sbuild (Debian sbuild) 0.78.1 (09 February 2019) on gcc131.bak.milne.osuosl.org +==============================================================================+ | hisat2 2.1.0-4 (armel) Thu, 13 Feb 2020 00:11:12 +0000 | +==============================================================================+ Package: hisat2 Version: 2.1.0-4 Source Version: 2.1.0-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: armel Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/unstable-amd64-sbuild-a6e7e314-b90a-4340-8b8a-c239dd8e01c1' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-MgajS0/resolver-3HTgyi' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://debian.oregonstate.edu/debian unstable InRelease [142 kB] Get:2 http://debian.oregonstate.edu/debian unstable/main Sources.diff/Index [27.9 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 Packages.diff/Index [27.9 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-12-0812.51.pdiff [15.6 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-12-1412.45.pdiff [16.3 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-12-2012.17.pdiff [11.7 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main Sources 2020-02-12-2012.17.pdiff [11.7 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-12-0812.51.pdiff [381 B] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-12-1412.45.pdiff [8629 B] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-12-2012.17.pdiff [29.4 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main armel Packages [7964 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 Packages 2020-02-12-2012.17.pdiff [29.4 kB] Fetched 8245 kB in 2s (4260 kB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. +------------------------------------------------------------------------------+ | 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://debian.oregonstate.edu/debian unstable/main hisat2 2.1.0-4 (dsc) [2105 B] Get:2 http://debian.oregonstate.edu/debian unstable/main hisat2 2.1.0-4 (tar) [2742 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main hisat2 2.1.0-4 (diff) [83.0 kB] Fetched 2827 kB in 0s (42.9 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hisat2-MgajS0/hisat2-2.1.0' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-MgajS0' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 12), help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel Filtered Build-Depends: debhelper-compat (= 12), help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-armel:amd64, libc-dev:armel, libstdc++-dev:armel 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 [430 B] Get:5 copy:/<>/apt_archive ./ Packages [513 B] Fetched 1900 B in 0s (99.9 kB/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 binutils-arm-linux-gnueabi bsdmainutils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libbsd0 libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libglib2.0-0 libgomp1:armel libgomp1-armel-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libreadline8 libsigsegv2 libsqlite3-0 libssl1.1 libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross m4 man-db mime-support pandoc pandoc-data po-debconf python3 python3-minimal python3.7 python3.7-minimal readline-common sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc wamerican | wordlist whois vacation gcc-9-locales cpp-doc dh-make binutils-multiarch g++-multilib g++-9-multilib gcc-9-doc manpages-dev flex bison gdb-arm-linux-gnueabi gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:armel libc-l10n:armel locales:armel glibc-doc manpages-dev:armel libstdc++-9-doc libstdc++-9-doc:armel libtool-doc gfortran | fortran95-compiler gcj-jdk libyaml-shell-perl 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 libidn2-0:armel libarchive-cpio-perl libglib2.0-data shared-mime-info xdg-user-dirs libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-arm-linux-gnueabi bsdmainutils build-essential cpp-9-arm-linux-gnueabi cpp-arm-linux-gnueabi cross-config crossbuild-essential-armel debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++ g++-9 g++-9-arm-linux-gnueabi g++-arm-linux-gnueabi gcc-10-base:armel gcc-10-cross-base gcc-9-arm-linux-gnueabi gcc-9-arm-linux-gnueabi-base gcc-9-base:armel gcc-9-cross-base gcc-arm-linux-gnueabi gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan5:armel libasan5-armel-cross libatomic1:armel libatomic1-armel-cross libbsd0 libc6:armel libc6-armel-cross libc6-dev libc6-dev:armel libc6-dev-armel-cross libconfig-auto-perl libconfig-inifiles-perl libcroco3 libcrypt-dev libcrypt-dev:armel libcrypt1:armel libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-9-dev:armel libgcc-9-dev-armel-cross libgcc-s1:armel libgcc-s1-armel-cross libglib2.0-0 libgomp1:armel libgomp1-armel-cross libicu63 libio-string-perl liblocale-gettext-perl libmagic-mgc libmagic1 libmpdec2 libpipeline1 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libreadline8 libsigsegv2 libsqlite3-0 libssl1.1 libstdc++-9-dev libstdc++-9-dev:armel libstdc++-9-dev-armel-cross libstdc++6:armel libstdc++6-armel-cross libsub-override-perl libtool libubsan1:armel libubsan1-armel-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-perl linux-libc-dev:armel linux-libc-dev-armel-cross 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:armel sensible-utils ucf 0 upgraded, 111 newly installed, 0 to remove and 0 not upgraded. Need to get 101 MB of archives. After this operation, 469 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [940 B] Get:2 http://debian.oregonstate.edu/debian unstable/main amd64 libbsd0 amd64 0.10.0-1 [107 kB] Get:3 http://debian.oregonstate.edu/debian unstable/main amd64 bsdmainutils amd64 11.1.2+b1 [191 kB] Get:4 http://debian.oregonstate.edu/debian unstable/main amd64 libuchardet0 amd64 0.0.6-3 [64.9 kB] Get:5 http://debian.oregonstate.edu/debian unstable/main amd64 groff-base amd64 1.22.4-4 [919 kB] Get:6 http://debian.oregonstate.edu/debian unstable/main amd64 libpipeline1 amd64 1.5.2-2 [33.9 kB] Get:7 http://debian.oregonstate.edu/debian unstable/main amd64 man-db amd64 2.9.0-2 [1307 kB] Get:8 http://debian.oregonstate.edu/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-4 [18.8 kB] Get:9 http://debian.oregonstate.edu/debian unstable/main amd64 libssl1.1 amd64 1.1.1d-2 [1540 kB] Get:10 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.7-minimal amd64 3.7.6-1+b1 [591 kB] Get:11 http://debian.oregonstate.edu/debian unstable/main amd64 libexpat1 amd64 2.2.9-1 [94.3 kB] Get:12 http://debian.oregonstate.edu/debian unstable/main amd64 python3.7-minimal amd64 3.7.6-1+b1 [1813 kB] Get:13 http://debian.oregonstate.edu/debian unstable/main amd64 python3-minimal amd64 3.7.5-3 [36.8 kB] Get:14 http://debian.oregonstate.edu/debian unstable/main amd64 mime-support all 3.64 [37.8 kB] Get:15 http://debian.oregonstate.edu/debian unstable/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:16 http://debian.oregonstate.edu/debian unstable/main amd64 readline-common all 8.0-3 [72.5 kB] Get:17 http://debian.oregonstate.edu/debian unstable/main amd64 libreadline8 amd64 8.0-3 [160 kB] Get:18 http://debian.oregonstate.edu/debian unstable/main amd64 libsqlite3-0 amd64 3.31.1-2 [661 kB] Get:19 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3.7-stdlib amd64 3.7.6-1+b1 [1735 kB] Get:20 http://debian.oregonstate.edu/debian unstable/main amd64 python3.7 amd64 3.7.6-1+b1 [351 kB] Get:21 http://debian.oregonstate.edu/debian unstable/main amd64 libpython3-stdlib amd64 3.7.5-3 [20.2 kB] Get:22 http://debian.oregonstate.edu/debian unstable/main amd64 python3 amd64 3.7.5-3 [62.1 kB] Get:23 http://debian.oregonstate.edu/debian unstable/main armel gcc-10-base armel 10-20200211-1 [195 kB] Get:24 http://debian.oregonstate.edu/debian unstable/main armel gcc-9-base armel 9.2.1-28 [195 kB] Get:25 http://debian.oregonstate.edu/debian unstable/main amd64 sensible-utils all 0.0.12+nmu1 [16.0 kB] Get:26 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic-mgc amd64 1:5.38-4 [262 kB] Get:27 http://debian.oregonstate.edu/debian unstable/main amd64 libmagic1 amd64 1:5.38-4 [120 kB] Get:28 http://debian.oregonstate.edu/debian unstable/main amd64 file amd64 1:5.38-4 [67.9 kB] Get:29 http://debian.oregonstate.edu/debian unstable/main amd64 gettext-base amd64 0.19.8.1-10 [123 kB] Get:30 http://debian.oregonstate.edu/debian unstable/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:31 http://debian.oregonstate.edu/debian unstable/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:32 http://debian.oregonstate.edu/debian unstable/main amd64 m4 amd64 1.4.18-4 [203 kB] Get:33 http://debian.oregonstate.edu/debian unstable/main amd64 autoconf all 2.69-11.1 [341 kB] Get:34 http://debian.oregonstate.edu/debian unstable/main amd64 autotools-dev all 20180224.1 [77.0 kB] Get:35 http://debian.oregonstate.edu/debian unstable/main amd64 automake all 1:1.16.1-4 [771 kB] Get:36 http://debian.oregonstate.edu/debian unstable/main amd64 autopoint all 0.19.8.1-10 [435 kB] Get:37 http://debian.oregonstate.edu/debian unstable/main amd64 binutils-arm-linux-gnueabi amd64 2.34-2 [2748 kB] Get:38 http://debian.oregonstate.edu/debian unstable/main amd64 libcrypt-dev amd64 1:4.4.10-10 [104 kB] Get:39 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev amd64 2.29-10 [2638 kB] Get:40 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev amd64 9.2.1-28 [1697 kB] Get:41 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9 amd64 9.2.1-28 [10.7 MB] Get:42 http://debian.oregonstate.edu/debian unstable/main amd64 g++ amd64 4:9.2.1-3.1 [1644 B] Get:43 http://debian.oregonstate.edu/debian unstable/main amd64 build-essential amd64 12.8 [7640 B] Get:44 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi-base amd64 9.2.1-21cross1 [195 kB] Get:45 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-9-arm-linux-gnueabi amd64 9.2.1-21cross1 [6813 kB] Get:46 http://debian.oregonstate.edu/debian unstable/main amd64 cpp-arm-linux-gnueabi amd64 4:9.2.1-3.1 [16.7 kB] Get:47 http://debian.oregonstate.edu/debian unstable/main amd64 cross-config all 2.6.15-3 [39.9 kB] Get:48 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-cross-base all 9.2.1-21cross1 [190 kB] Get:49 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-10-cross-base all 10-20200211-1cross1 [191 kB] Get:50 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-armel-cross all 2.29-9cross1 [1128 kB] Get:51 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-s1-armel-cross all 10-20200211-1cross1 [38.3 kB] Get:52 http://debian.oregonstate.edu/debian unstable/main amd64 libgomp1-armel-cross all 10-20200211-1cross1 [85.0 kB] Get:53 http://debian.oregonstate.edu/debian unstable/main amd64 libatomic1-armel-cross all 10-20200211-1cross1 [8668 B] Get:54 http://debian.oregonstate.edu/debian unstable/main amd64 libasan5-armel-cross all 9.2.1-21cross1 [341 kB] Get:55 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++6-armel-cross all 10-20200211-1cross1 [369 kB] Get:56 http://debian.oregonstate.edu/debian unstable/main amd64 libubsan1-armel-cross all 10-20200211-1cross1 [114 kB] Get:57 http://debian.oregonstate.edu/debian unstable/main amd64 libgcc-9-dev-armel-cross all 9.2.1-21cross1 [644 kB] Get:58 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-9-arm-linux-gnueabi amd64 9.2.1-21cross1 [7157 kB] Get:59 http://debian.oregonstate.edu/debian unstable/main amd64 gcc-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1464 B] Get:60 http://debian.oregonstate.edu/debian unstable/main amd64 linux-libc-dev-armel-cross all 5.4.8-1cross1 [1128 kB] Get:61 http://debian.oregonstate.edu/debian unstable/main amd64 libc6-dev-armel-cross all 2.29-9cross1 [2141 kB] Get:62 http://debian.oregonstate.edu/debian unstable/main amd64 libstdc++-9-dev-armel-cross all 9.2.1-21cross1 [1709 kB] Get:63 http://debian.oregonstate.edu/debian unstable/main amd64 g++-9-arm-linux-gnueabi amd64 9.2.1-21cross1 [7392 kB] Get:64 http://debian.oregonstate.edu/debian unstable/main amd64 g++-arm-linux-gnueabi amd64 4:9.2.1-3.1 [1180 B] Get:65 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-inifiles-perl all 3.000002-1 [52.0 kB] Get:66 http://debian.oregonstate.edu/debian unstable/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:67 http://debian.oregonstate.edu/debian unstable/main amd64 libicu63 amd64 63.2-2 [8301 kB] Get:68 http://debian.oregonstate.edu/debian unstable/main amd64 libxml2 amd64 2.9.4+dfsg1-8 [710 kB] Get:69 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-namespacesupport-perl all 1.12-1 [14.8 kB] Get:70 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-base-perl all 1.09-1 [20.4 kB] Get:71 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-sax-perl all 1.02+dfsg-1 [59.0 kB] Get:72 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-libxml-perl amd64 2.0134+dfsg-1+b1 [344 kB] Get:73 http://debian.oregonstate.edu/debian unstable/main amd64 libxml-simple-perl all 2.25-1 [72.0 kB] Get:74 http://debian.oregonstate.edu/debian unstable/main amd64 libyaml-perl all 1.30-1 [67.7 kB] Get:75 http://debian.oregonstate.edu/debian unstable/main amd64 libconfig-auto-perl all 0.44-1 [19.5 kB] Get:76 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-which-perl all 1.23-1 [16.6 kB] Get:77 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-homedir-perl all 1.004-1 [42.7 kB] Get:78 http://debian.oregonstate.edu/debian unstable/main amd64 libdebian-dpkgcross-perl all 2.6.15-3 [38.7 kB] Get:79 http://debian.oregonstate.edu/debian unstable/main amd64 dpkg-cross all 2.6.15-3 [49.3 kB] Get:80 http://debian.oregonstate.edu/debian unstable/main amd64 crossbuild-essential-armel all 12.8 [6640 B] Get:81 http://debian.oregonstate.edu/debian unstable/main amd64 libtool all 2.4.6-12 [547 kB] Get:82 http://debian.oregonstate.edu/debian unstable/main amd64 dh-autoreconf all 19 [16.9 kB] Get:83 http://debian.oregonstate.edu/debian unstable/main amd64 libdebhelper-perl all 12.9 [183 kB] Get:84 http://debian.oregonstate.edu/debian unstable/main amd64 libarchive-zip-perl all 1.67-1 [104 kB] Get:85 http://debian.oregonstate.edu/debian unstable/main amd64 libsub-override-perl all 0.09-2 [10.2 kB] Get:86 http://debian.oregonstate.edu/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.6.3-2 [23.7 kB] Get:87 http://debian.oregonstate.edu/debian unstable/main amd64 dh-strip-nondeterminism all 1.6.3-2 [14.7 kB] Get:88 http://debian.oregonstate.edu/debian unstable/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:89 http://debian.oregonstate.edu/debian unstable/main amd64 dwz amd64 0.13-5 [151 kB] Get:90 http://debian.oregonstate.edu/debian unstable/main amd64 libglib2.0-0 amd64 2.62.4-2 [1319 kB] Get:91 http://debian.oregonstate.edu/debian unstable/main amd64 libcroco3 amd64 0.6.13-1 [146 kB] Get:92 http://debian.oregonstate.edu/debian unstable/main amd64 gettext amd64 0.19.8.1-10 [1303 kB] Get:93 http://debian.oregonstate.edu/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get:94 http://debian.oregonstate.edu/debian unstable/main amd64 po-debconf all 1.0.21 [248 kB] Get:95 http://debian.oregonstate.edu/debian unstable/main amd64 debhelper all 12.9 [994 kB] Get:96 http://debian.oregonstate.edu/debian unstable/main amd64 help2man amd64 1.47.12 [180 kB] Get:97 http://debian.oregonstate.edu/debian unstable/main armel libgcc-s1 armel 10-20200211-1 [38.3 kB] Get:98 http://debian.oregonstate.edu/debian unstable/main armel libcrypt1 armel 1:4.4.10-10 [100 kB] Get:99 http://debian.oregonstate.edu/debian unstable/main armel libc6 armel 2.29-10 [2338 kB] Get:100 http://debian.oregonstate.edu/debian unstable/main armel libasan5 armel 9.2.1-28 [348 kB] Get:101 http://debian.oregonstate.edu/debian unstable/main armel libatomic1 armel 10-20200211-1 [8864 B] Get:102 http://debian.oregonstate.edu/debian unstable/main armel linux-libc-dev armel 5.4.13-1 [1040 kB] Get:103 http://debian.oregonstate.edu/debian unstable/main armel libcrypt-dev armel 1:4.4.10-10 [120 kB] Get:104 http://debian.oregonstate.edu/debian unstable/main armel libc6-dev armel 2.29-10 [2184 kB] Get:105 http://debian.oregonstate.edu/debian unstable/main armel libgomp1 armel 10-20200211-1 [86.7 kB] Get:106 http://debian.oregonstate.edu/debian unstable/main armel libstdc++6 armel 10-20200211-1 [408 kB] Get:107 http://debian.oregonstate.edu/debian unstable/main armel libubsan1 armel 10-20200211-1 [115 kB] Get:108 http://debian.oregonstate.edu/debian unstable/main armel libgcc-9-dev armel 9.2.1-28 [644 kB] Get:109 http://debian.oregonstate.edu/debian unstable/main armel libstdc++-9-dev armel 9.2.1-28 [1740 kB] Get:110 http://debian.oregonstate.edu/debian unstable/main amd64 pandoc-data all 2.5-3 [349 kB] Get:111 http://debian.oregonstate.edu/debian unstable/main amd64 pandoc amd64 2.5-3+b1 [15.7 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 101 MB in 2s (66.5 MB/s) Selecting previously unselected package libbsd0:amd64. (Reading database ... 12784 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.10.0-1_amd64.deb ... Unpacking libbsd0:amd64 (0.10.0-1) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../01-bsdmainutils_11.1.2+b1_amd64.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../02-libuchardet0_0.0.6-3_amd64.deb ... Unpacking libuchardet0:amd64 (0.0.6-3) ... Selecting previously unselected package groff-base. Preparing to unpack .../03-groff-base_1.22.4-4_amd64.deb ... Unpacking groff-base (1.22.4-4) ... Selecting previously unselected package libpipeline1:amd64. Preparing to unpack .../04-libpipeline1_1.5.2-2_amd64.deb ... Unpacking libpipeline1:amd64 (1.5.2-2) ... Selecting previously unselected package man-db. Preparing to unpack .../05-man-db_2.9.0-2_amd64.deb ... Unpacking man-db (2.9.0-2) ... 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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 (3.31.1-2) ... Setting up libmagic1:amd64 (1:5.38-4) ... Setting up linux-libc-dev:armel (5.4.13-1) ... Setting up libxml-namespacesupport-perl (1.12-1) ... Setting up gettext-base (0.19.8.1-10) ... Setting up file (1:5.38-4) ... Setting up libyaml-perl (1.30-1) ... Setting up libicu63:amd64 (63.2-2) ... Setting up linux-libc-dev-armel-cross (5.4.8-1cross1) ... Setting up gcc-9-arm-linux-gnueabi-base:amd64 (9.2.1-21cross1) ... Setting up libxml-sax-base-perl (1.09-1) ... Setting up libio-string-perl (1.08-3) ... Setting up gcc-10-base:armel (10-20200211-1) ... Setting up autotools-dev (20180224.1) ... Setting up cross-config (2.6.15-3) ... Setting up libsigsegv2:amd64 (2.12-2) ... Setting up cpp-9-arm-linux-gnueabi (9.2.1-21cross1) ... Setting up autopoint (0.19.8.1-10) ... Setting up gcc-9-cross-base (9.2.1-21cross1) ... Setting up gcc-10-cross-base (10-20200211-1cross1) ... Setting up libc6-armel-cross (2.29-9cross1) ... Setting up sensible-utils (0.0.12+nmu1) ... Setting up libcrypt-dev:amd64 (1:4.4.10-10) ... Setting up libuchardet0:amd64 (0.0.6-3) ... Setting up libsub-override-perl (0.09-2) ... Setting up libc6-dev:amd64 (2.29-10) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up pandoc-data (2.5-3) ... Setting up libc6-dev-armel-cross (2.29-9cross1) ... Setting up libfile-homedir-perl (1.004-1) ... Setting up libbsd0:amd64 (0.10.0-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (8.0-3) ... Setting up libxml2:amd64 (2.9.4+dfsg1-8) ... Setting up liblocale-gettext-perl (1.07-4) ... Setting up gcc-9-base:armel (9.2.1-28) ... Setting up libfile-stripnondeterminism-perl (1.6.3-2) ... Setting up libgomp1-armel-cross (10-20200211-1cross1) ... Setting up libstdc++-9-dev:amd64 (9.2.1-28) ... Setting up libtool (2.4.6-12) ... Setting up libreadline8:amd64 (8.0-3) ... Setting up libgcc-s1-armel-cross (10-20200211-1cross1) ... Setting up m4 (1.4.18-4) ... Setting up libstdc++6-armel-cross (10-20200211-1cross1) ... Setting up libatomic1-armel-cross (10-20200211-1cross1) ... Setting up help2man (1.47.12) ... Setting up libasan5-armel-cross (9.2.1-21cross1) ... Setting up cpp-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up pandoc (2.5-3+b1) ... Setting up libubsan1-armel-cross (10-20200211-1cross1) ... 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 libcroco3:amd64 (0.6.13-1) ... Setting up ucf (3.0038+nmu1) ... Setting up g++-9 (9.2.1-28) ... Setting up libgcc-9-dev-armel-cross (9.2.1-21cross1) ... Setting up autoconf (2.69-11.1) ... Setting up dh-strip-nondeterminism (1.6.3-2) ... Setting up g++ (4:9.2.1-3.1) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up dwz (0.13-5) ... Setting up groff-base (1.22.4-4) ... Setting up build-essential (12.8) ... 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 libstdc++-9-dev-armel-cross (9.2.1-21cross1) ... Setting up gcc-9-arm-linux-gnueabi (9.2.1-21cross1) ... Setting up man-db (2.9.0-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libxml-sax-perl (1.02+dfsg-1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up g++-9-arm-linux-gnueabi (9.2.1-21cross1) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up libxml-libxml-perl (2.0134+dfsg-1+b1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up gcc-arm-linux-gnueabi (4:9.2.1-3.1) ... 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 g++-arm-linux-gnueabi (4:9.2.1-3.1) ... Setting up libxml-simple-perl (2.25-1) ... Setting up libconfig-auto-perl (0.44-1) ... Setting up libdebian-dpkgcross-perl (2.6.15-3) ... Setting up dpkg-cross (2.6.15-3) ... Setting up crossbuild-essential-armel (12.8) ... Setting up libcrypt1:armel (1:4.4.10-10) ... Setting up libgcc-s1:armel (10-20200211-1) ... Setting up libc6:armel (2.29-10) ... Setting up libcrypt-dev:armel (1:4.4.10-10) ... Setting up libc6-dev:armel (2.29-10) ... Setting up libstdc++6:armel (10-20200211-1) ... Setting up libgomp1:armel (10-20200211-1) ... Setting up dh-autoreconf (19) ... Setting up libasan5:armel (9.2.1-28) ... Setting up libatomic1:armel (10-20200211-1) ... Setting up libubsan1:armel (10-20200211-1) ... Setting up debhelper (12.9) ... Setting up libgcc-9-dev:armel (9.2.1-28) ... Setting up libstdc++-9-dev:armel (9.2.1-28) ... Setting up sbuild-build-depends-main-dummy:armel (0.invalid.0) ... Processing triggers for libc-bin (2.29-10) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (armel included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 4.9.0-8-amd64 #1 SMP Debian 4.9.144-3.1 (2019-02-19) amd64 (x86_64) Toolchain package versions: binutils_2.34-2 dpkg-dev_1.19.7 g++-9_9.2.1-28 gcc-8_8.3.0-28 gcc-9_9.2.1-28 libc6-dev_2.29-10 libstdc++-9-dev_9.2.1-28 libstdc++-9-dev-armel-cross_9.2.1-21cross1 libstdc++6_10-20200211-1 libstdc++6-armel-cross_10-20200211-1cross1 linux-libc-dev_5.4.13-1 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_2.34-2 binutils-arm-linux-gnueabi_2.34-2 binutils-common_2.34-2 binutils-x86-64-linux-gnu_2.34-2 bsdmainutils_11.1.2+b1 bsdutils_1:2.34-0.1 build-essential_12.8 bzip2_1.0.8-2 coreutils_8.30-3+b1 cpp_4:9.2.1-3.1 cpp-8_8.3.0-28 cpp-9_9.2.1-28 cpp-9-arm-linux-gnueabi_9.2.1-21cross1 cpp-arm-linux-gnueabi_4:9.2.1-3.1 cross-config_2.6.15-3 crossbuild-essential-armel_12.8 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-cross_2.6.15-3 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_9.2.1-28 g++-9-arm-linux-gnueabi_9.2.1-21cross1 g++-arm-linux-gnueabi_4:9.2.1-3.1 gcc_4:9.2.1-3.1 gcc-10-base_10-20200211-1 gcc-10-cross-base_10-20200211-1cross1 gcc-8_8.3.0-28 gcc-8-base_8.3.0-28 gcc-9_9.2.1-28 gcc-9-arm-linux-gnueabi_9.2.1-21cross1 gcc-9-arm-linux-gnueabi-base_9.2.1-21cross1 gcc-9-base_9.2.1-28 gcc-9-cross-base_9.2.1-21cross1 gcc-arm-linux-gnueabi_4:9.2.1-3.1 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 libacl1_2.2.53-5 libapt-pkg5.0_1.8.4 libarchive-zip-perl_1.67-1 libasan5_9.2.1-28 libasan5-armel-cross_9.2.1-21cross1 libatomic1_10-20200211-1 libatomic1-armel-cross_10-20200211-1cross1 libattr1_1:2.4.48-5 libaudit-common_1:2.8.5-2 libaudit1_1:2.8.5-2+b1 libbinutils_2.34-2 libblkid1_2.34-0.1 libbsd0_0.10.0-1 libbz2-1.0_1.0.8-2 libc-bin_2.29-10 libc-dev-bin_2.29-10 libc6_2.29-10 libc6-armel-cross_2.29-9cross1 libc6-dev_2.29-10 libc6-dev-armel-cross_2.29-9cross1 libcap-ng0_0.7.9-2.1+b1 libcc1-0_10-20200211-1 libcom-err2_1.45.5-2 libconfig-auto-perl_0.44-1 libconfig-inifiles-perl_3.000002-1 libcroco3_0.6.13-1 libcrypt-dev_1:4.4.10-10 libcrypt1_1:4.4.10-10 libctf-nobfd0_2.34-2 libctf0_2.34-2 libdb5.3_5.3.28+dfsg1-0.6 libdebconfclient0_0.251 libdebhelper-perl_12.9 libdebian-dpkgcross-perl_2.6.15-3 libdpkg-perl_1.19.7 libelf1_0.176-1.1 libexpat1_2.2.9-1 libext2fs2_1.45.5-2 libfakeroot_1.24-1 libfdisk1_2.34-0.1 libffi6_3.2.1-9 libffi7_3.3-3 libfile-homedir-perl_1.004-1 libfile-stripnondeterminism-perl_1.6.3-2 libfile-which-perl_1.23-1 libgcc-8-dev_8.3.0-28 libgcc-9-dev_9.2.1-28 libgcc-9-dev-armel-cross_9.2.1-21cross1 libgcc-s1_10-20200211-1 libgcc-s1-armel-cross_10-20200211-1cross1 libgcc1_1:10-20200211-1 libgcrypt20_1.8.5-3 libgdbm-compat4_1.18.1-5 libgdbm6_1.18.1-5 libglib2.0-0_2.62.4-2 libgmp10_2:6.2.0+dfsg-3 libgnutls30_3.6.11.1-2 libgomp1_10-20200211-1 libgomp1-armel-cross_10-20200211-1cross1 libgpg-error0_1.36-7 libhogweed4_3.5.1+really3.4.1-1 libhogweed5_3.5.1+really3.5.1-2 libicu63_63.2-2 libidn2-0_2.2.0-2 libio-string-perl_1.08-3 libisl19_0.20-2 libisl22_0.22-2 libitm1_10-20200211-1 liblocale-gettext-perl_1.07-4 liblsan0_10-20200211-1 liblz4-1_1.9.2-2 liblzma5_5.2.4-1+b1 libmagic-mgc_1:5.38-4 libmagic1_1:5.38-4 libmount1_2.34-0.1 libmpc3_1.1.0-1 libmpdec2_2.4.2-2 libmpfr6_4.0.2-1 libmpx2_8.3.0-28 libncursesw6_6.1+20191019-1 libnettle6_3.5.1+really3.4.1-1 libnettle7_3.5.1+really3.5.1-2 libp11-kit0_0.23.20-1 libpam-modules_1.3.1-5 libpam-modules-bin_1.3.1-5 libpam-runtime_1.3.1-5 libpam0g_1.3.1-5 libpcre2-8-0_10.34-7 libpcre3_2:8.39-12+b1 libperl5.28_5.28.1-6 libperl5.30_5.30.0-9 libpipeline1_1.5.2-2 libpython3-stdlib_3.7.5-3 libpython3.7-minimal_3.7.6-1+b1 libpython3.7-stdlib_3.7.6-1+b1 libquadmath0_10-20200211-1 libreadline8_8.0-3 libseccomp2_2.4.2-2 libselinux1_3.0-1 libsemanage-common_3.0-1 libsemanage1_3.0-1 libsepol1_3.0-1 libsigsegv2_2.12-2 libsmartcols1_2.34-0.1 libsqlite3-0_3.31.1-2 libss2_1.45.5-2 libssl1.1_1.1.1d-2 libstdc++-9-dev_9.2.1-28 libstdc++-9-dev-armel-cross_9.2.1-21cross1 libstdc++6_10-20200211-1 libstdc++6-armel-cross_10-20200211-1cross1 libsub-override-perl_0.09-2 libsystemd0_244.2-1 libtasn1-6_4.15.0-2 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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 ucf_3.0038+nmu1 util-linux_2.34-0.1 xz-utils_5.2.4-1+b1 zlib1g_1:1.2.11.dfsg-1.2 +------------------------------------------------------------------------------+ | 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 CONFIG_SITE=/etc/dpkg-cross/cross-config.armel DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=helmut PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=unstable-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1003 SCHROOT_GROUP=helmut SCHROOT_SESSION_ID=unstable-amd64-sbuild-a6e7e314-b90a-4340-8b8a-c239dd8e01c1 SCHROOT_UID=1003 SCHROOT_USER=helmut SHELL=/bin/sh USER=helmut dpkg-buildpackage ----------------- Command: dpkg-buildpackage -aarmel -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 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-architecture: warning: specified GNU system type arm-linux-gnueabi does not match CC system type x86_64-linux-gnu, try setting a correct CC environment variable dpkg-source --before-build . dpkg-buildpackage: info: host architecture armel fakeroot debian/rules clean dh clean dh_auto_clean make -j1 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-arch dh build-arch dh_update_autotools_config -a dh_autoreconf -a dh_auto_configure -a debian/rules override_dh_auto_build make[1]: Entering directory '/<>' dh_auto_build -- BUILD_HOST='Debian' BUILD_TIME="11 February 2020" all doc make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=arm-linux-gnueabi-pkg-config CXX=arm-linux-gnueabi-g\+\+ CC=arm-linux-gnueabi-gcc BUILD_HOST=Debian "BUILD_TIME=11 February 2020" all doc make[2]: Entering directory '/<>' arm-linux-gnueabi-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="\"`arm-linux-gnueabi-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 -Wno-narrowing -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 In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/set:60, from gfm.h:32, from hisat2_build.cpp:35: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:61, from gbwt_graph.h:28, from gfm.h:64, from hisat2_build.cpp:35: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ arm-linux-gnueabi-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="\"`arm-linux-gnueabi-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 -Wno-narrowing -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 In file included from gfm.h:43, from hisat2_build.cpp:35: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from hisat2_build.cpp:30: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from hisat2_build.cpp:28: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hisat2_build.cpp:35: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from hisat2_build.cpp:28: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from hisat2_build.cpp:35: gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const string&, const string&, const string&, const string&, const string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool) [with TStr = SString; index_t = long long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:955:3: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ hgfm.h:1970:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:687:142: required from here gfm.h:1929:102: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 1929 | std::numeric_limits::max(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from gfm.h:43, from hisat2_build.cpp:35: blockwise_sa.h: In instantiation of ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’: blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ hgfm.h:1833:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hgfm.h:2180:26: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:687:142: required from here blockwise_sa.h:453:15: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 453 | mkeyQSortSuf(t, s, slen, 4, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~ 454 | this->verbose(), this->sanityCheck()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ blockwise_sa.h:453:15: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from blockwise_sa.h:29, from gfm.h:43, from hisat2_build.cpp:35: diff_sample.h: In instantiation of ‘void DifferenceCoverSample::build(int) [with TStr = SString]’: blockwise_sa.h:375:4: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:354:4: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:206:29: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ hgfm.h:1820:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hgfm.h:2180:26: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:687:142: required from here diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 813 | sanityCheckOrderedSufs(t, t.length(), sPrimeArr, sPrimeSz, v); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff_sample.h:813:43: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from ds.h:32, from sequence_io.h:28, from hisat2_build.cpp:28: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:447:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ hgfm.h:1833:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hgfm.h:2180:26: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:687:142: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hisat2_build.cpp:35: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = SString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:453:15: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ hgfm.h:1833:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hgfm.h:2180:26: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:687:142: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf2(const T&, TIndexOffU*, size_t, TIndexOffU*, int, bool, bool, size_t, EList*) [with T = SString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: diff_sample.h:772:30: required from ‘void DifferenceCoverSample::build(int) [with TStr = SString]’ blockwise_sa.h:375:4: required from ‘void KarkkainenBlockwiseSA::build() [with TStr = SString]’ blockwise_sa.h:354:4: required from ‘void KarkkainenBlockwiseSA::reset() [with TStr = SString]’ blockwise_sa.h:206:29: required from ‘KarkkainenBlockwiseSA::KarkkainenBlockwiseSA(const TStr&, TIndexOffU, int, uint32_t, uint32_t, bool, bool, bool, std::string, std::ostream&) [with TStr = SString; TIndexOffU = long long unsigned int; uint32_t = unsigned int; std::string = std::__cxx11::basic_string; std::ostream = std::basic_ostream]’ hgfm.h:1820:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hgfm.h:2180:26: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:687:142: required from here multikey_qsort.h:661:31: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 661 | sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from hisat2_build.cpp:28: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:447:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ hgfm.h:1833:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hgfm.h:2180:26: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:687:142: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:447:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ hgfm.h:1833:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hgfm.h:2180:26: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:687:142: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = SString; T2 = const unsigned char*; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:447:19: required from ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = SString]’ blockwise_sa.h:1098:15: required from ‘void KarkkainenBlockwiseSA::nextBlock(int, int) [with TStr = SString]’ blockwise_sa.h:297:17: required from ‘TIndexOffU KarkkainenBlockwiseSA::nextSuffix() [with TStr = SString; TIndexOffU = long long unsigned int]’ hgfm.h:1833:55: required from ‘static void HGFM::gbwt_worker(void*) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hgfm.h:2180:26: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long long unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:492:19: required from ‘void driver(const string&, EList >&, const string&, const string&, const string&, const string&, const string&, const string&, bool, int) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:687:142: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/set:60, from gfm.h:32, from hisat2_build.cpp:35: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::tuple<>}; _Key = long long unsigned int; _Val = std::pair; _KeyOfValue = std::_Select1st >; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:61, from gbwt_graph.h:28, from gfm.h:64, from hisat2_build.cpp:35: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = long long unsigned int; _Tp = long long unsigned int; _Compare = std::less; _Alloc = std::allocator >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/arm-linux-gnueabi/include/c++/9/set:60, from gfm.h:32, from hisat2_build.cpp:35: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple, std::allocator >&>, std::tuple<>}; _Key = std::__cxx11::basic_string; _Val = std::pair, long long unsigned int>; _KeyOfValue = std::_Select1st, long long unsigned int> >; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, long long unsigned int> >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:61, from gbwt_graph.h:28, from gfm.h:64, from hisat2_build.cpp:35: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In member function ‘std::map<_Key, _Tp, _Compare, _Alloc>::mapped_type& std::map<_Key, _Tp, _Compare, _Alloc>::operator[](const key_type&) [with _Key = std::__cxx11::basic_string; _Tp = long long unsigned int; _Compare = std::less >; _Alloc = std::allocator, long long unsigned int> >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::pair, long long unsigned int>, std::_Select1st, long long unsigned int> >, std::less >, std::allocator, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator, long long unsigned int> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from /usr/arm-linux-gnueabi/include/c++/9/set:60, from gfm.h:32, from hisat2_build.cpp:35: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h: In member function ‘std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::iterator std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_M_emplace_hint_unique(std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::const_iterator, _Args&& ...) [with _Args = {const std::piecewise_construct_t&, std::tuple::CompositeNodeIDs&>, std::tuple<>}; _Key = RefGraph::CompositeNodeIDs; _Val = std::pair::CompositeNodeIDs, long long unsigned int>; _KeyOfValue = std::_Select1st::CompositeNodeIDs, long long unsigned int> >; _Compare = std::less::CompositeNodeIDs>; _Alloc = std::allocator::CompositeNodeIDs, long long unsigned int> >]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_tree.h:2452:7: note: parameter passing for argument of type ‘std::_Rb_tree::CompositeNodeIDs, std::pair::CompositeNodeIDs, long long unsigned int>, std::_Select1st::CompositeNodeIDs, long long unsigned int> >, std::less::CompositeNodeIDs>, std::allocator::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator::CompositeNodeIDs, long long unsigned int> >’} changed in GCC 7.1 2452 | _Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>:: | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/map:61, from gbwt_graph.h:28, from gfm.h:64, from hisat2_build.cpp:35: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In static member function ‘static void RefGraph::reverseDeterminize(EList::Node>&, EList::Edge>&, index_t&, index_t) [with index_t = long long unsigned int]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree::CompositeNodeIDs, std::pair::CompositeNodeIDs, long long unsigned int>, std::_Select1st::CompositeNodeIDs, long long unsigned int> >, std::less::CompositeNodeIDs>, std::allocator::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator::CompositeNodeIDs, long long unsigned int> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree::CompositeNodeIDs, std::pair::CompositeNodeIDs, long long unsigned int>, std::_Select1st::CompositeNodeIDs, long long unsigned int> >, std::less::CompositeNodeIDs>, std::allocator::CompositeNodeIDs, long long unsigned int> > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator::CompositeNodeIDs, long long unsigned int> >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h: In constructor ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const string&, const string&, const string&, const string&, const string&, const string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long long unsigned int; local_index_t = short unsigned int]’: /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, /usr/arm-linux-gnueabi/include/c++/9/bits/stl_map.h:499:8: note: parameter passing for argument of type ‘std::_Rb_tree, std::_Select1st >, std::less, std::allocator > >::const_iterator’ {aka ‘std::_Rb_tree_const_iterator >’} changed in GCC 7.1 499 | __i = _M_t._M_emplace_hint_unique(__i, std::piecewise_construct, In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from edit.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from edit.h:29, from edit.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from edit.cpp:21: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from edit.h:29, from edit.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from gfm.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from gfm.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from gfm.cpp:21: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from gfm.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ arm-linux-gnueabi-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="\"`arm-linux-gnueabi-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 -Wno-narrowing -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 In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:45: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1753:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1753 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3068:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3068 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3069:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3069 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3085:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3085 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: hisat2.cpp:3826:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3826 | auto_ptr refs( | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: hisat2.cpp:3686:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6451 | int lastorig = -1; | ^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1542:4: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:5003:9: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1172 | if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1183 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1238 | if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1249 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2625 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2703 | if(alt_range.first >= alts.size()) { hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2868 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2909 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2985 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3021 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3026 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3278 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:492:66: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ group_walk.h:1478:3: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:4998:5: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:794:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 794 | while(new_top - top < tmp_gbwt_to_node.size()) { group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 801 | if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:817:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 817 | if(i + 1 < tmp_zOffs.size()) { group_walk.h:823:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 823 | while(new_bot2 - top < tmp_gbwt_to_node.size()) { group_walk.h:830:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 830 | if(new_bot2 - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = unsigned int]’: hi_aligner.h:2739:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2484 | if(ht_range.first >= haplotypes.size()) hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2499 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2537 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2561 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2568 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hisat2.cpp:45: spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: spliced_aligner.h:214:9: required from here spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 282 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_sw.cpp:25: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_bt.h:31, from aligner_bt.cpp:20: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from sse_util.cpp:20: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_swsse.cpp:22: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_swsse_loc_i16.cpp:56: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_swsse_ee_i16.cpp:56: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_swsse_loc_u8.cpp:56: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_swsse_ee_u8.cpp:56: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from edit.h:29, from splice_site.cpp:20: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = unsigned int]’: splice_site.cpp:722:59: required from here ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from splice_site.cpp:20: splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ arm-linux-gnueabi-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="\"`arm-linux-gnueabi-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 -Wno-narrowing -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 gfm.h:43, from hgfm.h:24, from hisat2.cpp:33: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:45: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1753:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1753 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3068:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3068 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3069:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3069 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3085:2: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3085 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const string&, const string&)’: hisat2.cpp:3826:9: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 3826 | auto_ptr refs( | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2.cpp:33: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hgfm.h:24, from hisat2.cpp:33: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hgfm.h:24, from hisat2.cpp:33: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hgfm.h:24, from hisat2.cpp:33: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long long unsigned int]’: hisat2.cpp:3686:17: required from ‘void driver(const char*, const string&, const string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2.cpp:4115:51: required from here gfm.h:6451:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6451 | int lastorig = -1; | ^~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hgfm.h:24, from hisat2.cpp:33: multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’: hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2125:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long long int’} and ‘long long unsigned int’ [-Wsign-compare] 2125 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hgfm.h:24, from hisat2.cpp:33: multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::advance(const GFM&, const BitPairReference&, SARangeWithOffs&, GWHit&, index_t, bool, EList, 16>*, EList, S>&, GroupWalkState&, WalkMetrics&, PerReadMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:1542:4: required from ‘bool GroupWalk2S::advanceElement(index_t, const GFM&, const BitPairReference&, SARangeWithOffs&, GroupWalkState&, WalkResult&, WalkMetrics&, PerReadMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:5003:9: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:1172:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1172 | if(new_node_bot - new_node_top < gws.map.size()) { group_walk.h:1183:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1183 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { group_walk.h:1238:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1238 | if(node_range.second - node_range.first < st.back().map_.size()) { group_walk.h:1249:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 1249 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2625:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2625 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2703:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2703 | if(alt_range.first >= alts.size()) { hi_aligner.h:2868:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2868 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:2909:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 2909 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:2985:31: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2985 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3021:32: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 3021 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3026:39: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 3026 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3278:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long long unsigned int’ [-Wsign-compare] 3278 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41, from spliced_aligner.h:23, from hisat2.cpp:45: group_walk.h: In instantiation of ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’: group_walk.h:492:66: required from ‘std::pair GWState::init(const GFM&, const BitPairReference&, SARangeWithOffs&, EList, S>&, GWHit&, index_t, bool, EList, 16>*, index_t, index_t, index_t, index_t, const EList >&, index_t, WalkMetrics&) [with int S = 16; index_t = short unsigned int; T = EListSlice]’ group_walk.h:1478:3: required from ‘void GroupWalk2S::init(const GFM&, const BitPairReference&, SARangeWithOffs&, RandomSource&, WalkMetrics&) [with index_t = short unsigned int; T = EListSlice; int S = 16]’ hi_aligner.h:4998:5: required from ‘bool HI_Aligner::getGenomeCoords_local(const GFM&, const ALTDB&, const BitPairReference&, RandomSource&, local_index_t, local_index_t, local_index_t, local_index_t, const EList >&, bool, index_t, index_t, EList&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool, bool&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4773:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here group_walk.h:794:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 794 | while(new_top - top < tmp_gbwt_to_node.size()) { group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 801 | if(new_top - top == tmp_gbwt_to_node.size()) { group_walk.h:817:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 817 | if(i + 1 < tmp_zOffs.size()) { group_walk.h:823:38: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 823 | while(new_bot2 - top < tmp_gbwt_to_node.size()) { group_walk.h:830:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 830 | if(new_bot2 - top < tmp_gbwt_to_node.size()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘void add_haplotypes(const EList >&, const EList >&, const EList&, Haplotype&, EList >&, index_t, bool, bool) [with index_t = long long unsigned int]’: hi_aligner.h:2739:39: required from ‘static index_t GenomeHit::alignWithALTs_recur(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, EList >&, EList&, int&, const char*, index_t, int, index_t, bool, EList&, index_t, ELList >&, Haplotype&, ELList*, index_t, index_t*, index_t, const GraphPolicy&, index_t&, ALT_TYPE) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:706:28: required from ‘static index_t GenomeHit::alignWithALTs(const EList >&, const EList >&, const EList&, index_t, const BTDnaString&, index_t, index_t, index_t, const BitPairReference&, SharedTempVars&, index_t, int, index_t, bool, const GraphPolicy&, EList&, ELList >&, EList >&, Haplotype&, ELList*, index_t, index_t*) [with index_t = long long unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2194:47: required from ‘static bool GenomeHit::adjustWithALT(index_t, index_t, const Coord&, SharedTempVars&, EList >&, const Read&, const GFM&, const ALTDB&, const BitPairReference&, const GraphPolicy&) [with index_t = long long unsigned int]’ hi_aligner.h:4796:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:3926:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3435:151: required from here hi_aligner.h:2484:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2484 | if(ht_range.first >= haplotypes.size()) hi_aligner.h:2499:37: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2499 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2537:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2537 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2561:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2561 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { hi_aligner.h:2568:41: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int’ [-Wsign-compare] 2568 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ In file included from hisat2.cpp:45: spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’: spliced_aligner.h:214:9: required from here spliced_aligner.h:282:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 282 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ spliced_aligner.h:642:65: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] 642 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { spliced_aligner.h:1298:105: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘int64_t’ {aka ‘long long int’} [-Wsign-compare] 1298 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { In file included from spliced_aligner.h:23, from hisat2.cpp:45: hi_aligner.h: In instantiation of ‘index_t HI_Aligner::globalGFMSearch(const GFM&, const Read&, const Scoring&, const ReportingParams&, bool, index_t, index_t&, index_t&, index_t&, index_t&, index_t&, EList >&, RandomSource&, bool&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int]’: spliced_aligner.h:936:25: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t) [with index_t = long long unsigned int; local_index_t = short unsigned int; int64_t = long long int]’ spliced_aligner.h:214:9: required from here hi_aligner.h:5792:85: warning: comparison of integer expressions of different signedness: ‘long long unsigned int’ and ‘const THitInt’ {aka ‘const long long int’} [-Wsign-compare] 5792 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from edit.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from edit.h:29, from edit.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from edit.cpp:21: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from edit.h:29, from edit.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from gfm.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from gfm.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from gfm.cpp:21: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from gfm.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:456:12: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 456 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:450:7: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 450 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from aligner_cache.h:59, from aligner_seed.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_seed.h:30, from aligner_seed.cpp:21: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from aligner_cache.h:59, from aligner_seed.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from random_util.h:25, from aligner_seed2.h:101, from aligner_seed2.cpp:22: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_seed2.cpp:22: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from random_util.h:25, from aligner_seed2.h:101, from aligner_seed2.cpp:22: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_sw.cpp:25: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_sw.cpp:25: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from aligner_result.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from ref_read.h:33, from reference.h:32, from aligner_result.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_result.cpp:22: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from ref_read.h:33, from reference.h:32, from aligner_result.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from aln_sink.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from read.h:25, from aln_sink.h:24, from aln_sink.cpp:22: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from aln_sink.h:25, from aln_sink.cpp:22: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from read.h:25, from aln_sink.h:24, from aln_sink.cpp:22: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from unique.h:38, from unique.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from unique.h:38, from unique.cpp:20: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from unique.h:38, from unique.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_bt.h:31, from aligner_bt.cpp:20: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_bt.h:25, from aligner_bt.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from sse_util.cpp:20: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_swsse.cpp:22: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_swsse.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_swsse_loc_i16.cpp:56: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_i16.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_swsse_ee_i16.cpp:56: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_i16.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_swsse_loc_u8.cpp:56: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_loc_u8.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_swsse.h:28, from aligner_sw.h:84, from aligner_swsse_ee_u8.cpp:56: sse_util.h: In member function ‘simde__m128i* EList_m128i::alloc(size_t)’: sse_util.h:220:41: warning: ‘new’ of type ‘simde__m128i’ with extended alignment 16 [-Waligned-new=] 220 | last_alloc_ = new simde__m128i[sz + 2]; | ^ sse_util.h:220:41: note: uses ‘void* operator new [](std::size_t)’, which does not have an alignment parameter sse_util.h:220:41: note: use ‘-faligned-new’ to enable C++17 over-aligned new support In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from read.h:25, from aligner_result.h:27, from aligner_sw_common.h:23, from aligner_sw.h:74, from aligner_swsse_ee_u8.cpp:56: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from random_util.h:25, from aligner_seed2.h:101, from aligner_driver.h:78, from aligner_driver.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from aligner_result.h:30, from aligner_seed2.h:102, from aligner_driver.h:78, from aligner_driver.cpp:20: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from random_util.h:25, from aligner_seed2.h:101, from aligner_driver.h:78, from aligner_driver.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from splice_site.cpp:20: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ splice_site.cpp: In member function ‘void SpliceSiteDB::read(const GFM&, const EList >&)’: splice_site.cpp:717:59: warning: ?: using integer constants in boolean context, the expression will always evaluate to ‘true’ [-Wint-in-bool-context] 717 | exons.back().init(ref, left, right, fw == '+' ? SPL_FW : SPL_RC); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~ In file included from ds.h:32, from edit.h:29, from splice_site.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from splice_site.cpp:20: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from edit.h:29, from splice_site.cpp:20: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = unsigned int]’: splice_site.cpp:722:59: required from here ds.h:663:14: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of non-trivially copyable type ‘class Exon’; use copy-assignment or copy-initialization instead [-Wclass-memaccess] 663 | std::memcpy(list_ + cur_, l, bytes); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from edit.h:30, from splice_site.cpp:20: splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ In file included from ds.h:32, from edit.h:29, from splice_site.cpp:20: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ arm-linux-gnueabi-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="\"`arm-linux-gnueabi-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 -Wno-narrowing -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 In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ arm-linux-gnueabi-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="\"`arm-linux-gnueabi-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 -Wno-narrowing -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 In file included from gfm.h:43, from hgfm.h:24, from hisat2_inspect.cpp:27: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from hgfm.h:24, from hisat2_inspect.cpp:27: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hgfm.h:24, from hisat2_inspect.cpp:27: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hgfm.h:24, from hisat2_inspect.cpp:27: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from hgfm.h:24, from hisat2_inspect.cpp:27: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from splice_site.h:34, from edit.h:30, from edit.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from splice_site.h:34, from edit.h:30, from edit.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/bits/locale_conv.h:41, from /usr/arm-linux-gnueabi/include/c++/9/locale:43, from /usr/arm-linux-gnueabi/include/c++/9/iomanip:43, from timer.h:26, from reference.h:36, from splice_site.h:32, from edit.h:30, from edit.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from edit.h:29, from edit.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from splice_site.h:34, from edit.h:30, from edit.cpp:21: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from edit.h:29, from edit.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ In file included from gfm.h:43, from gfm.cpp:21: blockwise_sa.h: In function ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 484 | this->verbose(), this->sanityCheck()); | ^ blockwise_sa.h: In member function ‘void KarkkainenBlockwiseSA::qsort(EList&) [with TStr = S2bDnaString]’: blockwise_sa.h:484:52: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] In file included from alphabet.h:27, from gfm.h:40, from gfm.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:11: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from gfm.cpp:21: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1098:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1098 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from gfm.cpp:21: gfm.h:1102:3: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] 1102 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ In file included from /usr/arm-linux-gnueabi/include/c++/9/memory:80, from gfm.h:28, from gfm.cpp:21: /usr/arm-linux-gnueabi/include/c++/9/bits/unique_ptr.h:53:28: note: declared here 53 | template class auto_ptr; | ^~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from gfm.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:63: note: in expansion of macro ‘OFF_MASK’ 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ^~~~~~~~ In file included from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from gfm.cpp:21: multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 764 | if(sanityCheck) sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ multikey_qsort.h:764:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] multikey_qsort.h: In instantiation of ‘void mkeyQSortSuf(const T&, TIndexOffU*, size_t, int, bool, bool, size_t) [with T = S2bDnaString; TIndexOffU = long long unsigned int; size_t = unsigned int]’: blockwise_sa.h:484:52: required from here multikey_qsort.h:496:40: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 496 | if(sanityCheck) sanityCheckOrderedSufs(host, hlen, s, slen, upto); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from ds.h:32, from sequence_io.h:28, from multikey_qsort.h:24, from diff_sample.h:26, from blockwise_sa.h:29, from gfm.h:43, from gfm.cpp:21: multikey_qsort.h: In instantiation of ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’: multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1160:49: note: in expansion of macro ‘OFF_MASK’ 1160 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1169:49: note: in expansion of macro ‘OFF_MASK’ 1169 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1071:40: note: in expansion of macro ‘OFF_MASK’ 1071 | OFF_MASK, begin, end); | ^~~~~~~~ multikey_qsort.h: In instantiation of ‘void selectionSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’: multikey_qsort.h:1067:33: required from ‘void bucketSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, uint8_t, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int; uint8_t = unsigned char]’ multikey_qsort.h:1166:20: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, size_t, size_t, size_t, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ multikey_qsort.h:763:18: required from ‘void mkeyQSortSufDcU8(const T1&, const T2&, size_t, TIndexOffU*, size_t, const DifferenceCoverSample&, int, bool, bool) [with T1 = S2bDnaString; T2 = S2bDnaString; size_t = unsigned int; TIndexOffU = long long unsigned int]’ blockwise_sa.h:478:56: required from here btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:914:10: note: in expansion of macro ‘OFF_MASK’ 914 | off = OFF_MASK; | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:923:29: note: in expansion of macro ‘OFF_MASK’ 923 | OFF_MASK, begin, end); | ^~~~~~~~ btypes.h:25:18: warning: conversion from ‘long long unsigned int’ to ‘size_t’ {aka ‘unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Woverflow] 25 | #define OFF_MASK 0xffffffffffffffff | ^~~~~~~~~~~~~~~~~~ multikey_qsort.h:1007:48: note: in expansion of macro ‘OFF_MASK’ 1007 | sanityCheckOrderedSufs(host1, hlen, s, slen, OFF_MASK, begin, end); | ^~~~~~~~ make[2]: Nothing to be done for 'doc'. make[2]: Leaving directory '/<>' help2man ./hisat2 --no-info --name \ 'graph-based alignment of short nucleotide reads to many genomes, wrapper script' \ > debian/hisat2.1 help2man: can't get `--help' info from ./hisat2 Try `--no-discard-stderr' if option outputs to stderr make[1]: *** [debian/rules:33: override_dh_auto_build] Error 2 make[1]: Leaving directory '/<>' make: *** [debian/rules:28: build-arch] Error 2 dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2020-02-13T00:19:57Z Finished -------- +------------------------------------------------------------------------------+ | Cleanup | +------------------------------------------------------------------------------+ Purging /<> Not cleaning session: cloned chroot in use E: Build failure (dpkg-buildpackage died) +------------------------------------------------------------------------------+ | Summary | +------------------------------------------------------------------------------+ Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any Build-Space: 59292 Build-Time: 489 Distribution: unstable Fail-Stage: build Foreign Architectures: armel Host Architecture: armel Install-Time: 25 Job: hisat2_2.1.0-4 Machine Architecture: amd64 Package: hisat2 Package-Time: 525 Source-Version: 2.1.0-4 Space: 59292 Status: attempted Version: 2.1.0-4 -------------------------------------------------------------------------------- Finished at 2020-02-13T00:19:57Z Build needed 00:08:45, 59292k disk space