sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | hisat2 2.2.1-5 (riscv64) Sun, 09 Feb 2025 07:53:51 +0000 | +==============================================================================+ Package: hisat2 Version: 2.2.1-5 Source Version: 2.2.1-5 Distribution: unstable Machine Architecture: amd64 Host Architecture: riscv64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-e859ec23-a0d5-4938-8bab-4f8d8b89fcd0' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-1RSwb8/resolver-eS0taT' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [205 kB] Get:2 http://localhost:3142/debian unstable/main Sources.diff/Index [63.6 kB] Get:3 http://localhost:3142/debian unstable/non-free Sources.diff/Index [63.3 kB] Get:4 http://localhost:3142/debian unstable/contrib Sources.diff/Index [63.3 kB] Get:5 http://localhost:3142/debian unstable/main amd64 Packages.diff/Index [63.6 kB] Get:6 http://localhost:3142/debian unstable/main Sources T-2025-02-09-0210.34-F-2025-02-09-0210.34.pdiff [17.4 kB] Get:7 http://localhost:3142/debian unstable/non-free Sources T-2025-02-09-0210.34-F-2025-02-09-0210.34.pdiff [31 B] Get:8 http://localhost:3142/debian unstable/contrib Sources T-2025-02-09-0210.34-F-2025-02-09-0210.34.pdiff [568 B] Get:6 http://localhost:3142/debian unstable/main Sources T-2025-02-09-0210.34-F-2025-02-09-0210.34.pdiff [17.4 kB] Get:9 http://localhost:3142/debian unstable/main amd64 Packages T-2025-02-09-0210.34-F-2025-02-09-0210.34.pdiff [15.9 kB] Get:8 http://localhost:3142/debian unstable/contrib Sources T-2025-02-09-0210.34-F-2025-02-09-0210.34.pdiff [568 B] Get:7 http://localhost:3142/debian unstable/non-free Sources T-2025-02-09-0210.34-F-2025-02-09-0210.34.pdiff [31 B] Get:9 http://localhost:3142/debian unstable/main amd64 Packages T-2025-02-09-0210.34-F-2025-02-09-0210.34.pdiff [15.9 kB] Get:10 http://localhost:3142/debian unstable/main riscv64 Packages [9672 kB] Fetched 10.2 MB in 3s (3343 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 6793 kB of source archives. Get:1 http://localhost:3142/debian unstable/main hisat2 2.2.1-5 (dsc) [2104 B] Get:2 http://localhost:3142/debian unstable/main hisat2 2.2.1-5 (tar) [6761 kB] Get:3 http://localhost:3142/debian unstable/main hisat2 2.2.1-5 (diff) [29.6 kB] Fetched 6793 kB in 0s (158 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hisat2-1RSwb8/hisat2-2.2.1' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-1RSwb8' 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-riscv64:amd64, libc-dev:riscv64, libstdc++-dev:riscv64 Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-riscv64:amd64, libc-dev:riscv64, libstdc++-dev:riscv64 dpkg-deb: warning: root directory /<>/sbuild-build-depends-main-dummy has unusual owner or group 1000:119 dpkg-deb: hint: you might need to pass --root-owner-group, see for further details dpkg-deb: warning: ignoring 1 warning about the control file(s) 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 [609 B] Ign:3 copy:/<>/apt_archive ./ Release.gpg Get:4 copy:/<>/apt_archive ./ Sources [792 B] Get:5 copy:/<>/apt_archive ./ Packages [810 B] Fetched 2211 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... Execute external solver... The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-riscv64-linux-gnu bsdextrautils cpp-14-riscv64-linux-gnu cpp-riscv64-linux-gnu crossbuild-essential-riscv64 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file g++-14-riscv64-linux-gnu g++-riscv64-linux-gnu gcc-14-base:riscv64 gcc-14-cross-base gcc-14-riscv64-linux-gnu gcc-14-riscv64-linux-gnu-base gcc-riscv64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:riscv64 libasan8-riscv64-cross libatomic1:riscv64 libatomic1-riscv64-cross libc6:riscv64 libc6-dev:riscv64 libc6-dev-riscv64-cross libc6-riscv64-cross libcrypt-dev:riscv64 libcrypt1:riscv64 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libffi8 libfile-stripnondeterminism-perl libgcc-14-dev:riscv64 libgcc-14-dev-riscv64-cross libgcc-s1:riscv64 libgcc-s1-riscv64-cross libgomp1:riscv64 libgomp1-riscv64-cross libicu72 libitm1:riscv64 libitm1-riscv64-cross liblocale-gettext-perl liblsan0:riscv64 liblsan0-riscv64-cross liblua5.4-0 libmagic-mgc libmagic1t64 libncursesw6 libnuma1 libpipeline1 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsimde-dev libsqlite3-0 libstdc++-14-dev:riscv64 libstdc++-14-dev-riscv64-cross libstdc++6:riscv64 libstdc++6-riscv64-cross libtool libtsan2:riscv64 libtsan2-riscv64-cross libubsan1:riscv64 libubsan1-riscv64-cross libuchardet0 libunistring5 libxml2 libyaml-0-2 linux-libc-dev-riscv64-cross m4 man-db media-types netbase pandoc pandoc-data po-debconf python3 python3-minimal python3.13 python3.13-minimal readline-common sensible-utils Suggested packages: autoconf-archive gnu-standards autoconf-doc binutils-doc gcc-14-locales cpp-14-doc cpp-doc dh-make gcc-14-doc manpages-dev flex bison gdb-riscv64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:riscv64 libc-l10n:riscv64 locales:riscv64 libnss-nis:riscv64 libnss-nisplus:riscv64 manpages-dev:riscv64 libstdc++-14-doc:riscv64 libtool-doc gfortran | fortran95-compiler gcj-jdk m4-doc apparmor less www-browser texlive-latex-recommended texlive-xetex texlive-luatex pandoc-citeproc texlive-latex-extra context wkhtmltopdf librsvg2-bin ghc nodejs php python ruby r-base-core libjs-mathjax libjs-katex citation-style-language-styles libmail-box-perl python3-doc python3-tk python3-venv python3.13-venv python3.13-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx libidn2-0:riscv64 libarchive-cpio-perl libgpm2 libltdl-dev libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-riscv64-linux-gnu bsdextrautils cpp-14-riscv64-linux-gnu cpp-riscv64-linux-gnu crossbuild-essential-riscv64 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file g++-14-riscv64-linux-gnu g++-riscv64-linux-gnu gcc-14-base:riscv64 gcc-14-cross-base gcc-14-riscv64-linux-gnu gcc-14-riscv64-linux-gnu-base gcc-riscv64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:riscv64 libasan8-riscv64-cross libatomic1:riscv64 libatomic1-riscv64-cross libc6:riscv64 libc6-dev:riscv64 libc6-dev-riscv64-cross libc6-riscv64-cross libcrypt-dev:riscv64 libcrypt1:riscv64 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libffi8 libfile-stripnondeterminism-perl libgcc-14-dev:riscv64 libgcc-14-dev-riscv64-cross libgcc-s1:riscv64 libgcc-s1-riscv64-cross libgomp1:riscv64 libgomp1-riscv64-cross libicu72 libitm1:riscv64 libitm1-riscv64-cross liblocale-gettext-perl liblsan0:riscv64 liblsan0-riscv64-cross liblua5.4-0 libmagic-mgc libmagic1t64 libncursesw6 libnuma1 libpipeline1 libpython3-stdlib libpython3.13-minimal libpython3.13-stdlib libreadline8t64 libsimde-dev libsqlite3-0 libstdc++-14-dev:riscv64 libstdc++-14-dev-riscv64-cross libstdc++6:riscv64 libstdc++6-riscv64-cross libtool libtsan2:riscv64 libtsan2-riscv64-cross libubsan1:riscv64 libubsan1-riscv64-cross libuchardet0 libunistring5 libxml2 libyaml-0-2 linux-libc-dev-riscv64-cross m4 man-db media-types netbase pandoc pandoc-data po-debconf python3 python3-minimal python3.13 python3.13-minimal readline-common sbuild-build-depends-main-dummy:riscv64 sensible-utils 0 upgraded, 96 newly installed, 0 to remove and 0 not upgraded. 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Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [952 B] Get:2 http://localhost:3142/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.2-1 [859 kB] Get:4 http://localhost:3142/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:5 http://localhost:3142/debian unstable/main amd64 python3.13-minimal amd64 3.13.2-1 [2205 kB] Get:6 http://localhost:3142/debian unstable/main amd64 python3-minimal amd64 3.13.1-2 [27.0 kB] Get:7 http://localhost:3142/debian unstable/main amd64 media-types all 11.0.0 [27.6 kB] Get:8 http://localhost:3142/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get:9 http://localhost:3142/debian unstable/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libncursesw6 amd64 6.5+20250125-2 [135 kB] Get:11 http://localhost:3142/debian unstable/main amd64 readline-common all 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unstable/main amd64 gettext-base amd64 0.23.1-1 [243 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:24 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get:25 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 2.40.4-3 [92.1 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get:27 http://localhost:3142/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get:28 http://localhost:3142/debian unstable/main amd64 m4 amd64 1.4.19-5 [294 kB] Get:29 http://localhost:3142/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get:30 http://localhost:3142/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get:31 http://localhost:3142/debian unstable/main amd64 automake all 1:1.17-3 [862 kB] Get:32 http://localhost:3142/debian unstable/main amd64 autopoint all 0.23.1-1 [770 kB] Get:33 http://localhost:3142/debian unstable/main amd64 binutils-riscv64-linux-gnu amd64 2.44-1 [1426 kB] Get:34 http://localhost:3142/debian unstable/main amd64 gcc-14-riscv64-linux-gnu-base amd64 14.2.0-12cross1 [48.5 kB] Get:35 http://localhost:3142/debian unstable/main amd64 cpp-14-riscv64-linux-gnu amd64 14.2.0-12cross1 [13.3 MB] Get:36 http://localhost:3142/debian unstable/main amd64 cpp-riscv64-linux-gnu amd64 4:14.2.0-1 [4848 B] Get:37 http://localhost:3142/debian unstable/main amd64 gcc-14-cross-base all 14.2.0-12cross1 [43.7 kB] Get:38 http://localhost:3142/debian unstable/main amd64 libc6-riscv64-cross all 2.40-4cross1 [1142 kB] Get:39 http://localhost:3142/debian unstable/main amd64 libgcc-s1-riscv64-cross all 14.2.0-12cross1 [56.7 kB] Get:40 http://localhost:3142/debian unstable/main amd64 libgomp1-riscv64-cross all 14.2.0-12cross1 [129 kB] Get:41 http://localhost:3142/debian unstable/main amd64 libitm1-riscv64-cross all 14.2.0-12cross1 [25.2 kB] Get:42 http://localhost:3142/debian unstable/main amd64 libatomic1-riscv64-cross all 14.2.0-12cross1 [8336 B] Get:43 http://localhost:3142/debian unstable/main amd64 libasan8-riscv64-cross all 14.2.0-12cross1 [2355 kB] Get:44 http://localhost:3142/debian unstable/main amd64 liblsan0-riscv64-cross all 14.2.0-12cross1 [1077 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libtsan2-riscv64-cross all 14.2.0-12cross1 [2231 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libstdc++6-riscv64-cross all 14.2.0-12cross1 [660 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libubsan1-riscv64-cross all 14.2.0-12cross1 [979 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libgcc-14-dev-riscv64-cross all 14.2.0-12cross1 [5173 kB] Get:49 http://localhost:3142/debian unstable/main amd64 gcc-14-riscv64-linux-gnu amd64 14.2.0-12cross1 [25.7 MB] Get:50 http://localhost:3142/debian unstable/main amd64 gcc-riscv64-linux-gnu amd64 4:14.2.0-1 [1444 B] Get:51 http://localhost:3142/debian unstable/main amd64 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unstable/main amd64 debhelper all 13.24.1 [920 kB] Get:72 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.37-1 [29.7 kB] Get:73 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.37-1 [75.6 kB] Get:74 http://localhost:3142/debian unstable/main riscv64 gcc-14-base riscv64 14.2.0-16 [48.9 kB] Get:75 http://localhost:3142/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:76 http://localhost:3142/debian unstable/main riscv64 libgcc-s1 riscv64 14.2.0-16 [56.6 kB] Get:77 http://localhost:3142/debian unstable/main riscv64 libc6 riscv64 2.40-6 [2442 kB] Get:78 http://localhost:3142/debian unstable/main riscv64 libasan8 riscv64 14.2.0-16 [2365 kB] Get:79 http://localhost:3142/debian unstable/main riscv64 libatomic1 riscv64 14.2.0-16 [8676 B] Get:80 http://localhost:3142/debian unstable/main riscv64 libcrypt1 riscv64 1:4.4.38-1 [106 kB] Get:81 http://localhost:3142/debian unstable/main riscv64 libcrypt-dev riscv64 1:4.4.38-1 [221 kB] Get:82 http://localhost:3142/debian unstable/main riscv64 libc6-dev riscv64 2.40-6 [3097 kB] Get:83 http://localhost:3142/debian unstable/main riscv64 libgomp1 riscv64 14.2.0-16 [131 kB] Get:84 http://localhost:3142/debian unstable/main riscv64 libitm1 riscv64 14.2.0-16 [25.7 kB] Get:85 http://localhost:3142/debian unstable/main riscv64 liblsan0 riscv64 14.2.0-16 [1078 kB] Get:86 http://localhost:3142/debian unstable/main riscv64 libtsan2 riscv64 14.2.0-16 [2243 kB] Get:87 http://localhost:3142/debian unstable/main riscv64 libstdc++6 riscv64 14.2.0-16 [708 kB] Get:88 http://localhost:3142/debian unstable/main riscv64 libubsan1 riscv64 14.2.0-16 [979 kB] Get:89 http://localhost:3142/debian unstable/main riscv64 libgcc-14-dev riscv64 14.2.0-16 [5186 kB] Get:90 http://localhost:3142/debian unstable/main amd64 liblua5.4-0 amd64 5.4.7-1+b2 [147 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libsimde-dev all 0.8.2-2 [467 kB] Get:93 http://localhost:3142/debian unstable/main riscv64 libstdc++-14-dev riscv64 14.2.0-16 [5278 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:95 http://localhost:3142/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get:96 http://localhost:3142/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Preconfiguring packages ... Fetched 159 MB in 1s (201 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 12871 files and directories currently installed.) Preparing to unpack .../liblocale-gettext-perl_1.07-7+b1_amd64.deb ... Unpacking liblocale-gettext-perl (1.07-7+b1) ... Selecting previously unselected package libpython3.13-minimal:amd64. Preparing to unpack .../libpython3.13-minimal_3.13.2-1_amd64.deb ... Unpacking libpython3.13-minimal:amd64 (3.13.2-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package python3.13-minimal. Preparing to unpack .../python3.13-minimal_3.13.2-1_amd64.deb ... Unpacking python3.13-minimal (3.13.2-1) ... Setting up libpython3.13-minimal:amd64 (3.13.2-1) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.13-minimal (3.13.2-1) ... Selecting previously unselected package python3-minimal. (Reading database ... 13220 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.13.1-2_amd64.deb ... Unpacking python3-minimal (3.13.1-2) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_11.0.0_all.deb ... Unpacking media-types (11.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libffi8:amd64. Preparing to unpack .../03-libffi8_3.4.6-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.6-1) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../04-libncursesw6_6.5+20250125-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5+20250125-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../05-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... 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Setting up liblsan0-riscv64-cross (14.2.0-12cross1) ... Setting up python3 (3.13.1-2) ... Setting up libtsan2-riscv64-cross (14.2.0-12cross1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up libgcc-14-dev-riscv64-cross (14.2.0-12cross1) ... Setting up libstdc++-14-dev-riscv64-cross (14.2.0-12cross1) ... Setting up debhelper (13.24.1) ... Setting up gcc-14-riscv64-linux-gnu (14.2.0-12cross1) ... Setting up g++-14-riscv64-linux-gnu (14.2.0-12cross1) ... Setting up gcc-riscv64-linux-gnu (4:14.2.0-1) ... Setting up g++-riscv64-linux-gnu (4:14.2.0-1) ... Setting up crossbuild-essential-riscv64 (12.12) ... Setting up libgcc-s1:riscv64 (14.2.0-16) ... Setting up libc6:riscv64 (2.40-6) ... Setting up libasan8:riscv64 (14.2.0-16) ... Setting up libtsan2:riscv64 (14.2.0-16) ... Setting up libstdc++6:riscv64 (14.2.0-16) ... Setting up liblsan0:riscv64 (14.2.0-16) ... Setting up libitm1:riscv64 (14.2.0-16) ... Setting up libcrypt1:riscv64 (1:4.4.38-1) ... Setting up libgomp1:riscv64 (14.2.0-16) ... Setting up libatomic1:riscv64 (14.2.0-16) ... Setting up libubsan1:riscv64 (14.2.0-16) ... Setting up libcrypt-dev:riscv64 (1:4.4.38-1) ... Setting up libc6-dev:riscv64 (2.40-6) ... Setting up libgcc-14-dev:riscv64 (14.2.0-16) ... Setting up libstdc++-14-dev:riscv64 (14.2.0-16) ... Setting up sbuild-build-depends-main-dummy:riscv64 (0.invalid.0) ... Processing triggers for libc-bin (2.40-6) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (riscv64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-31-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.128-1 (2025-02-07) amd64 (x86_64) Toolchain package versions: binutils_2.44-1 dpkg-dev_1.22.15 g++-14_14.2.0-16 gcc-14_14.2.0-16 libc6-dev_2.40-6 libstdc++-14-dev_14.2.0-16 libstdc++-14-dev-riscv64-cross_14.2.0-12cross1 libstdc++6_14.2.0-16 libstdc++6-riscv64-cross_14.2.0-12cross1 linux-libc-dev_6.12.12-1 Package versions: apt_2.9.28 autoconf_2.72-3 automake_1:1.17-3 autopoint_0.23.1-1 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 binutils_2.44-1 binutils-common_2.44-1 binutils-riscv64-linux-gnu_2.44-1 binutils-x86-64-linux-gnu_2.44-1 bsdextrautils_2.40.4-3 bsdutils_1:2.40.4-3 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-16 cpp-14-riscv64-linux-gnu_14.2.0-12cross1 cpp-14-x86-64-linux-gnu_14.2.0-16 cpp-riscv64-linux-gnu_4:14.2.0-1 cpp-x86-64-linux-gnu_4:14.2.0-1 crossbuild-essential-riscv64_12.12 dash_0.5.12-12 debconf_1.5.89 debhelper_13.24.1 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.1-1 diffutils_1:3.10-2 dpkg_1.22.15 dpkg-dev_1.22.15 dwz_0.15-1+b1 e2fsprogs_1.47.2-1 fakeroot_1.37-1 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-16 g++-14-riscv64-linux-gnu_14.2.0-12cross1 g++-14-x86-64-linux-gnu_14.2.0-16 g++-riscv64-linux-gnu_4:14.2.0-1 g++-x86-64-linux-gnu_4:14.2.0-1 gcc_4:14.2.0-1 gcc-14_14.2.0-16 gcc-14-base_14.2.0-16 gcc-14-cross-base_14.2.0-12cross1 gcc-14-riscv64-linux-gnu_14.2.0-12cross1 gcc-14-riscv64-linux-gnu-base_14.2.0-12cross1 gcc-14-x86-64-linux-gnu_14.2.0-16 gcc-riscv64-linux-gnu_4:14.2.0-1 gcc-x86-64-linux-gnu_4:14.2.0-1 gettext_0.23.1-1 gettext-base_0.23.1-1 grep_3.11-4 groff-base_1.23.0-7 gzip_1.13-1 help2man_1.49.3 hostname_3.25 init-system-helpers_1.68 intltool-debian_0.35.0+20060710.6 libacl1_2.3.2-2+b1 libapt-pkg6.0t64_2.9.28 libarchive-zip-perl_1.68-1 libasan8_14.2.0-16 libasan8-riscv64-cross_14.2.0-12cross1 libatomic1_14.2.0-16 libatomic1-riscv64-cross_14.2.0-12cross1 libattr1_1:2.5.2-2 libaudit-common_1:4.0.2-2 libaudit1_1:4.0.2-2+b1 libbinutils_2.44-1 libblkid1_2.40.4-3 libbsd0_0.12.2-2 libbz2-1.0_1.0.8-6 libc-bin_2.40-6 libc-dev-bin_2.40-6 libc6_2.40-6 libc6-dev_2.40-6 libc6-dev-riscv64-cross_2.40-4cross1 libc6-riscv64-cross_2.40-4cross1 libcap-ng0_0.8.5-4 libcap2_1:2.66-5+b1 libcc1-0_14.2.0-16 libcom-err2_1.47.2-1 libcrypt-dev_1:4.4.38-1 libcrypt1_1:4.4.38-1 libctf-nobfd0_2.44-1 libctf0_2.44-1 libdb5.3t64_5.3.28+dfsg2-9 libdebconfclient0_0.277 libdebhelper-perl_13.24.1 libdpkg-perl_1.22.15 libelf1t64_0.192-4 libexpat1_2.6.4-1 libext2fs2t64_1.47.2-1 libfakeroot_1.37-1 libffi8_3.4.6-1 libfile-stripnondeterminism-perl_1.14.1-1 libgcc-14-dev_14.2.0-16 libgcc-14-dev-riscv64-cross_14.2.0-12cross1 libgcc-s1_14.2.0-16 libgcc-s1-riscv64-cross_14.2.0-12cross1 libgdbm-compat4t64_1.24-2 libgdbm6t64_1.24-2 libgmp10_2:6.3.0+dfsg-3 libgomp1_14.2.0-16 libgomp1-riscv64-cross_14.2.0-12cross1 libgprofng0_2.44-1 libhogweed6t64_3.10-1+b1 libhwasan0_14.2.0-16 libicu72_72.1-6 libisl23_0.27-1 libitm1_14.2.0-16 libitm1-riscv64-cross_14.2.0-12cross1 libjansson4_2.14-2+b3 liblocale-gettext-perl_1.07-7+b1 liblsan0_14.2.0-16 liblsan0-riscv64-cross_14.2.0-12cross1 liblua5.4-0_5.4.7-1+b2 liblz4-1_1.10.0-3 liblzma5_5.6.3-1+b1 libmagic-mgc_1:5.45-3+b1 libmagic1t64_1:5.45-3+b1 libmd0_1.1.0-2+b1 libmount1_2.40.4-3 libmpc3_1.3.1-1+b3 libmpfr6_4.2.1-1+b2 libncursesw6_6.5+20250125-2 libnettle8t64_3.10-1+b1 libnuma1_2.0.18-1+b1 libpam-modules_1.7.0-2 libpam-modules-bin_1.7.0-2 libpam-runtime_1.7.0-2 libpam0g_1.7.0-2 libpcre2-8-0_10.45-1 libperl5.40_5.40.0-8 libpipeline1_1.5.8-1 libpython3-stdlib_3.13.1-2 libpython3.13-minimal_3.13.2-1 libpython3.13-stdlib_3.13.2-1 libquadmath0_14.2.0-16 libreadline8t64_8.2-6 libseccomp2_2.5.5-2 libselinux1_3.8-1 libsemanage-common_3.7-2.1 libsemanage2_3.7-2.1 libsepol2_3.8-1 libsframe1_2.44-1 libsimde-dev_0.8.2-2 libsmartcols1_2.40.4-3 libsqlite3-0_3.46.1-1 libss2_1.47.2-1 libssl3t64_3.4.0-2 libstdc++-14-dev_14.2.0-16 libstdc++-14-dev-riscv64-cross_14.2.0-12cross1 libstdc++6_14.2.0-16 libstdc++6-riscv64-cross_14.2.0-12cross1 libsystemd0_257.2-3 libtinfo6_6.5+20250125-2 libtool_2.5.4-3 libtsan2_14.2.0-16 libtsan2-riscv64-cross_14.2.0-12cross1 libubsan1_14.2.0-16 libubsan1-riscv64-cross_14.2.0-12cross1 libuchardet0_0.0.8-1+b2 libudev1_257.2-3 libunistring5_1.3-1 libuuid1_2.40.4-3 libxml2_2.12.7+dfsg+really2.9.14-0.2+b1 libxxhash0_0.8.3-2 libyaml-0-2_0.2.5-2 libzstd1_1.5.6+dfsg-2 linux-libc-dev_6.12.12-1 linux-libc-dev-riscv64-cross_6.12.6-1cross1 login_1:4.16.0-2+really2.40.4-3 login.defs_1:4.16.0-7 logsave_1.47.2-1 m4_1.4.19-5 make_4.4.1-1 man-db_2.13.0-1 mawk_1.3.4.20250131-1 media-types_11.0.0 mount_2.40.4-3 ncurses-base_6.5+20250125-2 ncurses-bin_6.5+20250125-2 netbase_6.4 openssl-provider-legacy_3.4.0-2 pandoc_3.1.11.1+ds-2 pandoc-data_3.1.11.1-3 passwd_1:4.16.0-7 patch_2.7.6-7 perl_5.40.0-8 perl-base_5.40.0-8 perl-modules-5.40_5.40.0-8 po-debconf_1.0.21+nmu1 python3_3.13.1-2 python3-minimal_3.13.1-2 python3.13_3.13.2-1 python3.13-minimal_3.13.2-1 readline-common_8.2-6 rpcsvc-proto_1.4.3-1 sbuild-build-depends-main-dummy_0.invalid.0 sed_4.9-2 sensible-utils_0.0.24 sqv_1.2.1-6 sysvinit-utils_3.13-1 tar_1.35+dfsg-3.1 tzdata_2025a-2 util-linux_2.40.4-3 xz-utils_5.6.3-1+b1 zlib1g_1:1.3.dfsg+really1.3.1-1+b1 +------------------------------------------------------------------------------+ | Build | +------------------------------------------------------------------------------+ Unpack source ------------- -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: hisat2 Binary: hisat2, python3-hisat2 Architecture: any all Version: 2.2.1-5 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 96871cfbd92f3e6d11393aba14344550f57ff8d2 29576 hisat2_2.2.1-5.debian.tar.xz Checksums-Sha256: f3f4f867d0a6b1f880d64efc19deaa5788c62050e0a4d614ce98b3492f702599 6761242 hisat2_2.2.1.orig.tar.gz 70d19cce728774d945e65a341721be568980cbd42c4449e8cb4677850c62607d 29576 hisat2_2.2.1-5.debian.tar.xz Files: 0d1fcfcaf7ba1e64eb68006bba5a3855 6761242 hisat2_2.2.1.orig.tar.gz 0168dcca6cecdd97887bb4330c189aaa 29576 hisat2_2.2.1-5.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEck1gkzcRPHEFUNdHPCZ2P2xn5uIFAmaNEIYACgkQPCZ2P2xn 5uKpuw/9HA+ly3oYGrYHwPjr4hsKtUAqP6YK1GgbrVylLefTL1kjIwr7m6hNGCzu 99X3wix8CRksJoEqqxw3TyVlMx9f4NQ247lKsJrejwGBK7S+GB5h2SgnKIYqUkKM Wgl/BkMQWgAYR1zHJ/nx+DD/gjx3ZqlG9JHzaECFTrIMdhHprWnOX5wGLZhaRpZA uKBFQqvYUVOIc5gyBZqP+tynQAqPk9cQ4YfcAU037Ew7ANtyxq+8DeXfgpn/t7lA /uba4uCfs7rxm4PmH/rroSrrny7nkF5YZiWd0wMIHkiWvty0fdgVJ1Y3rg/IgAgi 2fLJSRT7jVx2V8LfOcolXOMIC6pCsltpKG8WY42lZTB1nIUpR46i0OG+fVUAhd5N 4FsmK3YnBUBfY6Nx/CWq6SL1MzxdKoDxC88i4P8Ie6tZZxTJi5G0o8WCX/UgB4uS llD1hPGJVGszV4eTQyjNBk798Ac0+x2joThxuiwHedyG/41AyYXAUGJ7XJnITqPm GNeBvCZAJxtDyz9bmAPEAIteP9FczwWZHEB16IYB8pG+pwfRd7Dp/BFYQWwyVaD2 m6FEF/spuP9m5IdbwHbx2uEKxWGtm/bYBqSKdIGoyPFMMRu9aAlG70iaWKC2n+QL Aqq/FvUD9DBcfDfU5IqL07a2QYgECbcgR0gANrC9Yamz4Jzu7rc= =vP68 -----END PGP SIGNATURE----- dpkg-source: warning: cannot verify inline signature for ./hisat2_2.2.1-5.dsc: unsupported subcommand dpkg-source: info: extracting hisat2 in /<> dpkg-source: info: unpacking hisat2_2.2.1.orig.tar.gz dpkg-source: info: unpacking hisat2_2.2.1-5.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying no_imp 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.riscv64 DEB_BUILD_OPTIONS=nocheck HOME=/sbuild-nonexistent LANG=en_US.UTF-8 LC_ALL=C.UTF-8 LOGNAME=crossqa OLDPWD=/home/crossqa PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games SBUILD_CONFIG=/tmp/tmp.AyAEOSHiDW/sbuild.conf 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-e859ec23-a0d5-4938-8bab-4f8d8b89fcd0 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa XDG_SESSION_CLASS=user dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -ariscv64 -Pcross,nocheck -us -uc -B -rfakeroot --jobs-try=1 dpkg-buildpackage: info: source package hisat2 dpkg-buildpackage: info: source version 2.2.1-5 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Michael R. Crusoe dpkg-architecture: warning: specified GNU system type riscv64-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 riscv64 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="09 July 2024" all doc make -j1 "INSTALL=install --strip-program=true" PKG_CONFIG=riscv64-linux-gnu-pkg-config CXX=riscv64-linux-gnu-g\+\+ CC=riscv64-linux-gnu-gcc BUILD_HOST=Debian "BUILD_TIME=09 July 2024" all doc make[2]: Entering directory '/<>' riscv64-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="\"09 July 2024\"" -DCOMPILER_VERSION="\"`riscv64-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 -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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, | ~~ 1041 | snpfile, | ~~~~~~~~ 1042 | htfile, | ~~~~~~~ 1043 | ssfile, | ~~~~~~~ 1044 | exonfile, | ~~~~~~~~~ 1045 | svfile, | ~~~~~~~ 1046 | repeatfile, | ~~~~~~~~~~~ 1047 | is, | ~~~ 1048 | szs, | ~~~~ 1049 | sztot, | ~~~~~~ 1050 | refparams, | ~~~~~~~~~~ 1051 | fout1, | ~~~~~~ 1052 | fout2, | ~~~~~~ 1053 | outfile, | ~~~~~~~~ 1054 | useBlockwise, | ~~~~~~~~~~~~~ 1055 | bmax, | ~~~~~ 1056 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 1057 | bmaxDivN, | ~~~~~~~~~ 1058 | dcv, | ~~~~ 1059 | parent_szs, | ~~~~~~~~~~~ 1060 | parent_refnames, | ~~~~~~~~~~~~~~~~ 1061 | seed, | ~~~~~ 1062 | verbose); | ~~~~~~~~ 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]’ 1989 | _in6(NULL) | ^ 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]’ 535 | gfm = new HGFM( | ^~~~~~~~~~~~~~~~~~~~~ 536 | s, | ~~ 537 | packed, | ~~~~~~~ 538 | 1, // TODO: maybe not? | ~~~~~~~~~~~~~~~~~~~~~~~ 539 | lineRate, | ~~~~~~~~~ 540 | offRate, // suffix-array sampling rate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 541 | ftabChars, // number of chars in initial arrow-pair calc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 | localOffRate, | ~~~~~~~~~~~~~ 543 | localFtabChars, | ~~~~~~~~~~~~~~~ 544 | nthreads, | ~~~~~~~~~ 545 | snpfile, | ~~~~~~~~ 546 | htfile, | ~~~~~~~ 547 | ssfile, | ~~~~~~~ 548 | exonfile, | ~~~~~~~~~ 549 | svfile, | ~~~~~~~ 550 | repeatfile, | ~~~~~~~~~~~ 551 | outfile, // basename for .?.ht2 files | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 552 | reverse == 0, // fw | ~~~~~~~~~~~~~~~~~~~ 553 | !entireSA, // useBlockwise | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 | bmax, // block size for blockwise SA builder | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 556 | bmaxDivN, // block size as divisor of len | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 557 | noDc? 0 : dcv,// difference-cover period | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 558 | is, // list of input streams | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 | szs, // list of reference sizes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 | refparams, // reference read-in parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | localindex, // create local indexes? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | parent_szs, // parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 | parent_refnames, // parent refence names | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 | seed, // pseudo-random number generator seed | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 566 | -1, // override offRate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 567 | verbose, // be talkative | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 | sanityCheck); // verify results and internal consistency | ~~~~~~~~~~~~ hisat2_build.cpp:786:39: required from here 786 | driver >(infile, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 787 | infiles, | ~~~~~~~~ 788 | snp_fname, | ~~~~~~~~~~ 789 | ht_fname, | ~~~~~~~~~ 790 | ss_fname, | ~~~~~~~~~ 791 | exon_fname, | ~~~~~~~~~~~ 792 | sv_fname, | ~~~~~~~~~ 793 | dummy_fname, | ~~~~~~~~~~~~ 794 | outfile, | ~~~~~~~~ 795 | false, | ~~~~~~ 796 | REF_READ_FORWARD, | ~~~~~~~~~~~~~~~~~ 797 | true, // create local indexes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 798 | NULL, // no parent szs | ~~~~~~~~~~~~~~~~~~~~~~ 799 | NULL, // no parent refnames | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 | &parent_szs, // get parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 | &parent_refnames); // get parent refnames | ~~~~~~~~~~~~~~~~~ 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 ‘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]; | ^~~~~~~~~~~ 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]; | ^~~~~~~~~~~ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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; | ^~~~~~~~~~~~~~ riscv64-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="\"09 July 2024\"" -DCOMPILER_VERSION="\"`riscv64-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 -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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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]’ 1039 | initFromVector( | ~~~~~~~~~~~~~~~~~~~~^ 1040 | s, | ~~ 1041 | snpfile, | ~~~~~~~~ 1042 | htfile, | ~~~~~~~ 1043 | ssfile, | ~~~~~~~ 1044 | exonfile, | ~~~~~~~~~ 1045 | svfile, | ~~~~~~~ 1046 | repeatfile, | ~~~~~~~~~~~ 1047 | is, | ~~~ 1048 | szs, | ~~~~ 1049 | sztot, | ~~~~~~ 1050 | refparams, | ~~~~~~~~~~ 1051 | fout1, | ~~~~~~ 1052 | fout2, | ~~~~~~ 1053 | outfile, | ~~~~~~~~ 1054 | useBlockwise, | ~~~~~~~~~~~~~ 1055 | bmax, | ~~~~~ 1056 | bmaxSqrtMult, | ~~~~~~~~~~~~~ 1057 | bmaxDivN, | ~~~~~~~~~ 1058 | dcv, | ~~~~ 1059 | parent_szs, | ~~~~~~~~~~~ 1060 | parent_refnames, | ~~~~~~~~~~~~~~~~ 1061 | seed, | ~~~~~ 1062 | verbose); | ~~~~~~~~ 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]’ 1989 | _in6(NULL) | ^ 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]’ 535 | gfm = new HGFM( | ^~~~~~~~~~~~~~~~~~~~~ 536 | s, | ~~ 537 | packed, | ~~~~~~~ 538 | 1, // TODO: maybe not? | ~~~~~~~~~~~~~~~~~~~~~~~ 539 | lineRate, | ~~~~~~~~~ 540 | offRate, // suffix-array sampling rate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 541 | ftabChars, // number of chars in initial arrow-pair calc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 542 | localOffRate, | ~~~~~~~~~~~~~ 543 | localFtabChars, | ~~~~~~~~~~~~~~~ 544 | nthreads, | ~~~~~~~~~ 545 | snpfile, | ~~~~~~~~ 546 | htfile, | ~~~~~~~ 547 | ssfile, | ~~~~~~~ 548 | exonfile, | ~~~~~~~~~ 549 | svfile, | ~~~~~~~ 550 | repeatfile, | ~~~~~~~~~~~ 551 | outfile, // basename for .?.ht2 files | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 552 | reverse == 0, // fw | ~~~~~~~~~~~~~~~~~~~ 553 | !entireSA, // useBlockwise | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 554 | bmax, // block size for blockwise SA builder | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 555 | bmaxMultSqrt, // block size as multiplier of sqrt(len) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 556 | bmaxDivN, // block size as divisor of len | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 557 | noDc? 0 : dcv,// difference-cover period | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 558 | is, // list of input streams | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 559 | szs, // list of reference sizes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 560 | (TIndexOffU)sztot.first, // total size of all unambiguous ref chars | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 561 | refparams, // reference read-in parameters | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 562 | localindex, // create local indexes? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 563 | parent_szs, // parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 564 | parent_refnames, // parent refence names | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 | seed, // pseudo-random number generator seed | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 566 | -1, // override offRate | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 567 | verbose, // be talkative | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 568 | autoMem, // pass exceptions up to the toplevel so that we can adjust memory settings automatically | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 569 | sanityCheck); // verify results and internal consistency | ~~~~~~~~~~~~ hisat2_build.cpp:786:39: required from here 786 | driver >(infile, | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~ 787 | infiles, | ~~~~~~~~ 788 | snp_fname, | ~~~~~~~~~~ 789 | ht_fname, | ~~~~~~~~~ 790 | ss_fname, | ~~~~~~~~~ 791 | exon_fname, | ~~~~~~~~~~~ 792 | sv_fname, | ~~~~~~~~~ 793 | dummy_fname, | ~~~~~~~~~~~~ 794 | outfile, | ~~~~~~~~ 795 | false, | ~~~~~~ 796 | REF_READ_FORWARD, | ~~~~~~~~~~~~~~~~~ 797 | true, // create local indexes | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 798 | NULL, // no parent szs | ~~~~~~~~~~~~~~~~~~~~~~ 799 | NULL, // no parent refnames | ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 800 | &parent_szs, // get parent szs | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 801 | &parent_refnames); // get parent refnames | ~~~~~~~~~~~~~~~~~ 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 ‘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]; | ^~~~~~~~~~~ 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]; | ^~~~~~~~~~~ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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; | ^~~~~~~~~~~~~~ riscv64-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="\"09 July 2024\"" -DCOMPILER_VERSION="\"`riscv64-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 -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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:46: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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]’ 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ 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]’ 5901 | _gws_local.advanceElement( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ 5902 | off, | ~~~~ 5903 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5904 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5905 | _sas_local, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5906 | _gwstate_local, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5907 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5908 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5909 | prm); // per-read metrics | ~~~~ 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]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ 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]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ 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]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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]’ 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ 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]’ 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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>]’ 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, | ~~~~~~~~~~~ 2917 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 2918 | cmp_ht, | ~~~~~~~ 2919 | ht_list, | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ 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>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ 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]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ 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]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ spliced_aligner.h:408:18: warning: variable ‘another_spliced’ set but not used [-Wunused-but-set-variable] 408 | bool another_spliced = false; | ^~~~~~~~~~~~~~~ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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_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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 { | ^~~~ riscv64-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="\"09 July 2024\"" -DCOMPILER_VERSION="\"`riscv64-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 -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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76, from aligner_sw_driver.h:86, from hi_aligner.h:42, from spliced_aligner.h:23, from hisat2.cpp:46: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ 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 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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]’ 4088 | pairReads(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, wlm, prm, him, rnd, sink); | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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]’ 3815 | gfm.checkOrigs(os, false); | ~~~~~~~~~~~~~~^~~~~~~~~~~ hisat2.cpp:4351:26: required from here 4351 | driver >("DNA", bt2index, outfile); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 5525 | index_t numHits = getAnchorHits(gfm, | ^~~~~~~~~~~~~ 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]’ 4080 | found[rdi][fwi] = align(sc, pepol, tpol, gpol, gfm, altdb, repeatdb, ref, swa, ssdb, rdi, fw, wlm, prm, swm, him, rnd, sink); | ^~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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]’ 1517 | st.advance( | ~~~~~~~~~~^ 1518 | gfmFw, | ~~~~~~ 1519 | ref, | ~~~~ 1520 | sa, | ~~~ 1521 | hit_, | ~~~~~ 1522 | (index_t)range, | ~~~~~~~~~~~~~~~ 1523 | false, | ~~~~~~ 1524 | NULL, | ~~~~~ 1525 | st_, | ~~~~ 1526 | gws, | ~~~~ 1527 | met, | ~~~~ 1528 | prm); | ~~~~ 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]’ 5901 | _gws_local.advanceElement( | ~~~~~~~~~~~~~~~~~~~~~~~~~^ 5902 | off, | ~~~~ 5903 | gfm, // forward Bowtie index for walking left | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5904 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5905 | _sas_local, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5906 | _gwstate_local, // GroupWalk state; scratch space | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5907 | wr, // put the result here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5908 | met, // metrics | ~~~~~~~~~~~~~~~~~~~~~~~~ 5909 | prm); // per-read metrics | ~~~~ 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]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ 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]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ 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]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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]’ 494 | return init(gfm, ref, sa, sts, hit, range, reportList, res, met); | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 1453 | st_.back().init( | ~~~~~~~~~~~~~~~^ 1454 | gfmFw, // Bowtie index | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1455 | ref, // bitpair-encoded reference | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1456 | sa, // SA range with offsets | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1457 | st_, // EList | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1458 | hit_, // GWHit | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1459 | 0, // range 0 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1460 | false, // put resolved elements into res_? | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1461 | NULL, // put resolved elements here | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1462 | top, // GBW row at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1463 | bot, // GBW row at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1464 | node_top, // node at top | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1465 | node_bot, // node at bot | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1466 | sa.node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~ 1467 | 0, // # steps taken | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1468 | met); // update metrics here | ~~~~ 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]’ 5896 | _gws_local.init(gfm, ref, _sas_local, rnd, met); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 5664 | getGenomeCoords_local( | ^~~~~~~~~~~~~~~~~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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>]’ 2915 | add_haplotypes(alts, | ~~~~~~~~~~~~~~^~~~~~ 2916 | haplotypes, | ~~~~~~~~~~~ 2917 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 2918 | cmp_ht, | ~~~~~~~ 2919 | ht_list, | ~~~~~~~~ 2920 | rdlen); | ~~~~~~ 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>]’ 717 | alignWithALTs_recur( | ~~~~~~~~~~~~~~~~~~~^ 718 | alts, | ~~~~~ 719 | haplotypes, | ~~~~~~~~~~~ 720 | haplotype_maxrights, | ~~~~~~~~~~~~~~~~~~~~ 721 | joinedOff, | ~~~~~~~~~~ 722 | rdseq, | ~~~~~~ 723 | rdoff - base_rdoff, | ~~~~~~~~~~~~~~~~~~~ 724 | rdoff, | ~~~~~~ 725 | rdlen, | ~~~~~~ 726 | ref, | ~~~~ 727 | sharedVar.raw_refbufs, | ~~~~~~~~~~~~~~~~~~~~~~ 728 | ASSERT_ONLY(sharedVar.destU32,) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 729 | alt_edits, | ~~~~~~~~~~ 730 | best_rdoff, | ~~~~~~~~~~~ 731 | NULL, /* rfseq */ | ~~~~~~~~~~~~~~~~~ 732 | tidx, | ~~~~~ 733 | rfoff, | ~~~~~~ 734 | rflen, | ~~~~~~ 735 | left, | ~~~~~ 736 | edits, | ~~~~~~ 737 | mm, | ~~~ 738 | ht_llist, | ~~~~~~~~~ 739 | cmp_ht, | ~~~~~~~ 740 | candidate_edits, | ~~~~~~~~~~~~~~~~ 741 | 0, /* tmp_numNs */ | ~~~~~~~~~~~~~~~~~~ 742 | numNs, | ~~~~~~ 743 | 0, /* dep */ | ~~~~~~~~~~~~~~~ 744 | gpol, | ~~~~~ 745 | numALTsTried); | ~~~~~~~~~~~~~ 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]’ 2337 | index_t alignedLen = alignWithALTs( | ~~~~~~~~~~~~~^ 2338 | alts, | ~~~~~ 2339 | altdb.haplotypes(), | ~~~~~~~~~~~~~~~~~~~ 2340 | altdb.haplotype_maxrights(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2341 | genomeHit._joinedOff, | ~~~~~~~~~~~~~~~~~~~~~ 2342 | seq, | ~~~~ 2343 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2344 | genomeHit._rdoff, | ~~~~~~~~~~~~~~~~~ 2345 | genomeHit._len, | ~~~~~~~~~~~~~~~ 2346 | ref, | ~~~~ 2347 | sharedVars, | ~~~~~~~~~~~ 2348 | genomeHit._tidx, | ~~~~~~~~~~~~~~~~ 2349 | (int)genomeHit._toff, | ~~~~~~~~~~~~~~~~~~~~~ 2350 | reflen, | ~~~~~~~ 2351 | false, /* left? */ | ~~~~~~~~~~~~~~~~~~ 2352 | gpol, | ~~~~~ 2353 | *genomeHit._edits, | ~~~~~~~~~~~~~~~~~~ 2354 | sharedVars.ht_llist, | ~~~~~~~~~~~~~~~~~~~~ 2355 | *genomeHit._ht_list, | ~~~~~~~~~~~~~~~~~~~~ 2356 | sharedVars.cmp_ht, | ~~~~~~~~~~~~~~~~~~ 2357 | &candidate_edits); | ~~~~~~~~~~~~~~~~~ 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]’ 5692 | GenomeHit::adjustWithALT( | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^ 5693 | hitoff - hitlen + 1, | ~~~~~~~~~~~~~~~~~~~~ 5694 | hitlen, | ~~~~~~~ 5695 | coord, | ~~~~~~ 5696 | _sharedVars, | ~~~~~~~~~~~~ 5697 | _genomeHits, | ~~~~~~~~~~~~ 5698 | *this->_rds[ordi], | ~~~~~~~~~~~~~~~~~~ 5699 | gfm, | ~~~~ 5700 | altdb, | ~~~~~~ 5701 | ref, | ~~~~ 5702 | gpol); | ~~~~~ 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]’ 4107 | mate_found |= alignMate( | ^~~~~~~~~ hisat2.cpp:3537:48: required from here 3537 | int ret = splicedAligner.go( | ~~~~~~~~~~~~~~~~~^ 3538 | sc, | ~~~ 3539 | pepol, | ~~~~~~ 3540 | *multiseed_tpol, | ~~~~~~~~~~~~~~~~ 3541 | *gpol, | ~~~~~~ 3542 | gfm, | ~~~~ 3543 | rgfm, | ~~~~~ 3544 | *altdb, | ~~~~~~~ 3545 | *repeatdb, | ~~~~~~~~~~ 3546 | *raltdb, | ~~~~~~~~ 3547 | ref, | ~~~~ 3548 | rref, | ~~~~~ 3549 | sw, | ~~~ 3550 | *ssdb, | ~~~~~~ 3551 | wlm, | ~~~~ 3552 | prm, | ~~~~ 3553 | swmSeed, | ~~~~~~~~ 3554 | him, | ~~~~ 3555 | rnd, | ~~~~ 3556 | msinkwrap); | ~~~~~~~~~~ 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 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 1086 | index_t nelt = this->globalGFMSearch( | ~~~~~~~~~~~~~~~~~~~~~^ 1087 | gfm, // GFM index | ~~~~~~~~~~~~~~~~~~~~ 1088 | rd, // read to align | ~~~~~~~~~~~~~~~~~~~~~~~~ 1089 | sc, // scoring scheme | ~~~~~~~~~~~~~~~~~~~~~~~~~ 1090 | sink.reportingParams(), | ~~~~~~~~~~~~~~~~~~~~~~~ 1091 | hit.fw(), | ~~~~~~~~~ 1092 | extoff, | ~~~~~~~ 1093 | extlen, | ~~~~~~~ 1094 | top, | ~~~~ 1095 | bot, | ~~~~ 1096 | node_top, | ~~~~~~~~~ 1097 | node_bot, | ~~~~~~~~~ 1098 | this->_node_iedge_count, | ~~~~~~~~~~~~~~~~~~~~~~~~ 1099 | rnd, | ~~~~ 1100 | uniqueStop); | ~~~~~~~~~~~ spliced_aligner.h:331:9: required from here 331 | int64_t SplicedAligner::hybridSearch_recur( | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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_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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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 722 | _exons.push_back_array(exons.begin(), exons.size()); | ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 { | ^~~~ riscv64-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="\"09 July 2024\"" -DCOMPILER_VERSION="\"`riscv64-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 -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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ riscv64-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="\"09 July 2024\"" -DCOMPILER_VERSION="\"`riscv64-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 -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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ riscv64-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="\"09 July 2024\"" -DCOMPILER_VERSION="\"`riscv64-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 -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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76, from hisat2_repeat.cpp:37: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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/riscv64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | 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/riscv64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ In file included from aligner_sw.h:76: aligner_sw_nuc.h: At global scope: aligner_sw_nuc.h:191:17: warning: template-id not allowed for constructor in C++20 [-Wtemplate-id-cdtor] 191 | NBest() { nelt_ = nbest_ = n_ = 0; } | ^ aligner_sw_nuc.h:191:17: note: remove the ‘< >’ 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 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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 4754 | template void dump_tstr(const SString& ); | ^ 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]’ 3312 | query = getString(s_, i, rp.min_repeat_len); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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]’ 3545 | getString(s_, saElt, rp.min_repeat_len, query); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ repeat_builder.cpp:4753:16: required from here 4753 | template class RepeatBuilder >; | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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/riscv64-linux-gnu/include/c++/14/iostream:41, 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/riscv64-linux-gnu/include/c++/14/ostream:179:25: warning: ‘pos_in_chr’ may be used uninitialized [-Wmaybe-uninitialized] 179 | { 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 2025-02-09T08:02:03Z +------------------------------------------------------------------------------+ | Finished Timed Build Commands | +------------------------------------------------------------------------------+ rm -Rf /<>/ ----------------------------------------- I: Finished running 'rm -Rf /<>/'. Finished processing commands. -------------------------------------------------------------------------------- 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: n/a Build-Time: 468 Distribution: unstable Fail-Stage: build Foreign Architectures: riscv64 Host Architecture: riscv64 Install-Time: 13 Job: hisat2_2.2.1-5 Machine Architecture: amd64 Package: hisat2 Package-Time: 492 Source-Version: 2.2.1-5 Space: n/a Status: attempted Version: 2.2.1-5 -------------------------------------------------------------------------------- Finished at 2025-02-09T08:02:03Z Build needed 00:08:12, no disk space