sbuild (Debian sbuild) 0.85.0 (04 January 2023) on debian-ci-siliconvalley +==============================================================================+ | hisat2 2.2.1-5 (arm64) Fri, 03 Jan 2025 07:33:38 +0000 | +==============================================================================+ Package: hisat2 Version: 2.2.1-5 Source Version: 2.2.1-5 Distribution: unstable Machine Architecture: amd64 Host Architecture: arm64 Build Architecture: amd64 Build Profiles: cross nocheck Build Type: any I: NOTICE: Log filtering will replace 'var/run/schroot/mount/sid-amd64-sbuild-369edb16-63ea-411f-b444-81566466a189' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-uAsS9Y/resolver-DVsz7x' with '<>' +------------------------------------------------------------------------------+ | Update chroot | +------------------------------------------------------------------------------+ Get:1 http://localhost:3142/debian unstable InRelease [205 kB] Get:2 http://localhost:3142/debian unstable/contrib Sources [62.7 kB] Get:3 http://localhost:3142/debian unstable/non-free Sources [82.8 kB] Get:4 http://localhost:3142/debian unstable/main Sources [10.8 MB] Get:5 http://localhost:3142/debian unstable/non-free-firmware Sources [6884 B] Get:6 http://localhost:3142/debian unstable/main arm64 Packages [9913 kB] Get:7 http://localhost:3142/debian unstable/main amd64 Packages [9999 kB] Fetched 31.1 MB in 3s (11.6 MB/s) Reading package lists... Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: gpgv libffi8 libgcrypt20 libgnutls30t64 libgpg-error0 libidn2-0 libp11-kit0 libtasn1-6 libunistring5 Use 'apt autoremove' to remove them. The following NEW packages will be installed: sqv The following packages will be upgraded: apt base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu bsdutils coreutils cpp-14 cpp-14-x86-64-linux-gnu debconf debianutils dpkg dpkg-dev e2fsprogs g++-14 g++-14-x86-64-linux-gnu gcc-14 gcc-14-base gcc-14-x86-64-linux-gnu gpgv gzip init-system-helpers libacl1 libapt-pkg6.0t64 libasan8 libatomic1 libaudit-common libaudit1 libbinutils libblkid1 libc-bin libc-dev-bin libc6 libc6-dev libcap-ng0 libcap2 libcc1-0 libcom-err2 libctf-nobfd0 libctf0 libdebconfclient0 libdpkg-perl libext2fs2t64 libgcc-14-dev libgcc-s1 libgcrypt20 libgmp10 libgnutls30t64 libgomp1 libgpg-error0 libgprofng0 libhogweed6t64 libhwasan0 libidn2-0 libitm1 libjansson4 liblsan0 liblz4-1 liblzma5 libmd0 libmount1 libmpc3 libmpfr6 libnettle8t64 libp11-kit0 libpam-modules libpam-modules-bin libpam0g libpcre2-8-0 libperl5.40 libquadmath0 libseccomp2 libselinux1 libsemanage2 libsframe1 libsmartcols1 libss2 libssl3t64 libstdc++-14-dev libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtsan2 libubsan1 libudev1 libunistring5 libuuid1 libxxhash0 libzstd1 linux-libc-dev login login.defs logsave make mount ncurses-bin openssl-provider-legacy passwd perl perl-base perl-modules-5.40 sysvinit-utils tar tzdata util-linux xz-utils zlib1g 110 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 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Get:12 http://localhost:3142/debian unstable/main amd64 libtsan2 amd64 14.2.0-12 [2460 kB] Get:13 http://localhost:3142/debian unstable/main amd64 libubsan1 amd64 14.2.0-12 [1075 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libhwasan0 amd64 14.2.0-12 [1489 kB] Get:15 http://localhost:3142/debian unstable/main amd64 libquadmath0 amd64 14.2.0-12 [145 kB] Get:16 http://localhost:3142/debian unstable/main amd64 gcc-14 amd64 14.2.0-12 [534 kB] Get:17 http://localhost:3142/debian unstable/main amd64 g++-14 amd64 14.2.0-12 [20.5 kB] Get:18 http://localhost:3142/debian unstable/main amd64 g++-14-x86-64-linux-gnu amd64 14.2.0-12 [12.1 MB] Get:19 http://localhost:3142/debian unstable/main amd64 libstdc++-14-dev amd64 14.2.0-12 [2372 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libgcc-14-dev amd64 14.2.0-12 [2673 kB] Get:21 http://localhost:3142/debian unstable/main amd64 gcc-14-x86-64-linux-gnu amd64 14.2.0-12 [21.4 MB] Get:22 http://localhost:3142/debian unstable/main amd64 cpp-14-x86-64-linux-gnu amd64 14.2.0-12 [11.0 MB] Get:23 http://localhost:3142/debian unstable/main amd64 cpp-14 amd64 14.2.0-12 [1280 B] Get:24 http://localhost:3142/debian unstable/main amd64 libstdc++6 amd64 14.2.0-12 [714 kB] Get:25 http://localhost:3142/debian unstable/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libgprofng0 amd64 2.43.50.20241230-1 [809 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libctf0 amd64 2.43.50.20241230-1 [88.5 kB] Get:28 http://localhost:3142/debian unstable/main amd64 libctf-nobfd0 amd64 2.43.50.20241230-1 [155 kB] Get:29 http://localhost:3142/debian unstable/main amd64 libjansson4 amd64 2.14-2+b3 [39.8 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libsframe1 amd64 2.43.50.20241230-1 [77.6 kB] Get:31 http://localhost:3142/debian unstable/main amd64 libzstd1 amd64 1.5.6+dfsg-2 [300 kB] Get:32 http://localhost:3142/debian unstable/main 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Get:43 http://localhost:3142/debian unstable/main amd64 bsdutils amd64 1:2.40.2-13 [106 kB] Get:44 http://localhost:3142/debian unstable/main amd64 coreutils amd64 9.5-1+b1 [2922 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libxxhash0 amd64 0.8.2-2+b2 [26.6 kB] Get:46 http://localhost:3142/debian unstable/main amd64 liblz4-1 amd64 1.9.4-4 [60.1 kB] Get:47 http://localhost:3142/debian unstable/main amd64 liblzma5 amd64 5.6.3-1+b1 [272 kB] Get:48 http://localhost:3142/debian unstable/main amd64 openssl-provider-legacy amd64 3.3.2-2 [298 kB] Get:49 http://localhost:3142/debian unstable/main amd64 libssl3t64 amd64 3.3.2-2 [2271 kB] Get:50 http://localhost:3142/debian unstable/main amd64 libcap2 amd64 1:2.66-5+b1 [27.8 kB] Get:51 http://localhost:3142/debian unstable/main amd64 libsystemd0 amd64 257.1-5 [449 kB] Get:52 http://localhost:3142/debian unstable/main amd64 libudev1 amd64 257.1-5 [148 kB] Get:53 http://localhost:3142/debian unstable/main amd64 libapt-pkg6.0t64 amd64 2.9.21 [1115 kB] Get:54 http://localhost:3142/debian unstable/main amd64 tar amd64 1.35+dfsg-3.1 [815 kB] Get:55 http://localhost:3142/debian unstable/main amd64 dpkg amd64 1.22.12 [1533 kB] Get:56 http://localhost:3142/debian unstable/main amd64 gzip amd64 1.12-1.2 [134 kB] Get:57 http://localhost:3142/debian unstable/main amd64 ncurses-bin amd64 6.5-2+b1 [434 kB] Get:58 http://localhost:3142/debian unstable/main amd64 libperl5.40 amd64 5.40.0-8 [4320 kB] Get:59 http://localhost:3142/debian unstable/main amd64 perl amd64 5.40.0-8 [267 kB] Get:60 http://localhost:3142/debian unstable/main amd64 perl-base amd64 5.40.0-8 [1675 kB] Get:61 http://localhost:3142/debian unstable/main amd64 perl-modules-5.40 all 5.40.0-8 [3015 kB] Get:62 http://localhost:3142/debian unstable/main amd64 libuuid1 amd64 2.40.2-13 [36.1 kB] Get:63 http://localhost:3142/debian unstable/main amd64 libblkid1 amd64 2.40.2-13 [168 kB] Get:64 http://localhost:3142/debian unstable/main amd64 libmount1 amd64 2.40.2-13 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libpam-modules amd64 1.5.3-7+b1 [267 kB] Get:87 http://localhost:3142/debian unstable/main amd64 logsave amd64 1.47.2-1 [23.9 kB] Get:88 http://localhost:3142/debian unstable/main amd64 libext2fs2t64 amd64 1.47.2-1 [212 kB] Get:89 http://localhost:3142/debian unstable/main amd64 e2fsprogs amd64 1.47.2-1 [590 kB] Get:90 http://localhost:3142/debian unstable/main amd64 login amd64 1:4.16.0-2+really2.40.2-13 [81.9 kB] Get:91 http://localhost:3142/debian unstable/main amd64 libgpg-error0 amd64 1.51-3 [82.2 kB] Get:92 http://localhost:3142/debian unstable/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB] Get:93 http://localhost:3142/debian unstable/main amd64 gpgv amd64 2.2.45-2 [219 kB] Get:94 http://localhost:3142/debian unstable/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB] Get:95 http://localhost:3142/debian unstable/main amd64 libunistring5 amd64 1.3-1 [476 kB] Get:96 http://localhost:3142/debian unstable/main amd64 libidn2-0 amd64 2.3.7-2+b1 [129 kB] Get:97 http://localhost:3142/debian unstable/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB] Get:98 http://localhost:3142/debian unstable/main amd64 libtasn1-6 amd64 4.19.0-3+b3 [49.5 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libmd0 amd64 1.1.0-2+b1 [36.3 kB] Get:101 http://localhost:3142/debian unstable/main amd64 libtinfo6 amd64 6.5-2+b1 [344 kB] Get:102 http://localhost:3142/debian unstable/main amd64 login.defs all 1:4.16.0-7 [185 kB] Get:103 http://localhost:3142/debian unstable/main amd64 libsemanage2 amd64 3.7-2+b1 [91.2 kB] Get:104 http://localhost:3142/debian unstable/main amd64 passwd amd64 1:4.16.0-7 [1233 kB] Get:105 http://localhost:3142/debian unstable/main amd64 tzdata all 2024b-4 [256 kB] Get:106 http://localhost:3142/debian unstable/main amd64 xz-utils amd64 5.6.3-1+b1 [542 kB] Get:107 http://localhost:3142/debian unstable/main amd64 dpkg-dev all 1.22.12 [1332 kB] Get:108 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13032 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.21_amd64.deb ... Unpacking apt (2.9.21) over (2.9.8) ... Setting up apt (2.9.21) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13026 files and directories currently installed.) Preparing to unpack .../libc-bin_2.40-4_amd64.deb ... Unpacking libc-bin (2.40-4) over (2.40-3) ... Setting up libc-bin (2.40-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13026 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.11-1_amd64.deb ... Unpacking sysvinit-utils (3.11-1) over (3.10-3) ... Setting up sysvinit-utils (3.11-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13026 files and directories currently installed.) Preparing to unpack .../libpam0g_1.5.3-7+b1_amd64.deb ... Unpacking libpam0g:amd64 (1.5.3-7+b1) over (1.5.3-7) ... Setting up libpam0g:amd64 (1.5.3-7+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13027 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-7+b1_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-7+b1) over (1.5.3-7) ... Setting up libpam-modules-bin (1.5.3-7+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13028 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-7+b1_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-7+b1) over (1.5.3-7) ... Setting up libpam-modules:amd64 (1.5.3-7+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13029 files and directories currently installed.) Preparing to unpack .../logsave_1.47.2-1_amd64.deb ... Unpacking logsave (1.47.2-1) over (1.47.1-1) ... Preparing to unpack .../libext2fs2t64_1.47.2-1_amd64.deb ... Leaving 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Leaving 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:amd64 (1.47.2-1) over (1.47.1-1) ... Setting up libext2fs2t64:amd64 (1.47.2-1) ... (Reading database ... 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Setting up libgpg-error0:amd64 (1.51-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13029 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.11.0-7_amd64.deb ... Unpacking libgcrypt20:amd64 (1.11.0-7) over (1.11.0-6) ... Setting up libgcrypt20:amd64 (1.11.0-7) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13030 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.7-2+b1_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.7-2+b1) over (2.3.7-2) ... Setting up libidn2-0:amd64 (2.3.7-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.5-3_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-3) over (0.25.5-2) ... Setting up libp11-kit0:amd64 (0.25.5-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-3+b3_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-3+b3) over (4.19.0-3+b2) ... Setting up libtasn1-6:amd64 (4.19.0-3+b3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.8-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.8-2) over (3.8.6-2) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13031 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2+b1_amd64.deb ... Unpacking libmd0:amd64 (1.1.0-2+b1) over (1.1.0-2) ... Setting up libmd0:amd64 (1.1.0-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13032 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.5-2+b1_amd64.deb ... Unpacking libtinfo6:amd64 (6.5-2+b1) over (6.5-2) ... Setting up libtinfo6:amd64 (6.5-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13033 files and directories currently installed.) Preparing to unpack .../0-login.defs_1%3a4.16.0-7_all.deb ... Unpacking login.defs (1:4.16.0-7) over (1:4.16.0-4) ... Preparing to unpack .../1-libsemanage2_3.7-2+b1_amd64.deb ... Unpacking libsemanage2:amd64 (3.7-2+b1) over (3.7-2) ... Preparing to unpack .../2-passwd_1%3a4.16.0-7_amd64.deb ... Unpacking passwd (1:4.16.0-7) over (1:4.16.0-4) ... Preparing to unpack .../3-tzdata_2024b-4_all.deb ... Unpacking tzdata (2024b-4) over (2024b-3) ... Preparing to unpack .../4-xz-utils_5.6.3-1+b1_amd64.deb ... Unpacking xz-utils (5.6.3-1+b1) over (5.6.2-2) ... Preparing to unpack .../5-dpkg-dev_1.22.12_all.deb ... Unpacking dpkg-dev (1.22.12) over (1.22.11) ... Preparing to unpack .../6-libdpkg-perl_1.22.12_all.deb ... Unpacking libdpkg-perl (1.22.12) over (1.22.11) ... Preparing to unpack .../7-make_4.4.1-1_amd64.deb ... Unpacking make (4.4.1-1) over (4.3-4.1) ... Preparing to unpack .../8-libcom-err2_1.47.2-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.2-1) over (1.47.1-1) ... Preparing to unpack .../9-libss2_1.47.2-1_amd64.deb ... Unpacking libss2:amd64 (1.47.2-1) over (1.47.1-1) ... Setting up login.defs (1:4.16.0-7) ... Installing new version of config file /etc/login.defs ... Setting up binutils-common:amd64 (2.43.50.20241230-1) ... Setting up linux-libc-dev (6.12.8-1) ... Setting up libctf-nobfd0:amd64 (2.43.50.20241230-1) ... Setting up libcom-err2:amd64 (1.47.2-1) ... Setting up libgomp1:amd64 (14.2.0-12) ... Setting up libsframe1:amd64 (2.43.50.20241230-1) ... Setting up libjansson4:amd64 (2.14-2+b3) ... Setting up tzdata (2024b-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Jan 3 07:33:55 UTC 2025. Universal Time is now: Fri Jan 3 07:33:55 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up make (4.4.1-1) ... Setting up libmpfr6:amd64 (4.2.1-1+b2) ... Setting up xz-utils (5.6.3-1+b1) ... Setting up libquadmath0:amd64 (14.2.0-12) ... Setting up libmpc3:amd64 (1.3.1-1+b3) ... Setting up libatomic1:amd64 (14.2.0-12) ... Setting up libss2:amd64 (1.47.2-1) ... Setting up cpp-14-x86-64-linux-gnu (14.2.0-12) ... Setting up logsave (1.47.2-1) ... Setting up cpp-14 (14.2.0-12) ... Setting up libubsan1:amd64 (14.2.0-12) ... Setting up mount (2.40.2-13) ... Setting up perl-modules-5.40 (5.40.0-8) ... Setting up libhwasan0:amd64 (14.2.0-12) ... Setting up libasan8:amd64 (14.2.0-12) ... Setting up libsemanage2:amd64 (3.7-2+b1) ... Setting up libtsan2:amd64 (14.2.0-12) ... Setting up libbinutils:amd64 (2.43.50.20241230-1) ... Setting up libc-dev-bin (2.40-4) ... Setting up libcc1-0:amd64 (14.2.0-12) ... Setting up liblsan0:amd64 (14.2.0-12) ... Setting up libitm1:amd64 (14.2.0-12) ... Setting up login (1:4.16.0-2+really2.40.2-13) ... Setting up libctf0:amd64 (2.43.50.20241230-1) ... Setting up e2fsprogs (1.47.2-1) ... Setting up libperl5.40:amd64 (5.40.0-8) ... Setting up perl (5.40.0-8) ... Setting up libgprofng0:amd64 (2.43.50.20241230-1) ... Setting up libdpkg-perl (1.22.12) ... Setting up passwd (1:4.16.0-7) ... Setting up libc6-dev:amd64 (2.40-4) ... Setting up libgcc-14-dev:amd64 (14.2.0-12) ... Setting up libstdc++-14-dev:amd64 (14.2.0-12) ... Setting up binutils-x86-64-linux-gnu (2.43.50.20241230-1) ... Setting up binutils (2.43.50.20241230-1) ... Setting up dpkg-dev (1.22.12) ... Setting up gcc-14-x86-64-linux-gnu (14.2.0-12) ... Setting up gcc-14 (14.2.0-12) ... Setting up g++-14-x86-64-linux-gnu (14.2.0-12) ... Setting up g++-14 (14.2.0-12) ... Processing triggers for debianutils (5.21) ... Processing triggers for libc-bin (2.40-4) ... +------------------------------------------------------------------------------+ | 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 (19.0 MB/s) Download complete and in download only mode I: NOTICE: Log filtering will replace 'build/hisat2-uAsS9Y/hisat2-2.2.1' with '<>' I: NOTICE: Log filtering will replace 'build/hisat2-uAsS9Y' 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-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 Filtered Build-Depends: debhelper-compat (= 13), libsimde-dev, help2man, pandoc, python3:any, libc-dev, libstdc++-dev, build-essential:amd64, fakeroot:amd64, crossbuild-essential-arm64:amd64, libc-dev:arm64, libstdc++-dev:arm64 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 [786 B] Get:5 copy:/<>/apt_archive ./ Packages [802 B] Fetched 2197 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 packages were automatically installed and are no longer required: libgnutls30t64 libidn2-0 libp11-kit0 libtasn1-6 Use 'apt autoremove' to remove them. The following additional packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-14-aarch64-linux-gnu gcc-14-aarch64-linux-gnu-base gcc-14-base:arm64 gcc-14-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev:arm64 libgcc-14-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2 libhwasan0:arm64 libhwasan0-arm64-cross libicu72 libitm1:arm64 libitm1-arm64-cross libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross liblua5.4-0 libmagic-mgc libmagic1t64 libncursesw6 libnsl2 libnuma1 libpipeline1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 libsimde-dev libsqlite3-0 libstdc++-14-dev:arm64 libstdc++-14-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libtirpc-common libtirpc3t64 libtool libtsan2:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml2 libyaml-0-2 linux-libc-dev-arm64-cross m4 man-db media-types netbase pandoc pandoc-data po-debconf python3 python3-minimal python3.12 python3.12-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-aarch64-linux-gnu gcc-doc gettext-doc libasprintf-dev libgettextpo-dev groff glibc-doc:arm64 libc-l10n:arm64 locales:arm64 libnss-nis:arm64 libnss-nisplus:arm64 manpages-dev:arm64 krb5-doc krb5-user libstdc++-14-doc:arm64 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 python3.12-venv python3.12-doc binfmt-support readline-doc Recommended packages: curl | wget | lynx libidn2-0:arm64 libarchive-cpio-perl krb5-locales libgpm2 libltdl-dev libmail-sendmail-perl ca-certificates The following NEW packages will be installed: autoconf automake autopoint autotools-dev binutils-aarch64-linux-gnu bsdextrautils cpp-14-aarch64-linux-gnu cpp-aarch64-linux-gnu crossbuild-essential-arm64 debhelper dh-autoreconf dh-strip-nondeterminism dwz fakeroot file g++-14-aarch64-linux-gnu g++-aarch64-linux-gnu gcc-14-aarch64-linux-gnu gcc-14-aarch64-linux-gnu-base gcc-14-base:arm64 gcc-14-cross-base gcc-aarch64-linux-gnu gettext gettext-base groff-base help2man intltool-debian libarchive-zip-perl libasan8:arm64 libasan8-arm64-cross libatomic1:arm64 libatomic1-arm64-cross libc6:arm64 libc6-arm64-cross libc6-dev:arm64 libc6-dev-arm64-cross libcrypt-dev:arm64 libcrypt1:arm64 libdebhelper-perl libelf1t64 libexpat1 libfakeroot libfile-stripnondeterminism-perl libgcc-14-dev:arm64 libgcc-14-dev-arm64-cross libgcc-s1:arm64 libgcc-s1-arm64-cross libgomp1:arm64 libgomp1-arm64-cross libgssapi-krb5-2 libhwasan0:arm64 libhwasan0-arm64-cross libicu72 libitm1:arm64 libitm1-arm64-cross libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblocale-gettext-perl liblsan0:arm64 liblsan0-arm64-cross liblua5.4-0 libmagic-mgc libmagic1t64 libncursesw6 libnsl2 libnuma1 libpipeline1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 libsimde-dev libsqlite3-0 libstdc++-14-dev:arm64 libstdc++-14-dev-arm64-cross libstdc++6:arm64 libstdc++6-arm64-cross libtirpc-common libtirpc3t64 libtool libtsan2:arm64 libtsan2-arm64-cross libubsan1:arm64 libubsan1-arm64-cross libuchardet0 libxml2 libyaml-0-2 linux-libc-dev-arm64-cross m4 man-db media-types netbase pandoc pandoc-data po-debconf python3 python3-minimal python3.12 python3.12-minimal readline-common sbuild-build-depends-main-dummy:arm64 sensible-utils 0 upgraded, 104 newly installed, 0 to remove and 0 not upgraded. Need to get 135 MB of archives. After this operation, 681 MB of additional disk space will be used. Get:1 copy:/<>/apt_archive ./ sbuild-build-depends-main-dummy 0.invalid.0 [944 B] Get:2 http://localhost:3142/debian unstable/main amd64 liblocale-gettext-perl amd64 1.07-7+b1 [15.3 kB] Get:3 http://localhost:3142/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.8-3 [817 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 python3.12-minimal amd64 3.12.8-3 [2162 kB] Get:6 http://localhost:3142/debian unstable/main amd64 python3-minimal amd64 3.12.8-1 [26.9 kB] Get:7 http://localhost:3142/debian unstable/main amd64 media-types all 10.1.0 [26.9 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 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:10 http://localhost:3142/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:11 http://localhost:3142/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:12 http://localhost:3142/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:13 http://localhost:3142/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:14 http://localhost:3142/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:15 http://localhost:3142/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:16 http://localhost:3142/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:17 http://localhost:3142/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get:18 http://localhost:3142/debian unstable/main amd64 readline-common all 8.2-6 [69.4 kB] Get:19 http://localhost:3142/debian unstable/main amd64 libreadline8t64 amd64 8.2-6 [169 kB] Get:20 http://localhost:3142/debian unstable/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:21 http://localhost:3142/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.8-3 [1969 kB] Get:22 http://localhost:3142/debian unstable/main amd64 python3.12 amd64 3.12.8-3 [677 kB] Get:23 http://localhost:3142/debian unstable/main amd64 libpython3-stdlib amd64 3.12.8-1 [9788 B] Get:24 http://localhost:3142/debian unstable/main amd64 python3 amd64 3.12.8-1 [27.9 kB] Get:25 http://localhost:3142/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get:26 http://localhost:3142/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get:27 http://localhost:3142/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get:28 http://localhost:3142/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get:29 http://localhost:3142/debian unstable/main amd64 gettext-base amd64 0.22.5-3 [200 kB] Get:30 http://localhost:3142/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get:31 http://localhost:3142/debian unstable/main amd64 groff-base amd64 1.23.0-7 [1185 kB] Get:32 http://localhost:3142/debian unstable/main amd64 bsdextrautils amd64 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http://localhost:3142/debian unstable/main amd64 cpp-aarch64-linux-gnu amd64 4:14.2.0-1 [4844 B] Get:44 http://localhost:3142/debian unstable/main amd64 gcc-14-cross-base all 14.2.0-12cross1 [43.7 kB] Get:45 http://localhost:3142/debian unstable/main amd64 libc6-arm64-cross all 2.40-4cross1 [1141 kB] Get:46 http://localhost:3142/debian unstable/main amd64 libgcc-s1-arm64-cross all 14.2.0-12cross1 [54.1 kB] Get:47 http://localhost:3142/debian unstable/main amd64 libgomp1-arm64-cross all 14.2.0-12cross1 [91.7 kB] Get:48 http://localhost:3142/debian unstable/main amd64 libitm1-arm64-cross all 14.2.0-12cross1 [25.9 kB] Get:49 http://localhost:3142/debian unstable/main amd64 libatomic1-arm64-cross all 14.2.0-12cross1 [10.3 kB] Get:50 http://localhost:3142/debian unstable/main amd64 libasan8-arm64-cross all 14.2.0-12cross1 [435 kB] Get:51 http://localhost:3142/debian unstable/main amd64 liblsan0-arm64-cross all 14.2.0-12cross1 [202 kB] Get:52 http://localhost:3142/debian unstable/main amd64 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libstdc++-14-dev-arm64-cross all 14.2.0-12cross1 [2563 kB] Get:62 http://localhost:3142/debian unstable/main amd64 g++-14-aarch64-linux-gnu amd64 14.2.0-12cross1 [12.2 MB] Get:63 http://localhost:3142/debian unstable/main amd64 g++-aarch64-linux-gnu amd64 4:14.2.0-1 [1200 B] Get:64 http://localhost:3142/debian unstable/main amd64 crossbuild-essential-arm64 all 12.12 [3548 B] Get:65 http://localhost:3142/debian unstable/main amd64 libdebhelper-perl all 13.23 [90.6 kB] Get:66 http://localhost:3142/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get:67 http://localhost:3142/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get:68 http://localhost:3142/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get:69 http://localhost:3142/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get:70 http://localhost:3142/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get:71 http://localhost:3142/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:72 http://localhost:3142/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get:73 http://localhost:3142/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:74 http://localhost:3142/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:75 http://localhost:3142/debian unstable/main amd64 gettext amd64 0.22.5-3 [1600 kB] Get:76 http://localhost:3142/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get:77 http://localhost:3142/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get:78 http://localhost:3142/debian unstable/main amd64 debhelper all 13.23 [919 kB] Get:79 http://localhost:3142/debian unstable/main amd64 libfakeroot amd64 1.36.2-1 [29.6 kB] Get:80 http://localhost:3142/debian unstable/main amd64 fakeroot amd64 1.36.2-1 [75.4 kB] Get:81 http://localhost:3142/debian unstable/main arm64 gcc-14-base arm64 14.2.0-12 [48.3 kB] Get:82 http://localhost:3142/debian unstable/main amd64 help2man amd64 1.49.3 [198 kB] Get:83 http://localhost:3142/debian unstable/main arm64 libgcc-s1 arm64 14.2.0-12 [54.1 kB] Get:84 http://localhost:3142/debian unstable/main arm64 libc6 arm64 2.40-4 [2457 kB] Get:85 http://localhost:3142/debian unstable/main arm64 libasan8 arm64 14.2.0-12 [2577 kB] Get:86 http://localhost:3142/debian unstable/main arm64 libatomic1 arm64 14.2.0-12 [10.1 kB] Get:87 http://localhost:3142/debian unstable/main arm64 libcrypt1 arm64 1:4.4.36-5 [91.6 kB] Get:88 http://localhost:3142/debian unstable/main arm64 libcrypt-dev arm64 1:4.4.36-5 [122 kB] Get:89 http://localhost:3142/debian unstable/main arm64 libc6-dev arm64 2.40-4 [1591 kB] Get:90 http://localhost:3142/debian unstable/main arm64 libgomp1 arm64 14.2.0-12 [124 kB] Get:91 http://localhost:3142/debian unstable/main arm64 libitm1 arm64 14.2.0-12 [24.1 kB] Get:92 http://localhost:3142/debian unstable/main arm64 liblsan0 arm64 14.2.0-12 [1161 kB] Get:93 http://localhost:3142/debian unstable/main arm64 libtsan2 arm64 14.2.0-12 [2386 kB] Get:94 http://localhost:3142/debian unstable/main arm64 libstdc++6 arm64 14.2.0-12 [637 kB] Get:95 http://localhost:3142/debian unstable/main arm64 libubsan1 arm64 14.2.0-12 [1039 kB] Get:96 http://localhost:3142/debian unstable/main arm64 libhwasan0 arm64 14.2.0-12 [1442 kB] Get:97 http://localhost:3142/debian unstable/main arm64 libgcc-14-dev arm64 14.2.0-12 [2367 kB] Get:98 http://localhost:3142/debian unstable/main amd64 liblua5.4-0 amd64 5.4.7-1+b1 [147 kB] Get:99 http://localhost:3142/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get:100 http://localhost:3142/debian unstable/main amd64 libsimde-dev all 0.8.2-2 [467 kB] Get:101 http://localhost:3142/debian unstable/main arm64 libstdc++-14-dev arm64 14.2.0-12 [2312 kB] Get:102 http://localhost:3142/debian unstable/main amd64 libyaml-0-2 amd64 0.2.5-2 [52.5 kB] Get:103 http://localhost:3142/debian unstable/main amd64 pandoc-data all 3.1.11.1-3 [459 kB] Get:104 http://localhost:3142/debian unstable/main amd64 pandoc amd64 3.1.11.1+ds-2 [26.4 MB] Preconfiguring packages ... Fetched 135 MB in 1s (191 MB/s) Selecting previously unselected package liblocale-gettext-perl. (Reading database ... 13033 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 libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.8-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.8-3) ... 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 python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.8-3_amd64.deb ... Unpacking python3.12-minimal (3.12.8-3) ... Setting up libpython3.12-minimal:amd64 (3.12.8-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.8-3) ... Selecting previously unselected package python3-minimal. (Reading database ... 13368 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.8-1_amd64.deb ... Unpacking python3-minimal (3.12.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../03-libncursesw6_6.5-2+b1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2+b1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../05-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../07-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../08-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../09-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../10-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../11-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../12-readline-common_8.2-6_all.deb ... Unpacking readline-common (8.2-6) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../13-libreadline8t64_8.2-6_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-6) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../14-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.8-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.8-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.8-3_amd64.deb ... Unpacking python3.12 (3.12.8-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.8-1) ... Setting up python3-minimal (3.12.8-1) ... Selecting previously unselected package python3. (Reading database ... 13927 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.8-1_amd64.deb ... Unpacking python3 (3.12.8-1) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../02-libmagic-mgc_1%3a5.45-3+b1_amd64.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:amd64. 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Setting up libicu72:amd64 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-13) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up gcc-14-base:arm64 (14.2.0-12) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libyaml-0-2:amd64 (0.2.5-2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libdebhelper-perl (13.23) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libmagic1t64:amd64 (1:5.45-3+b1) ... Setting up gettext-base (0.22.5-3) ... Setting up m4 (1.4.19-4) ... Setting up binutils-aarch64-linux-gnu (2.43.50.20241230-1) ... Setting up gcc-14-cross-base (14.2.0-12cross1) ... Setting up file (1:5.45-3+b1) ... Setting up libfakeroot:amd64 (1.36.2-1) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up fakeroot (1.36.2-1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up autotools-dev (20220109.1) ... Setting up libc6-arm64-cross (2.40-4cross1) ... Setting up autopoint (0.22.5-3) ... Setting up libitm1-arm64-cross (14.2.0-12cross1) ... Setting up libncursesw6:amd64 (6.5-2+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up autoconf (2.72-3) ... Setting up linux-libc-dev-arm64-cross (6.12.6-1cross1) ... Setting up libnuma1:amd64 (2.0.18-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:amd64 (0.0.8-1+b2) ... Setting up liblua5.4-0:amd64 (5.4.7-1+b1) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up pandoc-data (3.1.11.1-3) ... Setting up gcc-14-aarch64-linux-gnu-base:amd64 (14.2.0-12cross1) ... Setting up readline-common (8.2-6) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up liblocale-gettext-perl (1.07-7+b1) ... Setting up libgcc-s1-arm64-cross (14.2.0-12cross1) ... Setting up libatomic1-arm64-cross (14.2.0-12cross1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up liblsan0-arm64-cross (14.2.0-12cross1) ... Setting up libgomp1-arm64-cross (14.2.0-12cross1) ... Setting up gettext (0.22.5-3) ... Setting up libtool (2.4.7-8) ... Setting up libhwasan0-arm64-cross (14.2.0-12cross1) ... Setting up libc6-dev-arm64-cross (2.40-4cross1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libstdc++6-arm64-cross (14.2.0-12cross1) ... Setting up help2man (1.49.3) ... Setting up dh-autoreconf (20) ... Setting up pandoc (3.1.11.1+ds-2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-6) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up cpp-14-aarch64-linux-gnu (14.2.0-12cross1) ... Setting up groff-base (1.23.0-7) ... Setting up libasan8-arm64-cross (14.2.0-12cross1) ... Setting up libtsan2-arm64-cross (14.2.0-12cross1) ... Setting up libubsan1-arm64-cross (14.2.0-12cross1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up cpp-aarch64-linux-gnu (4:14.2.0-1) ... Setting up libgcc-14-dev-arm64-cross (14.2.0-12cross1) ... Setting up libstdc++-14-dev-arm64-cross (14.2.0-12cross1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up gcc-14-aarch64-linux-gnu (14.2.0-12cross1) ... Setting up gcc-aarch64-linux-gnu (4:14.2.0-1) ... Setting up g++-14-aarch64-linux-gnu (14.2.0-12cross1) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-3) ... Setting up python3.12 (3.12.8-3) ... Setting up debhelper (13.23) ... Setting up g++-aarch64-linux-gnu (4:14.2.0-1) ... Setting up libpython3-stdlib:amd64 (3.12.8-1) ... Setting up python3 (3.12.8-1) ... Setting up crossbuild-essential-arm64 (12.12) ... Setting up libgcc-s1:arm64 (14.2.0-12) ... Setting up libc6:arm64 (2.40-4) ... Setting up libhwasan0:arm64 (14.2.0-12) ... Setting up libasan8:arm64 (14.2.0-12) ... Setting up libtsan2:arm64 (14.2.0-12) ... Setting up libstdc++6:arm64 (14.2.0-12) ... Setting up liblsan0:arm64 (14.2.0-12) ... Setting up libitm1:arm64 (14.2.0-12) ... Setting up libcrypt1:arm64 (1:4.4.36-5) ... Setting up libgomp1:arm64 (14.2.0-12) ... Setting up libatomic1:arm64 (14.2.0-12) ... Setting up libubsan1:arm64 (14.2.0-12) ... Setting up libcrypt-dev:arm64 (1:4.4.36-5) ... Setting up libc6-dev:arm64 (2.40-4) ... Setting up libgcc-14-dev:arm64 (14.2.0-12) ... Setting up libstdc++-14-dev:arm64 (14.2.0-12) ... Setting up sbuild-build-depends-main-dummy:arm64 (0.invalid.0) ... Processing triggers for libc-bin (2.40-4) ... +------------------------------------------------------------------------------+ | Check architectures | +------------------------------------------------------------------------------+ Arch check ok (arm64 included in any all) +------------------------------------------------------------------------------+ | Build environment | +------------------------------------------------------------------------------+ Kernel: Linux 6.1.0-26-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.112-1 (2024-09-30) amd64 (x86_64) Toolchain package versions: binutils_2.43.50.20241230-1 dpkg-dev_1.22.12 g++-14_14.2.0-12 gcc-14_14.2.0-12 libc6-dev_2.40-4 libstdc++-14-dev_14.2.0-12 libstdc++-14-dev-arm64-cross_14.2.0-12cross1 libstdc++6_14.2.0-12 libstdc++6-arm64-cross_14.2.0-12cross1 linux-libc-dev_6.12.8-1 Package versions: apt_2.9.21 autoconf_2.72-3 automake_1:1.16.5-1.3 autopoint_0.22.5-3 autotools-dev_20220109.1 base-files_13.6 base-passwd_3.6.6 bash_5.2.37-1 binutils_2.43.50.20241230-1 binutils-aarch64-linux-gnu_2.43.50.20241230-1 binutils-common_2.43.50.20241230-1 binutils-x86-64-linux-gnu_2.43.50.20241230-1 bsdextrautils_2.40.2-13 bsdutils_1:2.40.2-13 build-essential_12.12 bzip2_1.0.8-6 coreutils_9.5-1+b1 cpp_4:14.2.0-1 cpp-14_14.2.0-12 cpp-14-aarch64-linux-gnu_14.2.0-12cross1 cpp-14-x86-64-linux-gnu_14.2.0-12 cpp-aarch64-linux-gnu_4:14.2.0-1 cpp-x86-64-linux-gnu_4:14.2.0-1 crossbuild-essential-arm64_12.12 dash_0.5.12-9 debconf_1.5.89 debhelper_13.23 debian-archive-keyring_2023.4 debianutils_5.21 dh-autoreconf_20 dh-strip-nondeterminism_1.14.0-1 diffutils_1:3.10-1 dpkg_1.22.12 dpkg-dev_1.22.12 dwz_0.15-1+b1 e2fsprogs_1.47.2-1 fakeroot_1.36.2-1 file_1:5.45-3+b1 findutils_4.10.0-3 g++_4:14.2.0-1 g++-14_14.2.0-12 g++-14-aarch64-linux-gnu_14.2.0-12cross1 g++-14-x86-64-linux-gnu_14.2.0-12 g++-aarch64-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_14.2.0-12 gcc-14-aarch64-linux-gnu_14.2.0-12cross1 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python3-minimal_3.12.8-1 python3.12_3.12.8-3 python3.12-minimal_3.12.8-3 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_1.2.1-5 sysvinit-utils_3.11-1 tar_1.35+dfsg-3.1 tzdata_2024b-4 util-linux_2.40.2-13 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----- gpgv: Signature made Tue Jul 9 10:27:18 2024 UTC gpgv: using RSA key 724D609337113C710550D7473C26763F6C67E6E2 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./hisat2_2.2.1-5.dsc: no acceptable signature found dpkg-source: info: extracting hisat2 in /<> dpkg-source: info: unpacking hisat2_2.2.1.orig.tar.gz dpkg-source: info: unpacking hisat2_2.2.1-5.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.arm64 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.v29hQvaNv0/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-369edb16-63ea-411f-b444-81566466a189 SCHROOT_UID=1000 SCHROOT_USER=crossqa SHELL=/bin/sh USER=crossqa dpkg-buildpackage ----------------- Command: dpkg-buildpackage --sanitize-env -aarm64 -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 aarch64-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 arm64 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=aarch64-linux-gnu-pkg-config CXX=aarch64-linux-gnu-g\+\+ CC=aarch64-linux-gnu-gcc BUILD_HOST=Debian "BUILD_TIME=09 July 2024" all doc make[2]: Entering directory '/<>' aarch64-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="\"`aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall -DMASSIVE_DATA_RLCSA \ -I. -I third_party \ -o hisat2-build-s hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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 sequence_io.h:30, from hisat2_build.cpp:28: 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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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; | ^~~~~~~~~~~~~~ aarch64-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="\"`aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-build-l hisat2_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp diff_sample.cpp hisat2_build_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_build.cpp:35: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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 sequence_io.h:30, from hisat2_build.cpp:28: 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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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; | ^~~~~~~~~~~~~~ aarch64-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="\"`aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-s hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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 { | ^~~~ aarch64-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="\"`aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-align-l hisat2.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp qual.cpp pat.cpp read_qseq.cpp aligner_seed_policy.cpp aligner_seed.cpp aligner_seed2.cpp aligner_sw.cpp aligner_sw_driver.cpp aligner_cache.cpp aligner_result.cpp ref_coord.cpp mask.cpp pe.cpp aln_sink.cpp dp_framer.cpp scoring.cpp presets.cpp unique.cpp simple_func.cpp random_util.cpp aligner_bt.cpp sse_util.cpp aligner_swsse.cpp outq.cpp aligner_swsse_loc_i16.cpp aligner_swsse_ee_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse_ee_u8.cpp aligner_driver.cpp splice_site.cpp hisat2_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hgfm.h:24, from hisat2.cpp:33: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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 { | ^~~~ aarch64-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="\"`aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-s hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ aarch64-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="\"`aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN -Wall \ -I. -I third_party -I . \ -o hisat2-inspect-l hisat2_inspect.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_inspect.cpp:25: alt.h: In member function ‘bool ALT::repOk() const’: assert_helpers.h:227:18: warning: comparison of constant ‘1’ with boolean expression is always true [-Wbool-compare] 227 | if(!((a) <= (b))) { \ | ~~~~^~~~~~ alt.h:180:13: note: in expansion of macro ‘assert_leq’ 180 | assert_leq(fw, 1); | ^~~~~~~~~~ In file included from hgfm.h:24, from hisat2_inspect.cpp:27: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-linux-gnu/include/c++/14/bits/unique_ptr.h:59:28: note: declared here 59 | template class auto_ptr; | ^~~~~~~~ aarch64-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="\"`aarch64-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 -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -DSIMDE_ENABLE_OPENMP -fopenmp-simd -O3 -Wno-narrowing -Wdate-time -D_FORTIFY_SOURCE=2 -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \ -I. -I third_party \ -o hisat2-repeat hisat2_repeat.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp gfm.cpp reference.cpp ds.cpp multikey_qsort.cpp limit.cpp random_source.cpp tinythread.cpp mask.cpp qual.cpp aligner_bt.cpp scoring.cpp simple_func.cpp dp_framer.cpp aligner_result.cpp aligner_sw_driver.cpp aligner_sw.cpp aligner_swsse_ee_i16.cpp aligner_swsse_ee_u8.cpp aligner_swsse_loc_i16.cpp aligner_swsse_loc_u8.cpp aligner_swsse.cpp bit_packed_array.cpp repeat_builder.cpp diff_sample.cpp hisat2_repeat_main.cpp \ -lpthread -Wl,-z,relro -Wl,-z,now In file included from hisat2_repeat.cpp:36: gfm.h: In static member function ‘static std::pair*, GFM*> GFM::fromStrings(const EList >&, bool, int, bool, int32_t, int32_t, int32_t, const std::string&, bool, index_t, index_t, index_t, int, uint32_t, bool, bool, bool)’: gfm.h:1185:17: warning: ‘template class std::auto_ptr’ is deprecated: use 'std::unique_ptr' instead [-Wdeprecated-declarations] 1185 | auto_ptr ss(new stringstream()); | ^~~~~~~~ In file included from /usr/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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 ‘< >’ 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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-linux-gnu/include/c++/14/memory:78, from gfm.h:28: /usr/aarch64-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/aarch64-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/aarch64-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/aarch64-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 2025-01-03T07:42:26Z +------------------------------------------------------------------------------+ | 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: 495 Distribution: unstable Fail-Stage: build Foreign Architectures: arm64 Host Architecture: arm64 Install-Time: 12 Job: hisat2_2.2.1-5 Machine Architecture: amd64 Package: hisat2 Package-Time: 528 Source-Version: 2.2.1-5 Space: n/a Status: attempted Version: 2.2.1-5 -------------------------------------------------------------------------------- Finished at 2025-01-03T07:42:26Z Build needed 00:08:48, no disk space