisat2_2.1.0-4.debian.tar.xz Checksums-Sha256: 8e12e932bb64346eb5ae9c4392146622f30e15b7d043efaecdebd0daea60e143 2741828 hisat2_2.1.0.orig.tar.xz 70bafae685fc9da1cb39b4de0722b34459e95257f4d9dc3c4ed28d8e693c99cb 82992 hisat2_2.1.0-4.debian.tar.xz Files: c3ac50c4c5cf6621b31c18cbfedc70e3 2741828 hisat2_2.1.0.orig.tar.xz 6a78514d4a437024b7fb6aa3d19269bc 82992 hisat2_2.1.0-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAl5C4yMACgkQPCZ2P2xn 5uKjKw/8CD8pEyLyqrhE2koPub+5F6uuOxYkx2mBjBIBQPgBNQo/fF84/25Ue9aN jqKC3wpMiD5d+RXyaTWQBJ/MV3DoFW7/UwiWnPP06Bmn0IKplSvovc8FpohkdrTj l7K1NQ0uRk7PrFgjMzvPW98k7rzHNDIQw+0fG3j8qSjdi2+B/qrhOm1v69gZ+TIc JHeu/59OIytIu6NVvdIxR4RBoctS8Zg/FZhPZrJTIrfvgx7ml4m/eXdRvoIfdt4O Ir+YKHczRitobZL579trLPjb4FkJeKcbmRS9LjHMt1FIm8lIUQSsZ+mYeCq9yl8C dcHanLWHNPefPQ9P+reiitmelKEc4s66k6w0+4Qi7AYmuUervD1PBVF2UpDQHaSc 025SZQH5bQgjC9L8ch74wZIPd7DDkAjCCYZ9E+4oOK7Vfy6slAsLF0ZHfq90bte1 N59rMygIdvcH2ihU5EzXDy1bI5uzwPse4rhdgQ/mTglMfSYPJtBGBrmmXJrMjL5P l4bGq4ikSt3fOLPDXH+0azj0X65MyRCEcMUEW6Bm8AsfA0vFj3n2VZlzBv2a4fFy spI8N4a+FMTPqTtk5oKsfhkmmdSzndvkP/85pyYTqmTSjXsVpgrPGhkXszO8/sbl eucogeKNjZsQVWp+4vn5ra1Vqr+9WVprl/aLLXEzECCKQ9mbpRU= =G74b -----END PGP SIGNATURE----- gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/sbuild-nonexistent/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Tue Feb 11 17:23:47 2020 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./hisat2_2.1.0-4.dsc dpkg-source: info: extracting hisat2 in /<> dpkg-source: info: unpacking hisat2_2.1.0.orig.tar.xz dpkg-source: info: unpacking hisat2_2.1.0-4.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying hardening dpkg-source: info: applying reproducibile dpkg-source: info: applying fix-freebsd dpkg-source: info: applying compilerflags dpkg-source: info: applying simde dpkg-source: info: applying python3 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf HOME=/sbuild-nonexistent LANG=C.UTF-8 LC_ALL=C.UTF-8 LOGNAME=user42 PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1001 SCHROOT_GROUP=user42 SCHROOT_SESSION_ID=sid-amd64-sbuild-ff8c47ae-80f5-410b-9519-4c7bbb77f230 SCHROOT_UID=1001 SCHROOT_USER=user42 SHELL=/bin/sh USER=user42 dpkg-buildpackage ----------------- Command: dpkg-buildpackage -us -uc -b -rfakeroot dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.1.0-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean dh_auto_clean make -j4 clean make[1]: Entering directory '/<>' rm -f hisat2-build-s hisat2-build-l hisat2-align-s hisat2-align-l hisat2-inspect-s hisat2-inspect-l hisat2-build-s-debug hisat2-build-l-debug hisat2-align-s-debug hisat2-align-l-debug hisat2-inspect-s-debug hisat2-inspect-l-debug \ hisat2-build-s.exe hisat2-build-l.exe hisat2-align-s.exe hisat2-align-l.exe hisat2-inspect-s.exe hisat2-inspect-l.exe hisat2-build-s-debug.exe hisat2-build-l-debug.exe hisat2-align-s-debug.exe hisat2-align-l-debug.exe hisat2-inspect-s-debug.exe hisat2-inspect-l-debug.exe \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM make[1]: Leaving directory '/<>' dh_clean debian/rules build dh build dh_update_autotools_config dh_autoreconf dh_auto_configure debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="11 February 2020" all doc make -j4 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=11 February 2020" all doc make[2]: Entering directory '/<>' /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from In file included from hisat2_build.cpp:35: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ hisat2_build.cpp:35: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from hisat2_build.cpp:35: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; In file included from hisat2_build.cpp ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ :35: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from hisat2.cpp:33: In file included from ./hgfm.h:24: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ hisat2.cpp:1753:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr presets(new PresetsV0()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ hisat2.cpp:1753:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr presets(new PresetsV0()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ hisat2.cpp:3068:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) hisat2.cpp:3068:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7 ^ : note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' hisat2.cpp:3069:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations]# define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ auto_ptr ps(patsrcFact->create()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: hisat2.cpp:3069:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr ps(patsrcFact->create()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46:: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ hisat2.cpp:3085:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED;hisat2.cpp:3085:2: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ hisat2.cpphisat2.cpp:3826:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr refs( ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ :3826:9: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr refs( ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. 7 warnings generated. 7 warnings generated. In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from gfm.cpp:21: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from gfm.cpp:21: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from gfm.cpp:21: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from gfm.cpp:21: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from gfm.cpp:21: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from gfm.cpp:21: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from gfm.cpp:21: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from gfm.cpp:21: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now /usr/bin/g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \"" \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"11 February 2020\"" -DCOMPILER_VERSION="\"`/usr/bin/g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -fdebug-prefix-map=/<>=. -fstack-protector-strong -Wformat -Werror=format-security -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -DPOPCNT_CAPABILITY -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now make[2]: Nothing to be done for 'doc'. In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from hisat2_inspect.cpp:27: In file included from ./hgfm.h:24: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from In file included from aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; In file included from aligner_seed.cpp:21 ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ : In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: noteIn file included from : expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ aligner_seed.cpp:21: In file included from ./aligner_seed.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated2 warnings generated. . In file included from aligner_seed2.cpp:22: In file included from aligner_seed2.cpp:In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: 22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from In file included from aligner_seed2.cpp:22: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) : note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ ^ 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here : expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_sw.cpp:25: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: In file included from aligner_sw.cpp./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: :note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 25: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_result.cpp:22: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ aligner_result.cpp:1267:10: error: ordered comparison between pointer and zero ('const char *' and 'int') if(flag > 0) { ~~~~ ^ ~ aligner_result.cpp:1267:10: error: ordered comparison between pointer and zero ('const char *' and 'int') if(flag > 0) { ~~~~ ^ ~ 2 warnings and 1 error generated. 2 warnings and 1 error generated. In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from edit.cpp:21: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated herealn_sink.cpp } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ :22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7In file included from aln_sink.cpp:22: In file included from ./aln_sink.h:25: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)): note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note ^ : expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. In file included from gfm.cpp:21: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from gfm.cpp:21: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: ^ note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here unique.cpp:20: In file included from ./unique.h:38: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46 ^ : note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from gfm.cpp:21: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from gfm.cpp:21: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. 2 warnings generated. 2 warnings generated. In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here 30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46aligner_bt.cpp:20: In file included from ./aligner_bt.h:25: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ : note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse.cpp:21: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_loc_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_ee_i16.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_loc_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_swsse_ee_u8.cpp:56: In file included from ./aligner_sw.h:74: In file included from ./aligner_sw_common.h:23: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from aligner_driver.cpp:20: In file included from ./aligner_driver.h:78: In file included from ./aligner_seed2.h:102: In file included from ./aligner_result.h:30: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1098:3: warning: 'auto_ptr >' is deprecated [-Wdeprecated-declarations] auto_ptr ss(new stringstream()); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr >' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ In file included from splice_site.cpp:20: In file included from ./edit.h:30: In file included from ./splice_site.h:34: ./gfm.h:1102:3: warning: 'auto_ptr' is deprecated [-Wdeprecated-declarations] auto_ptr fb(new FileBuf(ss.get())); ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/c++/9/backward/auto_ptr.h:287:7: note: 'auto_ptr' has been explicitly marked deprecated here } _GLIBCXX_DEPRECATED; ^ /usr/bin/../lib/gcc/x86_64-linux-gnu/9/../../../../include/x86_64-linux-gnu/c++/9/bits/c++config.h:86:46: note: expanded from macro '_GLIBCXX_DEPRECATED' # define _GLIBCXX_DEPRECATED __attribute__ ((__deprecated__)) ^ 2 warnings generated. 2 warnings generated. make[2]: *** [Makefile:316: hisat2-align-s] Error 1 make[2]: *** Waiting for unfinished jobs.... make[2]: *** [Makefile:324: hisat2-align-l] Error 1 make[2]: Leaving directory '/<>' dh_auto_build: error: make -j4 "INSTALL=install --strip-program=true" BUILD_HOST=Debian "BUILD_TIME=11 February 2020" all doc returned exit code 2 make[1]: *** [debian/rules:32: override_dh_auto_build] Error 25 make[1]: Leaving directory '/<>' make: *** [debian/rules:28: build] Error 2 dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-02-25T15:06:26Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Type: binary Build-Space: 27488 Build-Time: 66 Distribution: unstable Fail-Stage: build Host Architecture: amd64 Install-Time: 8 Job: hisat2_2.1.0-4 Machine Architecture: amd64 Package: hisat2 Package-Time: 91 Source-Version: 2.1.0-4 Space: 27488 Status: attempted Version: 2.1.0-4 -------------------------------------------------------------------------------- Finished at 2020-02-25T15:06:26Z Build needed 00:01:31, 27488k disk space E: Build failure (dpkg-buildpackage died) DC-Status: Failed 92.316514127s DC-Time-Estimation: 92.316514127 versus expected 262 (r/m: 1.8380621005637854 ; m: 92.316514127)