sbuild (Debian sbuild) 0.81.2+deb11u1 (31 August 2022) on debian-ci-siliconvalley +==============================================================================+ | hisat2 2.2.1-4 (ppc64el) Sun, 09 Apr 2023 05:09:50 +0000 | +==============================================================================+ Package: hisat2 Version: 2.2.1-4 Source Version: 2.2.1-4 Distribution: unstable Machine Architecture: amd64 Host Architecture: ppc64el Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-ce035713-0fcf-415b-bc0f-00020e94cfff' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-wkcF8d/resolver-4Vpojn' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian sid InRelease [184 kB] Get:2 http://localhost:3142/debian sid/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian sid/main amd64 Packages.diff/Index [63.6 kB] Get:4 http://localhost:3142/debian sid/main Sources T-2023-04-09-0203.16-F-2023-04-09-0203.16.pdiff [1394 B] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-04-09-0203.16-F-2023-04-09-0203.16.pdiff [4248 B] Get:4 http://localhost:3142/debian sid/main Sources T-2023-04-09-0203.16-F-2023-04-09-0203.16.pdiff [1394 B] Get:5 http://localhost:3142/debian sid/main amd64 Packages T-2023-04-09-0203.16-F-2023-04-09-0203.16.pdiff [4248 B] Get:6 http://localhost:3142/debian sid/main ppc64el Packages [9223 kB] Fetched 9540 kB in 2s (5050 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 6792 kB of source archives. Get:1 http://localhost:3142/debian sid/main hisat2 2.2.1-4 (dsc) [2129 B] Get:2 http://localhost:3142/debian sid/main hisat2 2.2.1-4 (tar) [6761 kB] Get:3 http://localhost:3142/debian sid/main hisat2 2.2.1-4 (diff) [29.1 kB] Fetched 6792 kB in 0s (160 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hisat2-wkcF8d/hisat2-2.2.1' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-wkcF8d' with '<>' +------------------------------------------------------------------------------+ | Install package build dependencies | +------------------------------------------------------------------------------+ Setup apt archive ----------------- Merged Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-ppc64el:amd64, libc-dev:ppc64el, libstdc++-dev:ppc64el Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-ppc64el:amd64, libc-dev:ppc64el, libstdc++-dev:ppc64el 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 [441 B] Get:5 copy:/<>/apt_archive ./ Packages [520 B] Fetched 1918 B in 0s (0 B/s) Reading package lists... Reading package lists... Install main build dependencies (apt-based resolver) ---------------------------------------------------- Installing build dependencies Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-powerpc64le-linux-gnu bsdextrautils cpp-12-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cross-config crossbuild-essential-ppc64el debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-11-base:ppc64el gcc-12-base:ppc64el gcc-12-cross-base gcc-12-powerpc64le-linux-gnu gcc-12-powerpc64le-linux-gnu-base gcc-powerpc64le-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:ppc64el libasan8-ppc64el-cross libatomic1:ppc64el libatomic1-ppc64el-cross libc6:ppc64el libc6-dev:ppc64el libc6-dev-ppc64el-cross libc6-ppc64el-cross libcom-err2:ppc64el libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:ppc64el libcrypt1:ppc64el libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:ppc64el libgcc-12-dev-ppc64el-cross libgcc-s1:ppc64el libgcc-s1-ppc64el-cross libgomp1:ppc64el libgomp1-ppc64el-cross libgssapi-krb5-2:ppc64el libicu72 libio-string-perl libitm1:ppc64el libitm1-ppc64el-cross libk5crypto3:ppc64el libkeyutils1:ppc64el libkrb5-3:ppc64el libkrb5support0:ppc64el liblocale-gettext-perl liblsan0:ppc64el liblsan0-ppc64el-cross liblua5.3-0 libmagic-mgc libmagic1 libncursesw6 libnsl-dev:ppc64el libnsl2:ppc64el libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0:ppc64el libquadmath0-ppc64el-cross libreadline8 libsimde-dev libsqlite3-0 libssl3:ppc64el libstdc++-11-dev:ppc64el libstdc++-12-dev-ppc64el-cross libstdc++6:ppc64el libstdc++6-ppc64el-cross libsub-override-perl libtirpc-dev:ppc64el libtirpc3:ppc64el libtool libtsan0:ppc64el libtsan2-ppc64el-cross libubsan1:ppc64el libubsan1-ppc64el-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-0-2 libyaml-perl linux-libc-dev:ppc64el linux-libc-dev-ppc64el-cross m4 man-db media-types pandoc pandoc-data po-debconf python3 python3-minimal python3.11 python3.11-minimal readline-common sensible-utils ucf Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-12-locales cpp-12-doc cpp-doc dh-make binutils-multiarch gcc-12-doc manpages-dev flex bison gdb-powerpc64le-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:ppc64el libc-l10n:ppc64el locales:ppc64el libnss-nis:ppc64el libnss-nisplus:ppc64el manpages-dev:ppc64el krb5-doc:ppc64el krb5-user:ppc64el libstdc++-11-doc:ppc64el 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 libjs-katex citation-style-language-styles libmail-box-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx libidn2-0:ppc64el libarchive-cpio-perl krb5-locales:ppc64el libgpm2 libltdl-dev libwww-perl libxml-sax-expat-perl libyaml-libyaml-perl | libyaml-syck-perl libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-powerpc64le-linux-gnu bsdextrautils cpp-12-powerpc64le-linux-gnu cpp-powerpc64le-linux-gnu cross-config crossbuild-essential-ppc64el debhelper dh-autoreconf dh-strip-nondeterminism dpkg-cross dwz file g++-12-powerpc64le-linux-gnu g++-powerpc64le-linux-gnu gcc-11-base:ppc64el gcc-12-base:ppc64el gcc-12-cross-base gcc-12-powerpc64le-linux-gnu gcc-12-powerpc64le-linux-gnu-base gcc-powerpc64le-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan6:ppc64el libasan8-ppc64el-cross libatomic1:ppc64el libatomic1-ppc64el-cross libc6:ppc64el libc6-dev:ppc64el libc6-dev-ppc64el-cross libc6-ppc64el-cross libcom-err2:ppc64el libconfig-auto-perl libconfig-inifiles-perl libcrypt-dev:ppc64el libcrypt1:ppc64el libdebhelper-perl libdebian-dpkgcross-perl libelf1 libexpat1 libfile-homedir-perl libfile-stripnondeterminism-perl libfile-which-perl libgcc-11-dev:ppc64el libgcc-12-dev-ppc64el-cross libgcc-s1:ppc64el libgcc-s1-ppc64el-cross libgomp1:ppc64el libgomp1-ppc64el-cross libgssapi-krb5-2:ppc64el libicu72 libio-string-perl libitm1:ppc64el libitm1-ppc64el-cross libk5crypto3:ppc64el libkeyutils1:ppc64el libkrb5-3:ppc64el libkrb5support0:ppc64el liblocale-gettext-perl liblsan0:ppc64el liblsan0-ppc64el-cross liblua5.3-0 libmagic-mgc libmagic1 libncursesw6 libnsl-dev:ppc64el libnsl2:ppc64el libpipeline1 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0:ppc64el libquadmath0-ppc64el-cross libreadline8 libsimde-dev libsqlite3-0 libssl3:ppc64el libstdc++-11-dev:ppc64el libstdc++-12-dev-ppc64el-cross libstdc++6:ppc64el libstdc++6-ppc64el-cross libsub-override-perl libtirpc-dev:ppc64el libtirpc3:ppc64el libtool libtsan0:ppc64el libtsan2-ppc64el-cross libubsan1:ppc64el libubsan1-ppc64el-cross libuchardet0 libxml-libxml-perl libxml-namespacesupport-perl libxml-sax-base-perl libxml-sax-perl libxml-simple-perl libxml2 libyaml-0-2 libyaml-perl linux-libc-dev:ppc64el linux-libc-dev-ppc64el-cross m4 man-db media-types pandoc pandoc-data po-debconf python3 python3-minimal python3.11 python3.11-minimal readline-common sbuild-build-depends-main-dummy:ppc64el sensible-utils ucf 0 upgraded, 121 newly installed, 0 to remove and 0 not upgraded. Need to get 122 MB of archives. After this operation, 596 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:2 http://localhost:3142/debian sid/main amd64 liblocale-gettext-perl amd64 1.07-5 [15.4 kB] Get:3 http://localhost:3142/debian sid/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:4 http://localhost:3142/debian sid/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:5 http://localhost:3142/debian sid/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:6 http://localhost:3142/debian sid/main amd64 python3-minimal amd64 3.11.2-1 [26.0 kB] Get:7 http://localhost:3142/debian sid/main amd64 media-types all 10.0.0 [26.1 kB] Get:8 http://localhost:3142/debian sid/main amd64 libncursesw6 amd64 6.4-2 [134 kB] Get:9 http://localhost:3142/debian sid/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:10 http://localhost:3142/debian sid/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:11 http://localhost:3142/debian sid/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:12 http://localhost:3142/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:13 http://localhost:3142/debian sid/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:14 http://localhost:3142/debian sid/main amd64 libpython3-stdlib amd64 3.11.2-1 [9012 B] Get:15 http://localhost:3142/debian sid/main amd64 python3 amd64 3.11.2-1 [26.0 kB] Get:16 http://localhost:3142/debian sid/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:17 http://localhost:3142/debian sid/main amd64 libmagic-mgc amd64 1:5.44-3 [305 kB] Get:18 http://localhost:3142/debian sid/main amd64 libmagic1 amd64 1:5.44-3 [104 kB] Get:19 http://localhost:3142/debian sid/main amd64 file amd64 1:5.44-3 [42.5 kB] Get:20 http://localhost:3142/debian sid/main amd64 gettext-base amd64 0.21-12 [160 kB] Get:21 http://localhost:3142/debian sid/main amd64 libuchardet0 amd64 0.0.7-1 [67.8 kB] Get:22 http://localhost:3142/debian sid/main amd64 groff-base amd64 1.22.4-10 [916 kB] Get:23 http://localhost:3142/debian sid/main amd64 bsdextrautils amd64 2.38.1-5+b1 [86.6 kB] Get:24 http://localhost:3142/debian sid/main amd64 libpipeline1 amd64 1.5.7-1 [38.5 kB] Get:25 http://localhost:3142/debian sid/main amd64 man-db amd64 2.11.2-2 [1386 kB] Get:26 http://localhost:3142/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:27 http://localhost:3142/debian sid/main amd64 m4 amd64 1.4.19-3 [287 kB] Get:28 http://localhost:3142/debian sid/main amd64 autoconf all 2.71-3 [332 kB] Get:29 http://localhost:3142/debian sid/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:30 http://localhost:3142/debian sid/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get:31 http://localhost:3142/debian sid/main amd64 autopoint all 0.21-12 [495 kB] Get:32 http://localhost:3142/debian sid/main amd64 binutils-powerpc64le-linux-gnu amd64 2.40-2 [2757 kB] Get:33 http://localhost:3142/debian sid/main amd64 gcc-12-powerpc64le-linux-gnu-base amd64 12.2.0-14cross1 [37.7 kB] Get:34 http://localhost:3142/debian sid/main amd64 cpp-12-powerpc64le-linux-gnu amd64 12.2.0-14cross1 [8567 kB] Get:35 http://localhost:3142/debian sid/main amd64 cpp-powerpc64le-linux-gnu amd64 4:12.2.0-3 [3980 B] Get:36 http://localhost:3142/debian sid/main amd64 cross-config all 2.6.20 [16.3 kB] Get:37 http://localhost:3142/debian sid/main amd64 gcc-12-cross-base all 12.2.0-14cross1 [33.2 kB] Get:38 http://localhost:3142/debian sid/main amd64 libc6-ppc64el-cross all 2.36-8cross1 [1353 kB] Get:39 http://localhost:3142/debian sid/main amd64 libgcc-s1-ppc64el-cross all 12.2.0-14cross1 [30.9 kB] Get:40 http://localhost:3142/debian sid/main amd64 libgomp1-ppc64el-cross all 12.2.0-14cross1 [120 kB] Get:41 http://localhost:3142/debian sid/main amd64 libitm1-ppc64el-cross all 12.2.0-14cross1 [28.3 kB] Get:42 http://localhost:3142/debian sid/main amd64 libatomic1-ppc64el-cross all 12.2.0-14cross1 [9508 B] Get:43 http://localhost:3142/debian sid/main amd64 libasan8-ppc64el-cross all 12.2.0-14cross1 [2184 kB] Get:44 http://localhost:3142/debian sid/main amd64 liblsan0-ppc64el-cross all 12.2.0-14cross1 [980 kB] Get:45 http://localhost:3142/debian sid/main amd64 libtsan2-ppc64el-cross all 12.2.0-14cross1 [2264 kB] Get:46 http://localhost:3142/debian sid/main amd64 libstdc++6-ppc64el-cross all 12.2.0-14cross1 [660 kB] Get:47 http://localhost:3142/debian sid/main amd64 libubsan1-ppc64el-cross all 12.2.0-14cross1 [897 kB] Get:48 http://localhost:3142/debian sid/main amd64 libquadmath0-ppc64el-cross all 12.2.0-14cross1 [149 kB] Get:49 http://localhost:3142/debian sid/main amd64 libgcc-12-dev-ppc64el-cross all 12.2.0-14cross1 [1320 kB] Get:50 http://localhost:3142/debian sid/main amd64 gcc-12-powerpc64le-linux-gnu amd64 12.2.0-14cross1 [16.9 MB] Get:51 http://localhost:3142/debian sid/main amd64 gcc-powerpc64le-linux-gnu amd64 4:12.2.0-3 [1484 B] Get:52 http://localhost:3142/debian sid/main amd64 linux-libc-dev-ppc64el-cross all 6.1.4-1cross1 [1830 kB] Get:53 http://localhost:3142/debian sid/main amd64 libc6-dev-ppc64el-cross all 2.36-8cross1 [1810 kB] Get:54 http://localhost:3142/debian sid/main amd64 libstdc++-12-dev-ppc64el-cross all 12.2.0-14cross1 [2124 kB] Get:55 http://localhost:3142/debian sid/main amd64 g++-12-powerpc64le-linux-gnu amd64 12.2.0-14cross1 [9490 kB] Get:56 http://localhost:3142/debian sid/main amd64 g++-powerpc64le-linux-gnu amd64 4:12.2.0-3 [1184 B] Get:57 http://localhost:3142/debian sid/main amd64 libconfig-inifiles-perl all 3.000003-2 [45.9 kB] Get:58 http://localhost:3142/debian sid/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:59 http://localhost:3142/debian sid/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:60 http://localhost:3142/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get:61 http://localhost:3142/debian sid/main amd64 libxml-namespacesupport-perl all 1.12-2 [15.1 kB] Get:62 http://localhost:3142/debian sid/main amd64 libxml-sax-base-perl all 1.09-3 [20.6 kB] Get:63 http://localhost:3142/debian sid/main amd64 libxml-sax-perl all 1.02+dfsg-3 [59.4 kB] Get:64 http://localhost:3142/debian sid/main amd64 libxml-libxml-perl amd64 2.0207+dfsg+really+2.0134-1+b1 [322 kB] Get:65 http://localhost:3142/debian sid/main amd64 libxml-simple-perl all 2.25-2 [69.8 kB] Get:66 http://localhost:3142/debian sid/main amd64 libyaml-perl all 1.30-2 [63.4 kB] Get:67 http://localhost:3142/debian sid/main amd64 libconfig-auto-perl all 0.44-2 [19.2 kB] Get:68 http://localhost:3142/debian sid/main amd64 libfile-which-perl all 1.27-2 [15.1 kB] Get:69 http://localhost:3142/debian sid/main amd64 libfile-homedir-perl all 1.006-2 [42.4 kB] Get:70 http://localhost:3142/debian sid/main amd64 libdebian-dpkgcross-perl all 2.6.20 [15.3 kB] Get:71 http://localhost:3142/debian sid/main amd64 dpkg-cross all 2.6.20 [25.8 kB] Get:72 http://localhost:3142/debian sid/main amd64 crossbuild-essential-ppc64el all 12.9 [6716 B] Get:73 http://localhost:3142/debian sid/main amd64 libdebhelper-perl all 13.11.4 [81.2 kB] Get:74 http://localhost:3142/debian sid/main amd64 libtool all 2.4.7-5 [517 kB] Get:75 http://localhost:3142/debian sid/main amd64 dh-autoreconf all 20 [17.1 kB] Get:76 http://localhost:3142/debian sid/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:77 http://localhost:3142/debian sid/main amd64 libsub-override-perl all 0.09-4 [9304 B] Get:78 http://localhost:3142/debian sid/main amd64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get:79 http://localhost:3142/debian sid/main amd64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get:80 http://localhost:3142/debian sid/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get:81 http://localhost:3142/debian sid/main amd64 dwz amd64 0.15-1 [109 kB] Get:82 http://localhost:3142/debian sid/main amd64 gettext amd64 0.21-12 [1300 kB] Get:83 http://localhost:3142/debian sid/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:84 http://localhost:3142/debian sid/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:85 http://localhost:3142/debian sid/main amd64 debhelper all 13.11.4 [942 kB] Get:86 http://localhost:3142/debian sid/main ppc64el gcc-11-base ppc64el 11.3.0-12 [38.4 kB] Get:87 http://localhost:3142/debian sid/main ppc64el gcc-12-base ppc64el 12.2.0-14 [37.5 kB] Get:88 http://localhost:3142/debian sid/main amd64 help2man amd64 1.49.3 [198 kB] Get:89 http://localhost:3142/debian sid/main ppc64el libgcc-s1 ppc64el 12.2.0-14 [30.9 kB] Get:90 http://localhost:3142/debian sid/main ppc64el libc6 ppc64el 2.36-8 [2680 kB] Get:91 http://localhost:3142/debian sid/main ppc64el libasan6 ppc64el 11.3.0-12 [2038 kB] Get:92 http://localhost:3142/debian sid/main ppc64el libatomic1 ppc64el 12.2.0-14 [9800 B] Get:93 http://localhost:3142/debian sid/main ppc64el linux-libc-dev ppc64el 6.1.20-2 [1747 kB] Get:94 http://localhost:3142/debian sid/main ppc64el libcrypt1 ppc64el 1:4.4.33-2 [97.3 kB] Get:95 http://localhost:3142/debian sid/main ppc64el libcrypt-dev ppc64el 1:4.4.33-2 [131 kB] Get:96 http://localhost:3142/debian sid/main ppc64el libcom-err2 ppc64el 1.47.0-2 [20.2 kB] Get:97 http://localhost:3142/debian sid/main ppc64el libkrb5support0 ppc64el 1.20.1-1+b1 [35.7 kB] Get:98 http://localhost:3142/debian sid/main ppc64el libk5crypto3 ppc64el 1.20.1-1+b1 [89.5 kB] Get:99 http://localhost:3142/debian sid/main ppc64el libkeyutils1 ppc64el 1.6.3-2 [10.0 kB] Get:100 http://localhost:3142/debian sid/main ppc64el libssl3 ppc64el 3.0.8-1 [2027 kB] Get:101 http://localhost:3142/debian sid/main ppc64el libkrb5-3 ppc64el 1.20.1-1+b1 [364 kB] Get:102 http://localhost:3142/debian sid/main ppc64el libgssapi-krb5-2 ppc64el 1.20.1-1+b1 [148 kB] Get:103 http://localhost:3142/debian sid/main ppc64el libtirpc3 ppc64el 1.3.3+ds-1 [96.7 kB] Get:104 http://localhost:3142/debian sid/main ppc64el libnsl2 ppc64el 1.3.0-2 [44.8 kB] Get:105 http://localhost:3142/debian sid/main ppc64el libtirpc-dev ppc64el 1.3.3+ds-1 [209 kB] Get:106 http://localhost:3142/debian sid/main ppc64el libnsl-dev ppc64el 1.3.0-2 [73.6 kB] Get:107 http://localhost:3142/debian sid/main ppc64el libc6-dev ppc64el 2.36-8 [1814 kB] Get:108 http://localhost:3142/debian sid/main ppc64el libgomp1 ppc64el 12.2.0-14 [123 kB] Get:109 http://localhost:3142/debian sid/main ppc64el libitm1 ppc64el 12.2.0-14 [28.8 kB] Get:110 http://localhost:3142/debian sid/main ppc64el liblsan0 ppc64el 12.2.0-14 [981 kB] Get:111 http://localhost:3142/debian sid/main ppc64el libtsan0 ppc64el 11.3.0-12 [2021 kB] Get:112 http://localhost:3142/debian sid/main ppc64el libstdc++6 ppc64el 12.2.0-14 [705 kB] Get:113 http://localhost:3142/debian sid/main ppc64el libubsan1 ppc64el 12.2.0-14 [897 kB] Get:114 http://localhost:3142/debian sid/main ppc64el libquadmath0 ppc64el 12.2.0-14 [149 kB] Get:115 http://localhost:3142/debian sid/main ppc64el libgcc-11-dev ppc64el 11.3.0-12 [1268 kB] Get:116 http://localhost:3142/debian sid/main amd64 liblua5.3-0 amd64 5.3.6-2 [123 kB] Get:117 http://localhost:3142/debian sid/main amd64 libsimde-dev all 0.7.4~rc2-2 [377 kB] Get:118 http://localhost:3142/debian sid/main ppc64el libstdc++-11-dev ppc64el 11.3.0-12 [2056 kB] Get:119 http://localhost:3142/debian sid/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:120 http://localhost:3142/debian sid/main amd64 pandoc-data all 2.17.1.1-1.1 [417 kB] Get:121 http://localhost:3142/debian sid/main amd64 pandoc amd64 2.17.1.1-1.1 [21.3 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 122 MB in 1s (196 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 15279 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-5_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-5) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... 15609 files and directories currently installed.) 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Selecting previously unselected package libnsl-dev:ppc64el. Preparing to unpack .../091-libnsl-dev_1.3.0-2_ppc64el.deb ... Unpacking libnsl-dev:ppc64el (1.3.0-2) ... Selecting previously unselected package libc6-dev:ppc64el. Preparing to unpack .../092-libc6-dev_2.36-8_ppc64el.deb ... Unpacking libc6-dev:ppc64el (2.36-8) ... Selecting previously unselected package libgomp1:ppc64el. Preparing to unpack .../093-libgomp1_12.2.0-14_ppc64el.deb ... Unpacking libgomp1:ppc64el (12.2.0-14) ... Selecting previously unselected package libitm1:ppc64el. Preparing to unpack .../094-libitm1_12.2.0-14_ppc64el.deb ... Unpacking libitm1:ppc64el (12.2.0-14) ... Selecting previously unselected package liblsan0:ppc64el. Preparing to unpack .../095-liblsan0_12.2.0-14_ppc64el.deb ... Unpacking liblsan0:ppc64el (12.2.0-14) ... Selecting previously unselected package libtsan0:ppc64el. Preparing to unpack .../096-libtsan0_11.3.0-12_ppc64el.deb ... Unpacking libtsan0:ppc64el (11.3.0-12) ... Selecting previously unselected package libstdc++6:ppc64el. Preparing to unpack .../097-libstdc++6_12.2.0-14_ppc64el.deb ... Unpacking libstdc++6:ppc64el (12.2.0-14) ... Selecting previously unselected package libubsan1:ppc64el. Preparing to unpack .../098-libubsan1_12.2.0-14_ppc64el.deb ... Unpacking libubsan1:ppc64el (12.2.0-14) ... Selecting previously unselected package libquadmath0:ppc64el. Preparing to unpack .../099-libquadmath0_12.2.0-14_ppc64el.deb ... Unpacking libquadmath0:ppc64el (12.2.0-14) ... Selecting previously unselected package libgcc-11-dev:ppc64el. Preparing to unpack .../100-libgcc-11-dev_11.3.0-12_ppc64el.deb ... Unpacking libgcc-11-dev:ppc64el (11.3.0-12) ... Selecting previously unselected package liblua5.3-0:amd64. Preparing to unpack .../101-liblua5.3-0_5.3.6-2_amd64.deb ... Unpacking liblua5.3-0:amd64 (5.3.6-2) ... Selecting previously unselected package libsimde-dev. Preparing to unpack .../102-libsimde-dev_0.7.4~rc2-2_all.deb ... 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Setting up media-types (10.0.0) ... Setting up libpipeline1:amd64 (1.5.7-1) ... Setting up libsimde-dev (0.7.4~rc2-2) ... Setting up gcc-11-base:ppc64el (11.3.0-12) ... Setting up libfile-which-perl (1.27-2) ... Setting up libicu72:amd64 (72.1-3) ... Setting up gcc-12-cross-base (12.2.0-14cross1) ... Setting up bsdextrautils (2.38.1-5+b1) ... Setting up gcc-12-powerpc64le-linux-gnu-base:amd64 (12.2.0-14cross1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libc6-ppc64el-cross (2.36-8cross1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libmagic1:amd64 (1:5.44-3) ... Setting up linux-libc-dev:ppc64el (6.1.20-2) ... Setting up libxml-namespacesupport-perl (1.12-2) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up file (1:5.44-3) ... Setting up libgomp1-ppc64el-cross (12.2.0-14cross1) ... Setting up libyaml-perl (1.30-2) ... Setting up gcc-12-base:ppc64el (12.2.0-14) ... Setting up libxml-sax-base-perl (1.09-3) ... Setting up libio-string-perl (1.08-4) ... Setting up autotools-dev (20220109.1) ... Setting up cross-config (2.6.20) ... Setting up cpp-12-powerpc64le-linux-gnu (12.2.0-14cross1) ... Setting up autopoint (0.21-12) ... Setting up libncursesw6:amd64 (6.4-2) ... Setting up autoconf (2.71-3) ... Setting up libitm1-ppc64el-cross (12.2.0-14cross1) ... Setting up libatomic1-ppc64el-cross (12.2.0-14cross1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libuchardet0:amd64 (0.0.7-1) ... Setting up liblua5.3-0:amd64 (5.3.6-2) ... Setting up linux-libc-dev-ppc64el-cross (6.1.4-1cross1) ... Setting up libsub-override-perl (0.09-4) ... Setting up libgcc-s1-ppc64el-cross (12.2.0-14cross1) ... Setting up binutils-powerpc64le-linux-gnu (2.40-2) ... Setting up pandoc-data (2.17.1.1-1.1) ... Setting up libfile-homedir-perl (1.006-2) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Setting up liblocale-gettext-perl (1.07-5) ... Setting up cpp-powerpc64le-linux-gnu (4:12.2.0-3) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up gettext (0.21-12) ... Setting up libc6-dev-ppc64el-cross (2.36-8cross1) ... Setting up libtool (2.4.7-5) ... Setting up libquadmath0-ppc64el-cross (12.2.0-14cross1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libasan8-ppc64el-cross (12.2.0-14cross1) ... Setting up liblsan0-ppc64el-cross (12.2.0-14cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libtsan2-ppc64el-cross (12.2.0-14cross1) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up pandoc (2.17.1.1-1.1) ... Setting up ucf (3.0043+nmu1) ... Setting up libstdc++6-ppc64el-cross (12.2.0-14cross1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up dwz (0.15-1) ... Setting up groff-base (1.22.4-10) ... Setting up libubsan1-ppc64el-cross (12.2.0-14cross1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libgcc-12-dev-ppc64el-cross (12.2.0-14cross1) ... Setting up libxml-sax-perl (1.02+dfsg-3) ... 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 libxml-libxml-perl (2.0207+dfsg+really+2.0134-1+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-12-powerpc64le-linux-gnu (12.2.0-14cross1) ... Setting up libstdc++-12-dev-ppc64el-cross (12.2.0-14cross1) ... Setting up libpython3-stdlib:amd64 (3.11.2-1) ... Setting up python3.11 (3.11.2-6) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1) ... Setting up gcc-powerpc64le-linux-gnu (4:12.2.0-3) ... Setting up libxml-simple-perl (2.25-2) ... Setting up g++-12-powerpc64le-linux-gnu (12.2.0-14cross1) ... Setting up g++-powerpc64le-linux-gnu (4:12.2.0-3) ... Setting up libconfig-auto-perl (0.44-2) ... Setting up libdebian-dpkgcross-perl (2.6.20) ... Setting up dpkg-cross (2.6.20) ... Setting up crossbuild-essential-ppc64el (12.9) ... Setting up libgcc-s1:ppc64el (12.2.0-14) ... Setting up libc6:ppc64el (2.36-8) ... Setting up libstdc++6:ppc64el (12.2.0-14) ... Setting up liblsan0:ppc64el (12.2.0-14) ... Setting up libitm1:ppc64el (12.2.0-14) ... Setting up libtsan0:ppc64el (11.3.0-12) ... Setting up libkeyutils1:ppc64el (1.6.3-2) ... Setting up libssl3:ppc64el (3.0.8-1) ... Setting up libcrypt1:ppc64el (1:4.4.33-2) ... Setting up libcom-err2:ppc64el (1.47.0-2) ... Setting up libgomp1:ppc64el (12.2.0-14) ... Setting up libasan6:ppc64el (11.3.0-12) ... Setting up libkrb5support0:ppc64el (1.20.1-1+b1) ... Setting up libquadmath0:ppc64el (12.2.0-14) ... Setting up libatomic1:ppc64el (12.2.0-14) ... Setting up libk5crypto3:ppc64el (1.20.1-1+b1) ... Setting up libubsan1:ppc64el (12.2.0-14) ... Setting up libgcc-11-dev:ppc64el (11.3.0-12) ... Setting up libcrypt-dev:ppc64el (1:4.4.33-2) ... Setting up libkrb5-3:ppc64el (1.20.1-1+b1) ... Setting up libgssapi-krb5-2:ppc64el (1.20.1-1+b1) ... Setting up libtirpc3:ppc64el (1.3.3+ds-1) ... Setting up libtirpc-dev:ppc64el (1.3.3+ds-1) ... Setting up libnsl2:ppc64el (1.3.0-2) ... Setting up libnsl-dev:ppc64el (1.3.0-2) ... Setting up libc6-dev:ppc64el (2.36-8) ... Setting up libstdc++-11-dev:ppc64el (11.3.0-12) ... Setting up sbuild-build-depends-main-dummy:ppc64el (0.invalid.0) ... Processing triggers for libc-bin (2.36-8) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (ppc64el included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) amd64 (x86_64) Toolchain package versions: binutils_2.40-2 dpkg-dev_1.21.21 g++-11_11.3.0-12 g++-12_12.2.0-14 gcc-11_11.3.0-12 gcc-12_12.2.0-14 libc6-dev_2.36-8 libstdc++-11-dev_11.3.0-12 libstdc++-12-dev_12.2.0-14 libstdc++-12-dev-ppc64el-cross_12.2.0-14cross1 libstdc++6_12.2.0-14 libstdc++6-ppc64el-cross_12.2.0-14cross1 linux-libc-dev_6.1.20-2 Package versions: adduser_3.132 apt_2.6.0 autoconf_2.71-3 automake_1:1.16.5-1.3 autopoint_0.21-12 autotools-dev_20220109.1 base-files_12.4 base-passwd_3.6.1 bash_5.2.15-2+b1 binutils_2.40-2 binutils-common_2.40-2 binutils-powerpc64le-linux-gnu_2.40-2 binutils-x86-64-linux-gnu_2.40-2 bsdextrautils_2.38.1-5+b1 bsdutils_1:2.38.1-5+b1 build-essential_12.9 bzip2_1.0.8-5+b1 coreutils_9.1-1 cpp_4:12.2.0-3 cpp-11_11.3.0-12 cpp-12_12.2.0-14 cpp-12-powerpc64le-linux-gnu_12.2.0-14cross1 cpp-powerpc64le-linux-gnu_4:12.2.0-3 cross-config_2.6.20 crossbuild-essential-ppc64el_12.9 dash_0.5.12-2 debconf_1.5.82 debhelper_13.11.4 debian-archive-keyring_2023.3 debianutils_5.7-0.4 dh-autoreconf_20 dh-strip-nondeterminism_1.13.1-1 diffutils_1:3.8-4 dpkg_1.21.21 dpkg-cross_2.6.20 dpkg-dev_1.21.21 dwz_0.15-1 e2fsprogs_1.47.0-2 fakeroot_1.31-1.2 file_1:5.44-3 findutils_4.9.0-4 g++_4:12.2.0-3 g++-11_11.3.0-12 g++-12_12.2.0-14 g++-12-powerpc64le-linux-gnu_12.2.0-14cross1 g++-powerpc64le-linux-gnu_4:12.2.0-3 gcc_4:12.2.0-3 gcc-11_11.3.0-12 gcc-11-base_11.3.0-12 gcc-12_12.2.0-14 gcc-12-base_12.2.0-14 gcc-12-cross-base_12.2.0-14cross1 gcc-12-powerpc64le-linux-gnu_12.2.0-14cross1 gcc-12-powerpc64le-linux-gnu-base_12.2.0-14cross1 gcc-9-base_9.5.0-3 gcc-powerpc64le-linux-gnu_4:12.2.0-3 gettext_0.21-12 gettext-base_0.21-12 gpgv_2.2.40-1.1 grep_3.8-5 groff-base_1.22.4-10 gzip_1.12-1 help2man_1.49.3 hostname_3.23+nmu1 init-system-helpers_1.65.2 intltool-debian_0.35.0+20060710.6 libacl1_2.3.1-3 libapt-pkg6.0_2.6.0 libarchive-zip-perl_1.68-1 libasan6_11.3.0-12 libasan8_12.2.0-14 libasan8-ppc64el-cross_12.2.0-14cross1 libatomic1_12.2.0-14 libatomic1-ppc64el-cross_12.2.0-14cross1 libattr1_1:2.5.1-4 libaudit-common_1:3.0.9-1 libaudit1_1:3.0.9-1 libbinutils_2.40-2 libblkid1_2.38.1-5+b1 libbz2-1.0_1.0.8-5+b1 libc-bin_2.36-8 libc-dev-bin_2.36-8 libc6_2.36-8 libc6-dev_2.36-8 libc6-dev-ppc64el-cross_2.36-8cross1 libc6-ppc64el-cross_2.36-8cross1 libcap-ng0_0.8.3-1+b3 libcap2_1:2.66-3 libcc1-0_12.2.0-14 libcom-err2_1.47.0-2 libconfig-auto-perl_0.44-2 libconfig-inifiles-perl_3.000003-2 libcrypt-dev_1:4.4.33-2 libcrypt1_1:4.4.33-2 libctf-nobfd0_2.40-2 libctf0_2.40-2 libdb5.3_5.3.28+dfsg2-1 libdebconfclient0_0.268 libdebhelper-perl_13.11.4 libdebian-dpkgcross-perl_2.6.20 libdpkg-perl_1.21.21 libelf1_0.188-2.1 libexpat1_2.5.0-1 libext2fs2_1.47.0-2 libfakeroot_1.31-1.2 libffi8_3.4.4-1 libfile-find-rule-perl_0.34-3 libfile-homedir-perl_1.006-2 libfile-stripnondeterminism-perl_1.13.1-1 libfile-which-perl_1.27-2 libgcc-11-dev_11.3.0-12 libgcc-12-dev_12.2.0-14 libgcc-12-dev-ppc64el-cross_12.2.0-14cross1 libgcc-s1_12.2.0-14 libgcc-s1-ppc64el-cross_12.2.0-14cross1 libgcrypt20_1.10.1-3 libgdbm-compat4_1.23-3 libgdbm6_1.23-3 libgmp10_2:6.2.1+dfsg1-1.1 libgnutls30_3.7.9-1 libgomp1_12.2.0-14 libgomp1-ppc64el-cross_12.2.0-14cross1 libgpg-error0_1.46-1 libgprofng0_2.40-2 libgssapi-krb5-2_1.20.1-1+b1 libhogweed6_3.8.1-2 libicu72_72.1-3 libidn2-0_2.3.3-1+b1 libio-string-perl_1.08-4 libisl23_0.25-1 libitm1_12.2.0-14 libitm1-ppc64el-cross_12.2.0-14cross1 libjansson4_2.14-2 libk5crypto3_1.20.1-1+b1 libkeyutils1_1.6.3-2 libkrb5-3_1.20.1-1+b1 libkrb5support0_1.20.1-1+b1 liblocale-gettext-perl_1.07-5 liblsan0_12.2.0-14 liblsan0-ppc64el-cross_12.2.0-14cross1 liblua5.3-0_5.3.6-2 liblz4-1_1.9.4-1 liblzma5_5.4.1-0.2 libmagic-mgc_1:5.44-3 libmagic1_1:5.44-3 libmd0_1.0.4-2 libmount1_2.38.1-5+b1 libmpc3_1.3.1-1 libmpfr6_4.2.0-1 libncursesw6_6.4-2 libnettle8_3.8.1-2 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnumber-compare-perl_0.03-3 libp11-kit0_0.24.1-2 libpam-modules_1.5.2-6 libpam-modules-bin_1.5.2-6 libpam-runtime_1.5.2-6 libpam0g_1.5.2-6 libpcre2-8-0_10.42-1 libpcre3_2:8.39-15 libperl5.34_5.34.0-5 libperl5.36_5.36.0-7 libpipeline1_1.5.7-1 libpython3-stdlib_3.11.2-1 libpython3.11-minimal_3.11.2-6 libpython3.11-stdlib_3.11.2-6 libquadmath0_12.2.0-14 libquadmath0-ppc64el-cross_12.2.0-14cross1 libreadline8_8.2-1.3 libseccomp2_2.5.4-1+b3 libselinux1_3.4-1+b5 libsemanage-common_3.4-1 libsemanage2_3.4-1+b5 libsepol2_3.4-2 libsimde-dev_0.7.4~rc2-2 libsmartcols1_2.38.1-5+b1 libsqlite3-0_3.40.1-2 libss2_1.47.0-2 libssl3_3.0.8-1 libstdc++-11-dev_11.3.0-12 libstdc++-12-dev_12.2.0-14 libstdc++-12-dev-ppc64el-cross_12.2.0-14cross1 libstdc++6_12.2.0-14 libstdc++6-ppc64el-cross_12.2.0-14cross1 libsub-override-perl_0.09-4 libsystemd0_252.6-1 libtasn1-6_4.19.0-2 libtext-glob-perl_0.11-3 libtinfo6_6.4-2 libtirpc-common_1.3.3+ds-1 libtirpc-dev_1.3.3+ds-1 libtirpc3_1.3.3+ds-1 libtool_2.4.7-5 libtsan0_11.3.0-12 libtsan2_12.2.0-14 libtsan2-ppc64el-cross_12.2.0-14cross1 libubsan1_12.2.0-14 libubsan1-ppc64el-cross_12.2.0-14cross1 libuchardet0_0.0.7-1 libudev1_252.6-1 libunistring2_1.0-2 libuuid1_2.38.1-5+b1 libxml-libxml-perl_2.0207+dfsg+really+2.0134-1+b1 libxml-namespacesupport-perl_1.12-2 libxml-sax-base-perl_1.09-3 libxml-sax-perl_1.02+dfsg-3 libxml-simple-perl_2.25-2 libxml2_2.9.14+dfsg-1.1+b3 libxxhash0_0.8.1-1 libyaml-0-2_0.2.5-1 libyaml-perl_1.30-2 libzstd1_1.5.4+dfsg2-5 linux-libc-dev_6.1.20-2 linux-libc-dev-ppc64el-cross_6.1.4-1cross1 login_1:4.13+dfsg1-1+b1 logsave_1.47.0-2 m4_1.4.19-3 make_4.3-4.1 man-db_2.11.2-2 mawk_1.3.4.20200120-3.1 media-types_10.0.0 mount_2.38.1-5+b1 ncurses-base_6.4-2 ncurses-bin_6.4-2 pandoc_2.17.1.1-1.1 pandoc-data_2.17.1.1-1.1 passwd_1:4.13+dfsg1-1+b1 patch_2.7.6-7 perl_5.36.0-7 perl-base_5.36.0-7 perl-modules-5.34_5.34.0-5 perl-modules-5.36_5.36.0-7 po-debconf_1.0.21+nmu1 python3_3.11.2-1 python3-minimal_3.11.2-1 python3.11_3.11.2-6 python3.11-minimal_3.11.2-6 readline-common_8.2-1.3 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-1 sensible-utils_0.0.17+nmu1 sysvinit-utils_3.06-4 tar_1.34+dfsg-1.2 tzdata_2023c-2 ucf_3.0043+nmu1 usrmerge_35 util-linux_2.38.1-5+b1 util-linux-extra_2.38.1-5+b1 xz-utils_5.4.1-0.2 zlib1g_1:1.2.13.dfsg-1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hisat2 Binary: hisat2, python3-hisat2 Architecture: any all Version: 2.2.1-4 Maintainer: Debian Med Packaging Team Uploaders: Michael R. Crusoe Homepage: https://daehwankimlab.github.io/hisat2/ Standards-Version: 4.6.1 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 (= 13), libsimde-dev, help2man , pandoc , python3:any Package-List: hisat2 deb science optional arch=any python3-hisat2 deb python optional arch=all Checksums-Sha1: e09c36d93952eff1ebfd19545c38e173636bf662 6761242 hisat2_2.2.1.orig.tar.gz 4f025a697c5a41a55a237309454a55fd214a57bf 29056 hisat2_2.2.1-4.debian.tar.xz Checksums-Sha256: f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599 6761242 hisat2_2.2.1.orig.tar.gz b71212885b7b5445fcc60425eaa9fb22e1f1396f8a9241d6e430d0709d8c70b8 29056 hisat2_2.2.1-4.debian.tar.xz Files: 0d1fcfcaf7ba1e64eb68006bba5a3855 6761242 hisat2_2.2.1.orig.tar.gz 85767e7119a42490cc50c90a3d16dc95 29056 hisat2_2.2.1-4.debian.tar.xz -----BEGIN PGP SIGNATURE----- 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No public key dpkg-source: warning: cannot verify inline signature for ./hisat2_2.2.1-4.dsc: no acceptable signature found dpkg-source: info: extracting hisat2 in /<> dpkg-source: info: unpacking hisat2_2.2.1.orig.tar.gz dpkg-source: info: unpacking hisat2_2.2.1-4.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 dpkg-source: info: applying fix-manual dpkg-source: info: applying riscv5 Check disk space ---------------- Sufficient free space for build User Environment ---------------- APT_CONFIG=/var/lib/sbuild/apt.conf CONFIG_SITE=/etc/dpkg-cross/cross-config.ppc64el DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SCHROOT_ALIAS_NAME=unstable-amd64-sbuild SCHROOT_CHROOT_NAME=sid-amd64-sbuild SCHROOT_COMMAND=env SCHROOT_GID=1000 SCHROOT_GROUP=crossqa SCHROOT_SESSION_ID=sid-amd64-sbuild-ce035713-0fcf-415b-bc0f-00020e94cfff SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -appc64el -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.2.1-4 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-architecture: warning: specified GNU system type powerpc64le-linux-gnu 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 ppc64el 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-repeat 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-repeat-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-repeat.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-repeat-debug.exe \ hisat2-src.zip hisat2-bin.zip rm -f core.* .tmp.head rm -rf *.dSYM rm -rf .ht2lib-obj* rm -f libhisat2lib*.a libhisat2lib*.so make[1]: Leaving directory '/<>' dh_clean debian/rules binary-arch dh binary-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="14 October 2022" all doc make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=powerpc64le-linux-gnu-pkg-config CXX=powerpc64le-linux-gnu-g\+\+ CC=powerpc64le-linux-gnu-gcc BUILD_HOST=Debian "BUILD_TIME=14 October 2022" all doc make[2]: Entering directory '/<>' powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-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. -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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:786:39: required from here gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ In file included from hisat2_build.cpp:31: In function ‘RefRecord fastaRefReadAppend(FileBuf&, bool, TStr&, TIndexOffU&, RefReadInParams&, std::string*) [with TStr = SString]’, inlined from ‘void GFM::joinToDisk(EList&, EList&, index_t, const RefReadInParams&, TStr&, std::ostream&, std::ostream&) [with TStr = SString; index_t = unsigned int]’ at gfm.h:4629:38: ref_read.h:305:49: warning: array subscript -1 is below array bounds of ‘uint8_t []’ {aka ‘unsigned char []’} [-Warray-bounds] 305 | if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A'; | ~~~~~~~~~~~~^ In file included from sstring.h:26, from sequence_io.h:30, from hisat2_build.cpp:28: alphabet.h: In function ‘void GFM::joinToDisk(EList&, EList&, index_t, const RefReadInParams&, TStr&, std::ostream&, std::ostream&) [with TStr = SString; index_t = unsigned int]’: alphabet.h:36:16: note: while referencing ‘asc2dnacat’ 36 | extern uint8_t asc2dnacat[]; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-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. -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 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h: In instantiation of ‘void GFM::initFromVector(TStr&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, EList&, EList&, index_t, const RefReadInParams&, std::ofstream&, std::ofstream&, const std::string&, bool, index_t, index_t, index_t, int, EList*, EList >*, uint32_t, bool) [with TStr = SString; index_t = long unsigned int; std::string = std::__cxx11::basic_string; std::ofstream = std::basic_ofstream; uint32_t = unsigned int]’: gfm.h:1039:23: required from ‘GFM::GFM(TStr&, bool, int, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, index_t, index_t, index_t, int, EList&, EList&, index_t, const RefReadInParams&, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; uint32_t = unsigned int]’ hgfm.h:1989:14: required from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int; int32_t = int; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; uint32_t = unsigned int]’ hisat2_build.cpp:535:15: required from ‘void driver(const std::string&, EList >&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, int, bool, EList*, EList >*, EList*, EList >*) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2_build.cpp:786:39: required from here gfm.h:2167:33: warning: variable ‘template_len’ set but not used [-Wunused-but-set-variable] 2167 | index_t template_len = 0; | ^~~~~~~~~~~~ In file included from hisat2_build.cpp:31: In function ‘RefRecord fastaRefReadAppend(FileBuf&, bool, TStr&, TIndexOffU&, RefReadInParams&, std::string*) [with TStr = SString]’, inlined from ‘void GFM::joinToDisk(EList&, EList&, index_t, const RefReadInParams&, TStr&, std::ostream&, std::ostream&) [with TStr = SString; index_t = long unsigned int]’ at gfm.h:4629:38: ref_read.h:305:49: warning: array subscript -1 is below array bounds of ‘uint8_t []’ {aka ‘unsigned char []’} [-Warray-bounds] 305 | if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A'; | ~~~~~~~~~~~~^ In file included from sstring.h:26, from sequence_io.h:30, from hisat2_build.cpp:28: alphabet.h: In function ‘void GFM::joinToDisk(EList&, EList&, index_t, const RefReadInParams&, TStr&, std::ostream&, std::ostream&) [with TStr = SString; index_t = long unsigned int]’: alphabet.h:36:16: note: while referencing ‘asc2dnacat’ 36 | extern uint8_t asc2dnacat[]; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2259:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2257:41: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘HGFM::HGFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int; local_index_t = short unsigned int]’ at hgfm.h:2255:36: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:768:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:687:9, inlined from ‘void SString::install(const T*, size_t) [with T = char]’ at sstring.h:685:15, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:766:29: sstring.h:602:25: warning: ‘void operator delete(void*)’ called on pointer returned from a mismatched allocation function [-Wmismatched-new-delete] 602 | delete cs_; | ^~~~~~~~~~ In member function ‘void SString::resize(size_t) [with T = char]’, inlined from ‘RFM::RFM(TStr&, bool, int, int32_t, int32_t, int32_t, int32_t, int32_t, int, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, const std::string&, bool, bool, TIndexOffU, TIndexOffU, TIndexOffU, int, EList&, EList&, index_t, const RefReadInParams&, bool, EList*, EList >*, uint32_t, int32_t, bool, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at rfm.h:764:24: sstring.h:610:31: note: returned from ‘void* operator new [](std::size_t)’ 610 | cs_ = new T[sz+1]; | ^~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-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. -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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3168 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:46: hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, 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:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = unsigned int]’: hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2.cpp:4351:26: required from here gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: 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:1517:14: 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:5901:34: 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:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, 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:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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:717:28: 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:2337:47: 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:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, 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:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3161 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ 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:494:14: 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:1453:18: 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:5896:20: 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:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, 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:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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:2915:39: 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:717:28: 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:2337:47: 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:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, 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:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2675 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2713 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:331:9: required from here spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ In file included from gfm.h:59: In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = unsigned int]’, inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = unsigned int]’ at repeat.h:38:10, inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = unsigned int]’ at repeat.h:466:45, inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: repeat.h:41:20: warning: ‘cmp.RepeatCoord::fw’ may be used uninitialized [-Wmaybe-uninitialized] 41 | if(fw != o.fw) | ~~^~ repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’: repeat.h:464:30: note: ‘cmp’ declared here 464 | RepeatCoord cmp; | ^~~ In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = unsigned int]’, inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = unsigned int]’ at repeat.h:38:10, inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = unsigned int]’ at repeat.h:466:45, inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: repeat.h:43:26: warning: ‘cmp.RepeatCoord::alleleID’ may be used uninitialized [-Wmaybe-uninitialized] 43 | if(alleleID != o.alleleID) | ~~^~~~~~~~ repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = unsigned int; local_index_t = short unsigned int]’: repeat.h:464:30: note: ‘cmp’ declared here 464 | RepeatCoord cmp; | ^~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/bits/exception_ptr.h:43, from /usr/powerpc64le-linux-gnu/include/c++/12/exception:168, from /usr/powerpc64le-linux-gnu/include/c++/12/ios:39, from /usr/powerpc64le-linux-gnu/include/c++/12/ostream:38, from /usr/powerpc64le-linux-gnu/include/c++/12/iostream:39, from pat.cpp:21: In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ In file included from pat.cpp:26: pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset 20 into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [21, 25] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [22, 26] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [23, 27] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [24, 28] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [25, 29] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [26, 30] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [27, 31] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [28, 32] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [29, 33] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [30, 34] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/bits/exception_ptr.h:43, from /usr/powerpc64le-linux-gnu/include/c++/12/exception:168, from /usr/powerpc64le-linux-gnu/include/c++/12/stdexcept:38, from pat.h:25, from read_qseq.cpp:20: In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset 20 into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [21, 25] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [22, 26] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [23, 27] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [24, 28] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [25, 29] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [26, 30] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [27, 31] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [28, 32] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [29, 33] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [30, 34] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:70: aligner_swsse_loc_i16.cpp: In member function ‘TAlScore SwAligner::alignGatherLoc16(int&, bool)’: aligner_swsse_loc_i16.cpp:415:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 415 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp:497:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 497 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp: In member function ‘TAlScore SwAligner::alignNucleotidesLocalSseI16(int&, bool)’: aligner_swsse_loc_i16.cpp:1045:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 1045 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp:1123:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 1123 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:70: aligner_swsse_ee_i16.cpp: In member function ‘TAlScore SwAligner::alignGatherEE16(int&, bool)’: aligner_swsse_ee_i16.cpp:405:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 405 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp:480:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 480 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp: In member function ‘TAlScore SwAligner::alignNucleotidesEnd2EndSseI16(int&, bool)’: aligner_swsse_ee_i16.cpp:873:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 873 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp:954:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 954 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:31: required from here ds.h:663:28: 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); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-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. -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 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void parseOptions(int, const char**)’: hisat2.cpp:1823:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1823 | auto_ptr presets(new PresetsV0()); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void multiseedSearchWorker_hisat2(void*)’: hisat2.cpp:3167:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3167 | auto_ptr patsrcFact(createPatsrcFactory(patsrc, tid)); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3168:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3168 | auto_ptr ps(patsrcFact->create()); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp:3189:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 3189 | auto_ptr bmapq(new_mapq(mapqv, scoreMin, sc)); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ hisat2.cpp: In function ‘void driver(const char*, const std::string&, const std::string&)’: hisat2.cpp:4035:9: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 4035 | auto_ptr refs( | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from spliced_aligner.h:23, from hisat2.cpp:46: hi_aligner.h: In instantiation of ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hisat2.cpp:3537:48: required from here hi_aligner.h:4385:84: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4385 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4404:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefId’ {aka ‘long int’} [-Wsign-compare] 4404 | if(positions[p].first.tid != res.refid()) continue; | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4405:63: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 4405 | if(positions[p].first.toff + 1000 < res.refoff() || | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:4406:52: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 4406 | res.refoff() + 1000 < positions[p].first.toff) continue; | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ hi_aligner.h:4407:88: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4407 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4489:92: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4489 | if(sink.bestPair() >= estScore && sink.numBestPair().first > rp.khits) | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4578:69: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4578 | align2repeat = (numBestPair == 0 || numBestPair > rp.khits); | ~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4584:83: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4584 | align2repeat = (rs->size() == 0 || sink.numBestUnp(rdi).first > rp.khits); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h:4614:55: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 4614 | if(sink.numBestUnp(rdi).first > rp.khits) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::pairReads(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, WalkMetrics&, PerReadMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4088:17: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:5990:51: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5990 | if(_repeatConcordant[r].first == left.off() && | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:5991:52: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5991 | _repeatConcordant[r].second == left2.off()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h: In instantiation of ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:5661:33: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 5661 | if(nelt > 0 && nelt <= rp.kseeds && hitlen > max_hitlen) { | ~~~~~^~~~~~~~~~~~ hi_aligner.h:5688:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘TRefOff’ {aka ‘long int’} [-Wsign-compare] 5688 | if(coord.off() + pepol.maxFragLen() * 2 < toff || toff + pepol.maxFragLen() * 2 < coord.off()) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ gfm.h: In instantiation of ‘void GFM::checkOrigs(const EList >&, bool) const [with index_t = long unsigned int]’: hisat2.cpp:3815:17: required from ‘void driver(const char*, const std::string&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’ hisat2.cpp:4351:26: required from here gfm.h:6935:13: warning: variable ‘lastorig’ set but not used [-Wunused-but-set-variable] 6935 | int lastorig = -1; | ^~~~~~~~ hi_aligner.h: In instantiation of ‘index_t HI_Aligner::getAnchorHits(const GFM&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const ALTDB&, const RepeatDB&, const BitPairReference&, RandomSource&, index_t, bool, EList >&, index_t, SharedTempVars&, WalkMetrics&, PerReadMetrics&, HIMetrics&, bool) [with index_t = long unsigned int; local_index_t = short unsigned int]’: hi_aligner.h:5525:23: required from ‘bool HI_Aligner::align(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4080:31: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:5150:32: warning: comparison of integer expressions of different signedness: ‘TRefId’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 5150 | if(coord.ref() == numeric_limits::max()) | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 unsigned int]’: hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:2267:47: warning: comparison of integer expressions of different signedness: ‘TRefOff’ {aka ‘long int’} and ‘long unsigned int’ [-Wsign-compare] 2267 | findSSOffs(gfm, altdb, (coord.joinedOff() >= width ? (index_t)(coord.joinedOff() - width) : 0), (index_t)(coord.joinedOff() + width), ssOffs); | ~~~~~~~~~~~~~~~~~~^~~~~~~~ In file included from aligner_seed2.h:109, from aligner_driver.h:78, from hi_aligner.h:41: 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:1517:14: 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:5901:34: 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 unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here group_walk.h:1147:60: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1147 | if(new_node_bot - new_node_top < gws.map.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1158:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1158 | for(index_t j = 0; j + 1 < gws.map.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~ group_walk.h:1213:69: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1213 | if(node_range.second - node_range.first < st.back().map_.size()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:1224:58: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1224 | for(index_t j = 0; j + 1 < st.back().map_.size(); j++) { | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ 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 unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’: hi_aligner.h:717:28: 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 unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2337:47: 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 unsigned int]’ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:2801:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2801 | if(rfoff >= contig_len) return 0; | ~~~~~~^~~~~~~~~~~~~ hi_aligner.h:2879:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2879 | if(alt_range.first >= alts.size()) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ hi_aligner.h:3044:42: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3044 | for(int i = 0; i < alt.len; i++) { | ~~^~~~~~~~~ hi_aligner.h:3085:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3085 | if(rd_i == rdoff && prev_alt_type == ALT_SPLICESITE) { | ~~~~~^~~~~~~~ hi_aligner.h:3161:31: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3161 | if(alignedLen == next_rdlen) return rdlen; | ~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3197:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3197 | if(mm_max_rd_i + rdoff > best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ hi_aligner.h:3202:39: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 3202 | } else if(mm_max_rd_i + rdoff == best_rdoff) { | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~ hi_aligner.h:3454:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare] 3454 | if(best_rdoff < rdoff + rd_i) { | ~~~~~~~~~~~^~~~~~~~~~~~~~ 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:494:14: 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:1453:18: 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:5896:20: 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 unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:5664:17: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here group_walk.h:785:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 785 | if(i + 1 < tmp_zOffs.size() && new_top == tmp_zOffs[i+1]) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:789:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 789 | if(new_top - top == tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ group_walk.h:795:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 795 | if(i + 1 < tmp_zOffs.size()) { | ~~~~~~^~~~~~~~~~~~~~~~~~ group_walk.h:801:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 801 | if(new_bot - top < tmp_gbwt_to_node.size()) { | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ 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 unsigned int]’: hi_aligner.h:2915:39: 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 unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:717:28: 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 unsigned int; BTDnaString = SDnaStringExpandable<1024, 2>]’ hi_aligner.h:2337:47: 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 unsigned int]’ hi_aligner.h:5692:54: required from ‘bool HI_Aligner::alignMate(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, bool, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, index_t, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hi_aligner.h:4107:39: required from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ hisat2.cpp:3537:48: required from here hi_aligner.h:2660:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2660 | if(ht_range.first >= haplotypes.size()) | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ hi_aligner.h:2675:37: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2675 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2713:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2713 | if(ht_list[h].first == ht_range.first) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ hi_aligner.h:2737:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 2737 | for(; ht_range.second < haplotypes.size(); ht_range.second++) { | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ hi_aligner.h:2744:41: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare] 2744 | if(ht_list[h].first == ht_range.second) { | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~ spliced_aligner.h: In instantiation of ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’: spliced_aligner.h:331:9: required from here spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ spliced_aligner.h:782:65: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 782 | tempHit.score() + sc.sc(0) * hit.rdoff() >= hit.score()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ spliced_aligner.h:1465:105: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int64_t’ {aka ‘long int’} [-Wsign-compare] 1465 | combinedHit.score() + sc.sc(0) * (rdlen - hit.rdoff() - hit.len() - hit.trim5()) >= hit.score()) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ 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 unsigned int; local_index_t = short unsigned int]’: spliced_aligner.h:1086:53: required from ‘int64_t SplicedAligner::hybridSearch_recur(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const ALTDB&, const RepeatDB&, const BitPairReference&, SwAligner&, SpliceSiteDB&, index_t, const GenomeHit&, index_t, index_t, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&, bool, index_t) [with index_t = long unsigned int; local_index_t = short unsigned int; int64_t = long int]’ spliced_aligner.h:331:9: required from here hi_aligner.h:6719:85: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘const THitInt’ {aka ‘const long int’} [-Wsign-compare] 6719 | if(node_range.first < node_range.second && node_range.second - node_range.first <= rp.kseeds) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ In file included from gfm.h:59: In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long unsigned int]’, inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long unsigned int]’ at repeat.h:38:10, inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = long unsigned int]’ at repeat.h:466:45, inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: repeat.h:41:20: warning: ‘cmp.RepeatCoord::fw’ may be used uninitialized [-Wmaybe-uninitialized] 41 | if(fw != o.fw) | ~~^~ repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: repeat.h:464:30: note: ‘cmp’ declared here 464 | RepeatCoord cmp; | ^~~ In member function ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long unsigned int]’, inlined from ‘bool RepeatCoord::operator<(const RepeatCoord&) const [with index_t = long unsigned int]’ at repeat.h:38:10, inlined from ‘size_t EList::bsearchLoBound(const T&) const [with T = RepeatCoord; int S = 128]’ at ds.h:919:18, inlined from ‘bool RepeatDB::findCoords(index_t, index_t, index_t, index_t, index_t, const EList&, const ALTDB&, EList, RepeatCoord > >&, index_t, index_t) const [with index_t = long unsigned int]’ at repeat.h:466:45, inlined from ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’ at hi_aligner.h:4391:44: repeat.h:43:26: warning: ‘cmp.RepeatCoord::alleleID’ may be used uninitialized [-Wmaybe-uninitialized] 43 | if(alleleID != o.alleleID) | ~~^~~~~~~~ repeat.h: In member function ‘int HI_Aligner::go(const Scoring&, const PairedEndPolicy&, const TranscriptomePolicy&, const GraphPolicy&, const GFM&, const GFM*, const ALTDB&, const RepeatDB&, const ALTDB&, const BitPairReference&, const BitPairReference*, SwAligner&, SpliceSiteDB&, WalkMetrics&, PerReadMetrics&, SwMetrics&, HIMetrics&, RandomSource&, AlnSinkWrap&) [with index_t = long unsigned int; local_index_t = short unsigned int]’: repeat.h:464:30: note: ‘cmp’ declared here 464 | RepeatCoord cmp; | ^~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/bits/exception_ptr.h:43, from /usr/powerpc64le-linux-gnu/include/c++/12/exception:168, from /usr/powerpc64le-linux-gnu/include/c++/12/ios:39, from /usr/powerpc64le-linux-gnu/include/c++/12/ostream:38, from /usr/powerpc64le-linux-gnu/include/c++/12/iostream:39, from pat.cpp:21: In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ In file included from pat.cpp:26: pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset 20 into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [21, 25] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [22, 26] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [23, 27] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [24, 28] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [25, 29] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [26, 30] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [27, 31] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [28, 32] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [29, 33] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’ at pat.h:1298:21: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ pat.h: In member function ‘virtual bool FastaContinuousPatternSource::read(Read&, TReadId&, TReadId&, bool&, bool&)’: pat.h:1297:46: note: at offset [30, 34] into destination object ‘cbuf’ of size 20 1297 | char cbuf[20]; | ^~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/bits/exception_ptr.h:43, from /usr/powerpc64le-linux-gnu/include/c++/12/exception:168, from /usr/powerpc64le-linux-gnu/include/c++/12/stdexcept:38, from pat.h:25, from read_qseq.cpp:20: In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset 20 into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [21, 25] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [22, 26] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [23, 27] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [24, 28] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [25, 29] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [26, 30] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [27, 31] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [28, 32] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [29, 33] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ In function ‘std::_Require >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]’, inlined from ‘void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algobase.h:182:11, inlined from ‘void std::__reverse(_RandomAccessIterator, _RandomAccessIterator, random_access_iterator_tag) [with _RandomAccessIterator = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1107:18, inlined from ‘void std::reverse(_BIter, _BIter) [with _BIter = char*]’ at /usr/powerpc64le-linux-gnu/include/c++/12/bits/stl_algo.h:1134:21, inlined from ‘char* itoa10(const T&, char*) [with T = long unsigned int]’ at util.h:48:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:63:9, inlined from ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’ at read_qseq.cpp:28:5: /usr/powerpc64le-linux-gnu/include/c++/12/bits/move.h:205:11: warning: writing 1 byte into a region of size 0 [-Wstringop-overflow=] 205 | __a = _GLIBCXX_MOVE(__b); | ^ read_qseq.cpp: In member function ‘int QseqPatternSource::parseName(Read&, Read*, bool, bool, bool, bool, int)’: read_qseq.cpp:62:22: note: at offset [30, 34] into destination object ‘cbuf’ of size 20 62 | char cbuf[20]; | ^~~~ 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:70: aligner_swsse_loc_i16.cpp: In member function ‘TAlScore SwAligner::alignGatherLoc16(int&, bool)’: aligner_swsse_loc_i16.cpp:415:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 415 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp:497:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 497 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp: In member function ‘TAlScore SwAligner::alignNucleotidesLocalSseI16(int&, bool)’: aligner_swsse_loc_i16.cpp:1045:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 1045 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp:1123:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 1123 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:70: aligner_swsse_ee_i16.cpp: In member function ‘TAlScore SwAligner::alignGatherEE16(int&, bool)’: aligner_swsse_ee_i16.cpp:405:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 405 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp:480:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 480 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp: In member function ‘TAlScore SwAligner::alignNucleotidesEnd2EndSseI16(int&, bool)’: aligner_swsse_ee_i16.cpp:873:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 873 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp:954:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 954 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: ds.h: In instantiation of ‘void EList::push_back_array(const T*, size_t) [with T = Exon; int S = 128; size_t = long unsigned int]’: splice_site.cpp:722:31: required from here ds.h:663:28: 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); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ splice_site.h:377:7: note: ‘class Exon’ declared here 377 | class Exon { | ^~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-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. -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:227:18: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: 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: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:227:18: 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); | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 \ -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-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. -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 hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ In file included from edit.h:26, from edit.cpp:21: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: 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: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:227:18: 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); | ^~~~~~~~~~ gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ powerpc64le-linux-gnu-g++ -O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -DCOMPILER_OPTIONS="\"-O3 -funroll-loops -g3 -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11\"" -std=c++11 \ -fno-strict-aliasing -DHISAT2_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"Debian\"" -DBUILD_TIME="\"14 October 2022\"" -DCOMPILER_VERSION="\"`powerpc64le-linux-gnu-g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DBOWTIE_MM -g -O2 -ffile-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. -I third_party \ -o hisat2-repeat hisat2_repeat.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 mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_repeat.cpp:36: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from hisat2_repeat.cpp:32: In function ‘RefRecord fastaRefReadAppend(FileBuf&, bool, TStr&, TIndexOffU&, RefReadInParams&, std::string*) [with TStr = SString]’, inlined from ‘static void GFM::join(EList&, EList&, index_t, const RefReadInParams&, uint32_t, TStr&, bool, bool) [with TStr = SString; index_t = long unsigned int]’ at gfm.h:4518:38, inlined from ‘void driver(const std::string&, EList >&, const std::string&, bool, bool, bool) [with TStr = SString]’ at hisat2_repeat.cpp:582:36: ref_read.h:305:49: warning: array subscript -1 is below array bounds of ‘uint8_t []’ {aka ‘unsigned char []’} [-Warray-bounds] 305 | if(rparms.nsToAs && asc2dnacat[c] >= 2) c = 'A'; | ~~~~~~~~~~~~^ In file included from sstring.h:26, from sequence_io.h:30, from hisat2_repeat.cpp:29: alphabet.h: In function ‘void driver(const std::string&, EList >&, const std::string&, bool, bool, bool) [with TStr = SString]’: alphabet.h:36:16: note: while referencing ‘asc2dnacat’ 36 | extern uint8_t asc2dnacat[]; | ^~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadSizes(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&)’: ref_read.cpp:367:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 367 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ ref_read.cpp: In function ‘std::pair fastaRefReadFragsNames(EList&, EList&, const RefReadInParams&, BitpairOutFileBuf*, TIndexOff&, EList >&)’: ref_read.cpp:440:22: warning: comparison of integer expressions of different signedness: ‘int64_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 440 | if(i + 1 >= recs.size() || recs[i+1].first) { | ~~~~~~^~~~~~~~~~~~~~ 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ reference.cpp: In member function ‘int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const’: reference.cpp:522:26: warning: variable ‘origBufOff’ set but not used [-Wunused-but-set-variable] 522 | uint64_t origBufOff = bufOff; | ^~~~~~~~~~ reference.cpp:516:14: warning: variable ‘binarySearched’ set but not used [-Wunused-but-set-variable] 516 | bool binarySearched = false; | ^~~~~~~~~~~~~~ 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:70: aligner_swsse_ee_i16.cpp: In member function ‘TAlScore SwAligner::alignGatherEE16(int&, bool)’: aligner_swsse_ee_i16.cpp:405:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 405 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp:480:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 480 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp: In member function ‘TAlScore SwAligner::alignNucleotidesEnd2EndSseI16(int&, bool)’: aligner_swsse_ee_i16.cpp:873:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 873 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_ee_i16.cpp:954:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 954 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:70: aligner_swsse_loc_i16.cpp: In member function ‘TAlScore SwAligner::alignGatherLoc16(int&, bool)’: aligner_swsse_loc_i16.cpp:415:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 415 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp:497:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 497 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp: In member function ‘TAlScore SwAligner::alignNucleotidesLocalSseI16(int&, bool)’: aligner_swsse_loc_i16.cpp:1045:49: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 1045 | vlo = _mm_slli_epi16(vlo, NBITS_PER_WORD-1); // all elts = 0x8000 | ~~~~~~~~~~~~~~^~ aligner_swsse_loc_i16.cpp:1123:55: warning: suggest parentheses around ‘-’ in operand of ‘&’ [-Wparentheses] 1123 | vf = _mm_slli_epi16(vf, NBITS_PER_WORD-1); | ~~~~~~~~~~~~~~^~ 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:75, 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 std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, from bit_packed_array.cpp:24: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | 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:75, from repeat_builder.cpp:26: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/memory:76, from gfm.h:28: /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ gfm.h:1189:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1189 | auto_ptr fb(new FileBuf(ss.get())); | ^~~~~~~~ /usr/powerpc64le-linux-gnu/include/c++/12/bits/unique_ptr.h:64:28: note: declared here 64 | template class auto_ptr; | ^~~~~~~~ repeat_builder.cpp: In function ‘std::string reverse_complement(const std::string&)’: repeat_builder.cpp:88:30: warning: array subscript has type ‘char’ [-Wchar-subscripts] 88 | rev[i] = asc2dnacomp[nt]; | ^~ repeat_builder.cpp: In function ‘std::string reverseComplement(const std::string&)’: repeat_builder.cpp:200:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] 200 | rc.push_back(asc2dnacomp[str[si - 1]]); | ^ repeat_builder.cpp: In member function ‘int CoordHelper::mapJoinedOffToSeq(TIndexOffU)’: repeat_builder.cpp:403:29: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 403 | for(size_t i = 0; i < num_cached_; i++) { | ~~^~~~~~~~~~~~~ repeat_builder.cpp: In function ‘size_t extract_kmer(const std::string&, size_t, size_t)’: repeat_builder.cpp:1217:53: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1217 | kmer = (kmer << 2) | asc2dna[seq[offset + i]]; | ^ repeat_builder.cpp: In function ‘size_t next_kmer(size_t, char, size_t)’: repeat_builder.cpp:1225:34: warning: array subscript has type ‘char’ [-Wchar-subscripts] 1225 | kmer = (kmer << 2) | asc2dna[base]; | ^~~~ repeat_builder.cpp: In function ‘void find_gap_pos(const std::string&, const std::string&, EList&, EList&, bool, size_t, size_t, size_t&, size_t&, bool)’: repeat_builder.cpp:1275:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1275 | for(int i = seq_len - 1; i >= gap_len; i--) { | ~~^~~~~~~~~~ repeat_builder.cpp:1277:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare] 1277 | if(i == seq_len - 1) ed2[i] = add; | ~~^~~~~~~~~~~~~~ repeat_builder.cpp: In member function ‘void RB_SWAligner::makePadString(const std::string&, const std::string&, std::string&, size_t)’: repeat_builder.cpp:2915:39: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2915 | pad[i] = "CGTA"[asc2dna[ref[i]]]; | ^ repeat_builder.cpp:2919:43: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2919 | pad[i] = "CGTA"[asc2dna[pad[i]]]; | ^ repeat_builder.cpp:2926:25: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 2926 | for(size_t i = 0; i < head_len; i++) { | ~~^~~~~~~~~~ repeat_builder.cpp:2929:67: warning: array subscript has type ‘char’ [-Wchar-subscripts] 2929 | pad[pad_start + i] = "CGTA"[asc2dna[pad[pad_start + i]]]; | ^ repeat_builder.cpp: In member function ‘int RB_SWAligner::alignStrings(const std::string&, const std::string&, EList&, Coord&)’: repeat_builder.cpp:3065:13: warning: variable ‘max_match_len’ set but not used [-Wunused-but-set-variable] 3065 | int max_match_len = 0; | ^~~~~~~~~~~~~ In file included from repeat_builder.cpp:31: repeat_builder.cpp: In instantiation of ‘RepeatBuilder::RepeatBuilder(TStr&, const EList&, const EList >&, bool, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:4753:16: required from here repeat_builder.h:947:17: warning: ‘RepeatBuilder >::coordHelper_’ will be initialized after [-Wreorder] 947 | CoordHelper coordHelper_; | ^~~~~~~~~~~~ repeat_builder.h:940:10: warning: ‘bool RepeatBuilder >::forward_only_’ [-Wreorder] 940 | bool forward_only_; | ^~~~~~~~~~~~~ repeat_builder.cpp:3167:1: warning: when initialized here [-Wreorder] 3167 | RepeatBuilder::RepeatBuilder(TStr& s, | ^~~~~~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’: repeat_builder.cpp:4753:16: required from here repeat_builder.cpp:3396:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3396 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3426:29: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3426 | if(spos != string::npos) { | ~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3553:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3553 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp:3563:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare] 3563 | if(pos != string::npos) { | ~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void RepeatBuilder::saveConsensus(const RepeatParameter&, const std::string&) [with TStr = SString; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:4753:16: required from here repeat_builder.cpp:4114:34: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘const int’ [-Wsign-compare] 4114 | if((oskip + out_len) == output_width) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ repeat_builder.cpp: In instantiation of ‘void dump_tstr(const TStr&) [with TStr = SString]’: repeat_builder.cpp:4754:46: required from here repeat_builder.cpp:309:38: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare] 309 | for(size_t j = 0; (j < print_width) && (i + j < s_len); j++) { | ~~~^~~~~~~~~~~~~~ repeat_builder.cpp:310:46: warning: array subscript has type ‘char’ [-Wchar-subscripts] 310 | buf.push_back("ACGTN"[s[i + j]]); | ~~~~~~~^ repeat_builder.cpp: In instantiation of ‘std::string getString(const TStr&, TIndexOffU, size_t) [with TStr = SString; std::string = std::__cxx11::basic_string; TIndexOffU = long unsigned int; size_t = long unsigned int]’: repeat_builder.cpp:3312:30: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ repeat_builder.cpp:4753:16: required from here repeat_builder.cpp:272:33: warning: array subscript has type ‘char’ [-Wchar-subscripts] 272 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ repeat_builder.cpp: In instantiation of ‘void getString(const TStr&, TIndexOffU, size_t, std::string&) [with TStr = SString; TIndexOffU = long unsigned int; size_t = long unsigned int; std::string = std::__cxx11::basic_string]’: repeat_builder.cpp:3545:22: required from ‘void RepeatBuilder::build(const RepeatParameter&) [with TStr = SString]’ repeat_builder.cpp:4753:16: required from here repeat_builder.cpp:286:25: warning: array subscript has type ‘char’ [-Wchar-subscripts] 286 | char nt = "ACGT"[ref[start + i]]; | ~~~~~~^ In file included from /usr/powerpc64le-linux-gnu/include/c++/12/iostream:39, from repeat_builder.cpp:21: In member function ‘std::basic_ostream<_CharT, _Traits>::__ostream_type& std::basic_ostream<_CharT, _Traits>::operator<<(long unsigned int) [with _CharT = char; _Traits = std::char_traits]’, inlined from ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’ at repeat_builder.cpp:3678:31: /usr/powerpc64le-linux-gnu/include/c++/12/ostream:171:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized] 171 | { return _M_insert(__n); } | ~~~~~~~~~^~~~~ repeat_builder.cpp: In member function ‘void RepeatBuilder::writeAllele(TIndexOffU, TIndexOffU, Range, const std::string&, TIndexOffU, const EList&, std::ostream&) [with TStr = SString]’: repeat_builder.cpp:3664:20: note: ‘pos_in_chr’ was declared here 3664 | TIndexOffU pos_in_chr; | ^~~~~~~~~~ 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:32: override_dh_auto_build] Error 126 make[1]: Leaving directory '/<>' make: *** [debian/rules:27: binary-arch] Error 2 dpkg-buildpackage: error: debian/rules binary-arch subprocess returned exit status 2 -------------------------------------------------------------------------------- Build finished at 2023-04-09T05:16:41Z 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: 74532 Build-Time: 388 Distribution: unstable Fail-Stage: build Foreign Architectures: ppc64el Host Architecture: ppc64el Install-Time: 13 Job: hisat2_2.2.1-4 Machine Architecture: amd64 Package: hisat2 Package-Time: 411 Source-Version: 2.2.1-4 Space: 74532 Status: attempted Version: 2.2.1-4 -------------------------------------------------------------------------------- Finished at 2023-04-09T05:16:41Z Build needed 00:06:51, 74532k disk space