Fri Jan 3 07:58:17 UTC 2025 I: starting to build bifrost/trixie/i386 on jenkins on '2025-01-03 07:57' Fri Jan 3 07:58:17 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/i386_4/47116/console.log Fri Jan 3 07:58:17 UTC 2025 I: Downloading source for trixie/bifrost=1.3.1-1 --2025-01-03 07:58:18-- http://deb.debian.org/debian/pool/main/b/bifrost/bifrost_1.3.1-1.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2099 (2.0K) [text/prs.lines.tag] Saving to: ‘bifrost_1.3.1-1.dsc’ 0K .. 100% 326M=0s 2025-01-03 07:58:18 (326 MB/s) - ‘bifrost_1.3.1-1.dsc’ saved [2099/2099] Fri Jan 3 07:58:18 UTC 2025 I: bifrost_1.3.1-1.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: bifrost Binary: bifrost, libbifrost0, libbifrost-dev Architecture: any Version: 1.3.1-1 Maintainer: Debian Med Packaging Team Uploaders: Andreas Tille Homepage: https://github.com/pmelsted/bifrost Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/bifrost Vcs-Git: https://salsa.debian.org/med-team/bifrost.git Testsuite: autopkgtest Build-Depends: debhelper-compat (= 13), d-shlibs, cmake, zlib1g-dev Package-List: bifrost deb python optional arch=any libbifrost-dev deb libdevel optional arch=any libbifrost0 deb libs optional arch=any Checksums-Sha1: 9daeeab211c6f2bd19b8ac6ad12dac770e8f100f 349856 bifrost_1.3.1.orig.tar.gz bf0657121971cc5635e117f45f620bff5202026e 253052 bifrost_1.3.1-1.debian.tar.xz Checksums-Sha256: d6a9baacddba8e9508336c5adff15a8a482774c724fc0710392fed7bb9ad1e8b 349856 bifrost_1.3.1.orig.tar.gz 6b7fa56dd267ab84746d3169cf7a53471c6954176250fe88a7b074cc5fdb9676 253052 bifrost_1.3.1-1.debian.tar.xz Files: 71940660817cb6a0af24663bf00cc5db 349856 bifrost_1.3.1.orig.tar.gz efb8eacd113e4b5f264cea30b0fac580 253052 bifrost_1.3.1-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmWXu9kRHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtHTbA/9GvD2gJsMd07oSzjZDNKKJro4Ah4HmBgv RvwYiR3GsIMQz8zgDkaW7CSOALqkaoypeGaNxVHIo7h4lrQYD7SNPMY92J0lToaW etQnjYW3a9Hiz+YejPMngKmNoQx+SLFHQ3wcFcU71sd/B1VfT5TvxB2rwpyKXB15 X6AKrzE1wkIrpmfW969602vNWoxDLp2D45hdpOKV2NuwVy717cuUFwAQpqyMDd08 drfpI8HBleUOdeC0XozdsRgXSf41i+6wlqseRWGPtWSXJDxB7A8ssNOPDnzxRvFs OOzIldoRhULsNgx+KSRSCeVUyhIYyVdgqWCgrjwiMT3TIxDAthdDwamadRfiSU97 n5Eol+doT0kOT2xM0lBCGylGLwhN5CDSXpab1435PINUiP8iTL34tqvAgyzZFLvp 4rIYwRiJrWzhOUFTurKqTOG6w5Du+4PgTT90FvOioAkuNBftQ0iaCCxmI9UPHPRx RiZKWfn6ClYMshvUZ3SV08u3MyOiQgNW76g8l0Mb7YeozAb899Vq2in2ih0KIDNe rQo+lnWvVWLXCRjXsQlIB83ZlbTnc+vvv2odNc6XdIC1xhAF3SkVN0lLeISgFXDK mgY32kM/oKk0KXkjIFwt99M1G+qWyktiFToE+9IdlgL/iShMznwajQOZwYjHrCfA SRlnI8+EJGc= =Lib9 -----END PGP SIGNATURE----- Fri Jan 3 07:58:18 UTC 2025 I: Checking whether the package is not for us Fri Jan 3 07:58:18 UTC 2025 I: Starting 1st build on remote node ionos16-i386.debian.net. Fri Jan 3 07:58:18 UTC 2025 I: Preparing to do remote build '1' on ionos16-i386.debian.net. Fri Jan 3 08:00:21 UTC 2025 I: Deleting $TMPDIR on ionos16-i386.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Feb 5 02:21:31 -12 2026 I: pbuilder-time-stamp: 1770301291 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/trixie-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [bifrost_1.3.1-1.dsc] I: copying [./bifrost_1.3.1.orig.tar.gz] I: copying [./bifrost_1.3.1-1.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Jan 5 08:20:41 2024 gpgv: using RSA key F1F007320A035541F0A663CA578A0494D1C646D1 gpgv: issuer "tille@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./bifrost_1.3.1-1.dsc: no acceptable signature found dpkg-source: info: extracting bifrost in bifrost-1.3.1 dpkg-source: info: unpacking bifrost_1.3.1.orig.tar.gz dpkg-source: info: unpacking bifrost_1.3.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying add_soname.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/6636/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=22 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='9b3aeea3105e46d2a5e9f433360d2b7f' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='6636' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.g14CJuRX/pbuilderrc_NGEG --distribution trixie --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/trixie-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.g14CJuRX/b1 --logfile b1/build.log bifrost_1.3.1-1.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://213.165.73.152:3128' I: uname -a Linux ionos16-i386 6.1.0-28-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.119-1 (2024-11-22) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/6636/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 13), d-shlibs, cmake, zlib1g-dev dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19951 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs; however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on zlib1g-dev; however: Package zlib1g-dev is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} cmake{a} cmake-data{a} d-shlibs{a} debhelper{a} dh-autoreconf{a} dh-strip-nondeterminism{a} dwz{a} file{a} gettext{a} gettext-base{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13t64{a} libbrotli1{a} libcom-err2{a} libcurl4t64{a} libdebhelper-perl{a} libelf1t64{a} libexpat1{a} libfile-stripnondeterminism-perl{a} libgssapi-krb5-2{a} libicu72{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap-2.5-0{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtool{a} libuchardet0{a} libuv1t64{a} libxml2{a} m4{a} man-db{a} po-debconf{a} procps{a} sensible-utils{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl krb5-locales libarchive-cpio-perl libldap-common libltdl-dev libmail-sendmail-perl libsasl2-modules linux-sysctl-defaults lynx psmisc publicsuffix wget 0 packages upgraded, 55 newly installed, 0 to remove and 0 not upgraded. Need to get 39.7 MB of archives. After unpacking 142 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main i386 libproc2-0 i386 2:4.0.4-6 [65.7 kB] Get: 2 http://deb.debian.org/debian trixie/main i386 procps i386 2:4.0.4-6 [876 kB] Get: 3 http://deb.debian.org/debian trixie/main i386 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian trixie/main i386 libmagic-mgc i386 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main i386 libmagic1t64 i386 1:5.45-3+b1 [115 kB] Get: 6 http://deb.debian.org/debian trixie/main i386 file i386 1:5.45-3+b1 [43.2 kB] Get: 7 http://deb.debian.org/debian trixie/main i386 gettext-base i386 0.22.5-3 [201 kB] Get: 8 http://deb.debian.org/debian trixie/main i386 libuchardet0 i386 0.0.8-1+b2 [69.2 kB] Get: 9 http://deb.debian.org/debian trixie/main i386 groff-base i386 1.23.0-7 [1199 kB] Get: 10 http://deb.debian.org/debian trixie/main i386 bsdextrautils i386 2.40.2-13 [95.9 kB] Get: 11 http://deb.debian.org/debian trixie/main i386 libpipeline1 i386 1.5.8-1 [41.2 kB] Get: 12 http://deb.debian.org/debian trixie/main i386 man-db i386 2.13.0-1 [1428 kB] Get: 13 http://deb.debian.org/debian trixie/main i386 m4 i386 1.4.19-4 [293 kB] Get: 14 http://deb.debian.org/debian trixie/main i386 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian trixie/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main i386 autopoint all 0.22.5-3 [723 kB] Get: 18 http://deb.debian.org/debian trixie/main i386 cmake-data all 3.30.5-1 [2223 kB] Get: 19 http://deb.debian.org/debian trixie/main i386 libicu72 i386 72.1-5+b1 [9583 kB] Get: 20 http://deb.debian.org/debian trixie/main i386 libxml2 i386 2.12.7+dfsg+really2.9.14-0.2+b1 [734 kB] Get: 21 http://deb.debian.org/debian trixie/main i386 libarchive13t64 i386 3.7.4-1.1 [390 kB] Get: 22 http://deb.debian.org/debian trixie/main i386 libbrotli1 i386 1.1.0-2+b6 [308 kB] Get: 23 http://deb.debian.org/debian trixie/main i386 libkrb5support0 i386 1.21.3-3 [34.9 kB] Get: 24 http://deb.debian.org/debian trixie/main i386 libcom-err2 i386 1.47.2~rc1-2 [24.0 kB] Get: 25 http://deb.debian.org/debian trixie/main i386 libk5crypto3 i386 1.21.3-3 [83.6 kB] Get: 26 http://deb.debian.org/debian trixie/main i386 libkeyutils1 i386 1.6.3-4 [9600 B] Get: 27 http://deb.debian.org/debian trixie/main i386 libkrb5-3 i386 1.21.3-3 [350 kB] Get: 28 http://deb.debian.org/debian trixie/main i386 libgssapi-krb5-2 i386 1.21.3-3 [146 kB] Get: 29 http://deb.debian.org/debian trixie/main i386 libsasl2-modules-db i386 2.1.28+dfsg1-8 [20.6 kB] Get: 30 http://deb.debian.org/debian trixie/main i386 libsasl2-2 i386 2.1.28+dfsg1-8 [61.0 kB] Get: 31 http://deb.debian.org/debian trixie/main i386 libldap-2.5-0 i386 2.5.19+dfsg-1 [200 kB] Get: 32 http://deb.debian.org/debian trixie/main i386 libnghttp2-14 i386 1.64.0-1 [82.4 kB] Get: 33 http://deb.debian.org/debian trixie/main i386 libpsl5t64 i386 0.21.2-1.1+b1 [57.7 kB] Get: 34 http://deb.debian.org/debian trixie/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b5 [62.4 kB] Get: 35 http://deb.debian.org/debian trixie/main i386 libssh2-1t64 i386 1.11.1-1 [256 kB] Get: 36 http://deb.debian.org/debian trixie/main i386 libcurl4t64 i386 8.11.1-1 [393 kB] Get: 37 http://deb.debian.org/debian trixie/main i386 libexpat1 i386 2.6.4-1 [107 kB] Get: 38 http://deb.debian.org/debian trixie/main i386 libjsoncpp26 i386 1.9.6-3 [90.0 kB] Get: 39 http://deb.debian.org/debian trixie/main i386 librhash1 i386 1.4.5-1 [144 kB] Get: 40 http://deb.debian.org/debian trixie/main i386 libuv1t64 i386 1.48.0-7 [157 kB] Get: 41 http://deb.debian.org/debian trixie/main i386 cmake i386 3.30.5-1 [12.5 MB] Get: 42 http://deb.debian.org/debian trixie/main i386 d-shlibs all 0.109 [11.1 kB] Get: 43 http://deb.debian.org/debian trixie/main i386 libdebhelper-perl all 13.23 [90.6 kB] Get: 44 http://deb.debian.org/debian trixie/main i386 libtool all 2.4.7-8 [517 kB] Get: 45 http://deb.debian.org/debian trixie/main i386 dh-autoreconf all 20 [17.1 kB] Get: 46 http://deb.debian.org/debian trixie/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 47 http://deb.debian.org/debian trixie/main i386 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 48 http://deb.debian.org/debian trixie/main i386 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 49 http://deb.debian.org/debian trixie/main i386 libelf1t64 i386 0.192-4 [195 kB] Get: 50 http://deb.debian.org/debian trixie/main i386 dwz i386 0.15-1+b1 [116 kB] Get: 51 http://deb.debian.org/debian trixie/main i386 gettext i386 0.22.5-3 [1631 kB] Get: 52 http://deb.debian.org/debian trixie/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 53 http://deb.debian.org/debian trixie/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 54 http://deb.debian.org/debian trixie/main i386 debhelper all 13.23 [919 kB] Get: 55 http://deb.debian.org/debian trixie/main i386 zlib1g-dev i386 1:1.3.dfsg+really1.3.1-1+b1 [916 kB] Fetched 39.7 MB in 6s (6512 kB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:i386. (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 ... 19951 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-6_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.4-6_i386.deb ... Unpacking procps (2:4.0.4-6) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../02-sensible-utils_0.0.24_all.deb ... Unpacking sensible-utils (0.0.24) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../03-libmagic-mgc_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:i386. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3+b1_i386.deb ... Unpacking libmagic1t64:i386 (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3+b1_i386.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.22.5-3_i386.deb ... Unpacking gettext-base (0.22.5-3) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../07-libuchardet0_0.0.8-1+b2_i386.deb ... Unpacking libuchardet0:i386 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-7_i386.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.2-13_i386.deb ... Unpacking bsdextrautils (2.40.2-13) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../10-libpipeline1_1.5.8-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.0-1_i386.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-4_i386.deb ... Unpacking m4 (1.4.19-4) ... Selecting previously unselected package autoconf. Preparing to unpack .../13-autoconf_2.72-3_all.deb ... Unpacking autoconf (2.72-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../14-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../15-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../16-autopoint_0.22.5-3_all.deb ... Unpacking autopoint (0.22.5-3) ... Selecting previously unselected package cmake-data. Preparing to unpack .../17-cmake-data_3.30.5-1_all.deb ... Unpacking cmake-data (3.30.5-1) ... Selecting previously unselected package libicu72:i386. Preparing to unpack .../18-libicu72_72.1-5+b1_i386.deb ... Unpacking libicu72:i386 (72.1-5+b1) ... Selecting previously unselected package libxml2:i386. Preparing to unpack .../19-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_i386.deb ... Unpacking libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:i386. Preparing to unpack .../20-libarchive13t64_3.7.4-1.1_i386.deb ... Unpacking libarchive13t64:i386 (3.7.4-1.1) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../21-libbrotli1_1.1.0-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.1.0-2+b6) ... Selecting previously unselected package libkrb5support0:i386. Preparing to unpack .../22-libkrb5support0_1.21.3-3_i386.deb ... Unpacking libkrb5support0:i386 (1.21.3-3) ... Selecting previously unselected package libcom-err2:i386. Preparing to unpack .../23-libcom-err2_1.47.2~rc1-2_i386.deb ... Unpacking libcom-err2:i386 (1.47.2~rc1-2) ... Selecting previously unselected package libk5crypto3:i386. Preparing to unpack .../24-libk5crypto3_1.21.3-3_i386.deb ... Unpacking libk5crypto3:i386 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:i386. Preparing to unpack .../25-libkeyutils1_1.6.3-4_i386.deb ... Unpacking libkeyutils1:i386 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:i386. Preparing to unpack .../26-libkrb5-3_1.21.3-3_i386.deb ... Unpacking libkrb5-3:i386 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:i386. Preparing to unpack .../27-libgssapi-krb5-2_1.21.3-3_i386.deb ... Unpacking libgssapi-krb5-2:i386 (1.21.3-3) ... Selecting previously unselected package libsasl2-modules-db:i386. Preparing to unpack .../28-libsasl2-modules-db_2.1.28+dfsg1-8_i386.deb ... Unpacking libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Selecting previously unselected package libsasl2-2:i386. Preparing to unpack .../29-libsasl2-2_2.1.28+dfsg1-8_i386.deb ... Unpacking libsasl2-2:i386 (2.1.28+dfsg1-8) ... Selecting previously unselected package libldap-2.5-0:i386. Preparing to unpack .../30-libldap-2.5-0_2.5.19+dfsg-1_i386.deb ... Unpacking libldap-2.5-0:i386 (2.5.19+dfsg-1) ... Selecting previously unselected package libnghttp2-14:i386. Preparing to unpack .../31-libnghttp2-14_1.64.0-1_i386.deb ... Unpacking libnghttp2-14:i386 (1.64.0-1) ... Selecting previously unselected package libpsl5t64:i386. Preparing to unpack .../32-libpsl5t64_0.21.2-1.1+b1_i386.deb ... Unpacking libpsl5t64:i386 (0.21.2-1.1+b1) ... Selecting previously unselected package librtmp1:i386. Preparing to unpack .../33-librtmp1_2.4+20151223.gitfa8646d.1-2+b5_i386.deb ... Unpacking librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Selecting previously unselected package libssh2-1t64:i386. Preparing to unpack .../34-libssh2-1t64_1.11.1-1_i386.deb ... Unpacking libssh2-1t64:i386 (1.11.1-1) ... Selecting previously unselected package libcurl4t64:i386. Preparing to unpack .../35-libcurl4t64_8.11.1-1_i386.deb ... Unpacking libcurl4t64:i386 (8.11.1-1) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../36-libexpat1_2.6.4-1_i386.deb ... Unpacking libexpat1:i386 (2.6.4-1) ... Selecting previously unselected package libjsoncpp26:i386. Preparing to unpack .../37-libjsoncpp26_1.9.6-3_i386.deb ... Unpacking libjsoncpp26:i386 (1.9.6-3) ... Selecting previously unselected package librhash1:i386. Preparing to unpack .../38-librhash1_1.4.5-1_i386.deb ... Unpacking librhash1:i386 (1.4.5-1) ... Selecting previously unselected package libuv1t64:i386. Preparing to unpack .../39-libuv1t64_1.48.0-7_i386.deb ... Unpacking libuv1t64:i386 (1.48.0-7) ... Selecting previously unselected package cmake. Preparing to unpack .../40-cmake_3.30.5-1_i386.deb ... Unpacking cmake (3.30.5-1) ... Selecting previously unselected package d-shlibs. Preparing to unpack .../41-d-shlibs_0.109_all.deb ... Unpacking d-shlibs (0.109) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../42-libdebhelper-perl_13.23_all.deb ... Unpacking libdebhelper-perl (13.23) ... Selecting previously unselected package libtool. Preparing to unpack .../43-libtool_2.4.7-8_all.deb ... Unpacking libtool (2.4.7-8) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../44-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... Selecting previously unselected package libarchive-zip-perl. Preparing to unpack .../45-libarchive-zip-perl_1.68-1_all.deb ... Unpacking libarchive-zip-perl (1.68-1) ... Selecting previously unselected package libfile-stripnondeterminism-perl. Preparing to unpack .../46-libfile-stripnondeterminism-perl_1.14.0-1_all.deb ... Unpacking libfile-stripnondeterminism-perl (1.14.0-1) ... Selecting previously unselected package dh-strip-nondeterminism. Preparing to unpack .../47-dh-strip-nondeterminism_1.14.0-1_all.deb ... Unpacking dh-strip-nondeterminism (1.14.0-1) ... Selecting previously unselected package libelf1t64:i386. Preparing to unpack .../48-libelf1t64_0.192-4_i386.deb ... Unpacking libelf1t64:i386 (0.192-4) ... Selecting previously unselected package dwz. Preparing to unpack .../49-dwz_0.15-1+b1_i386.deb ... Unpacking dwz (0.15-1+b1) ... Selecting previously unselected package gettext. Preparing to unpack .../50-gettext_0.22.5-3_i386.deb ... Unpacking gettext (0.22.5-3) ... Selecting previously unselected package intltool-debian. Preparing to unpack .../51-intltool-debian_0.35.0+20060710.6_all.deb ... Unpacking intltool-debian (0.35.0+20060710.6) ... Selecting previously unselected package po-debconf. Preparing to unpack .../52-po-debconf_1.0.21+nmu1_all.deb ... Unpacking po-debconf (1.0.21+nmu1) ... Selecting previously unselected package debhelper. Preparing to unpack .../53-debhelper_13.23_all.deb ... Unpacking debhelper (13.23) ... Selecting previously unselected package zlib1g-dev:i386. Preparing to unpack .../54-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_i386.deb ... Unpacking zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libexpat1:i386 (2.6.4-1) ... Setting up libpipeline1:i386 (1.5.8-1) ... Setting up libkeyutils1:i386 (1.6.3-4) ... Setting up libicu72:i386 (72.1-5+b1) ... Setting up bsdextrautils (2.40.2-13) ... Setting up libmagic-mgc (1:5.45-3+b1) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libdebhelper-perl (13.23) ... Setting up libbrotli1:i386 (1.1.0-2+b6) ... Setting up libuv1t64:i386 (1.48.0-7) ... Setting up libmagic1t64:i386 (1:5.45-3+b1) ... Setting up libpsl5t64:i386 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:i386 (1.64.0-1) ... Setting up gettext-base (0.22.5-3) ... Setting up m4 (1.4.19-4) ... Setting up libcom-err2:i386 (1.47.2~rc1-2) ... Setting up file (1:5.45-3+b1) ... Setting up libelf1t64:i386 (0.192-4) ... Setting up libkrb5support0:i386 (1.21.3-3) ... Setting up libsasl2-modules-db:i386 (2.1.28+dfsg1-8) ... Setting up autotools-dev (20220109.1) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libjsoncpp26:i386 (1.9.6-3) ... Setting up libproc2-0:i386 (2:4.0.4-6) ... Setting up autopoint (0.22.5-3) ... Setting up d-shlibs (0.109) ... Setting up libk5crypto3:i386 (1.21.3-3) ... Setting up libsasl2-2:i386 (2.1.28+dfsg1-8) ... Setting up autoconf (2.72-3) ... Setting up zlib1g-dev:i386 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up dwz (0.15-1+b1) ... Setting up sensible-utils (0.0.24) ... Setting up libuchardet0:i386 (0.0.8-1+b2) ... Setting up procps (2:4.0.4-6) ... Setting up cmake-data (3.30.5-1) ... Setting up librhash1:i386 (1.4.5-1) ... Setting up libkrb5-3:i386 (1.21.3-3) ... Setting up libssh2-1t64:i386 (1.11.1-1) ... Setting up libxml2:i386 (2.12.7+dfsg+really2.9.14-0.2+b1) ... 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 gettext (0.22.5-3) ... Setting up libtool (2.4.7-8) ... Setting up libldap-2.5-0:i386 (2.5.19+dfsg-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libgssapi-krb5-2:i386 (1.21.3-3) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up groff-base (1.23.0-7) ... Setting up libarchive13t64:i386 (3.7.4-1.1) ... Setting up libcurl4t64:i386 (8.11.1-1) ... 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 cmake (3.30.5-1) ... Setting up debhelper (13.23) ... Processing triggers for libc-bin (2.40-4) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/bifrost-1.3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../bifrost_1.3.1-1_source.changes dpkg-buildpackage: info: source package bifrost dpkg-buildpackage: info: source version 1.3.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/bifrost-1.3.1' dh_auto_configure -- -DCOMPILATION_ARCH=OFF cd obj-i686-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DCOMPILATION_ARCH=OFF .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.5 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- The C compiler identification is GNU 14.2.0 -- The CXX compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE Disabling native architecture compilation (including AVX2) Build type: Release Maximum k-mer size: 31 Maximum g-mer size: 31 -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.3.1") -- Configuring done (1.7s) -- Generating done (0.0s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu make[1]: Leaving directory '/build/reproducible-path/bifrost-1.3.1' dh_auto_build cd obj-i686-linux-gnu && make -j22 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/bifrost-1.3.1 -B/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' make -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/depend make -f src/CMakeFiles/bifrost_dynamic.dir/build.make src/CMakeFiles/bifrost_dynamic.dir/depend make[3]: Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bifrost-1.3.1 /build/reproducible-path/bifrost-1.3.1/src /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src/CMakeFiles/bifrost_static.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/bifrost-1.3.1 /build/reproducible-path/bifrost-1.3.1/src /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src/CMakeFiles/bifrost_dynamic.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' make -f src/CMakeFiles/bifrost_dynamic.dir/build.make src/CMakeFiles/bifrost_dynamic.dir/build make[3]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' make -f src/CMakeFiles/bifrost_static.dir/build.make src/CMakeFiles/bifrost_static.dir/build make[3]: Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' [ 12%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o [ 12%] Building CXX object src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o [ 15%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o [ 15%] Building CXX object src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o [ 18%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o [ 21%] Building CXX object src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o [ 21%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o [ 25%] Building CXX object src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o [ 28%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp [ 34%] Building CXX object src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o [ 31%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o [ 40%] Building CXX object src/CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o [ 46%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o [ 46%] Building CXX object src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_static.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_static.dir/BitContainer.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp [ 50%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o [ 37%] Building CXX object src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp [ 53%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o -MF CMakeFiles/bifrost_static.dir/ColorSet.cpp.o.d -o CMakeFiles/bifrost_static.dir/ColorSet.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp [ 56%] Building CXX object src/CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -MF CMakeFiles/bifrost_static.dir/Bifrost.cpp.o.d -o CMakeFiles/bifrost_static.dir/Bifrost.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp [ 59%] Building CXX object src/CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o [ 62%] Building CXX object src/CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o -MF CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o.d -o CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o -MF CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o.d -o CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/CompressedSequence.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o -MF CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o.d -o CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o -MF CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o.d -o CMakeFiles/bifrost_static.dir/GFA_Parser.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/GFA_Parser.cpp [ 65%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o -MF CMakeFiles/bifrost_static.dir/Kmer.cpp.o.d -o CMakeFiles/bifrost_static.dir/Kmer.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/Kmer.cpp [ 68%] Building CXX object src/CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o -MF CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o.d -o CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/KmerIterator.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o -MF CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o.d -o CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o -MF CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o.d -o CMakeFiles/bifrost_static.dir/TinyBitmap.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/TinyBitmap.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/CompressedSequence.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -O3 -MD -MT src/CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o -MF CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o.d -o CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/GFA_Parser.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/GFA_Parser.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/Kmer.cpp In file included from /build/reproducible-path/bifrost-1.3.1/src/CompressedSequence.cpp:3: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/Kmer.hpp:21, from /build/reproducible-path/bifrost-1.3.1/src/KmerIterator.cpp:3: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:149: src/CMakeFiles/bifrost_static.dir/CompressedSequence.cpp.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:205: src/CMakeFiles/bifrost_static.dir/KmerIterator.cpp.o] Error 1 In file included from /build/reproducible-path/bifrost-1.3.1/src/Kmer.hpp:21, from /build/reproducible-path/bifrost-1.3.1/src/Kmer.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/Kmer.hpp:21, from /build/reproducible-path/bifrost-1.3.1/src/Kmer.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompressedSequence.cpp:3: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ [ 75%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o [ 75%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp cd /build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu/src && /usr/bin/c++ -DMAX_GMER_SIZE=32 -DMAX_KMER_SIZE=32 -Dbifrost_dynamic_EXPORTS -I/build/reproducible-path/bifrost-1.3.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/bifrost-1.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -O3 -MD -MT src/CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o -MF CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o.d -o CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o -c /build/reproducible-path/bifrost-1.3.1/src/KmerIterator.cpp make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:191: src/CMakeFiles/bifrost_dynamic.dir/Kmer.cpp.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:191: src/CMakeFiles/bifrost_static.dir/Kmer.cpp.o] Error 1 In file included from /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:12, from /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_u32(uint64_t, uint32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:12: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 46 | return ((__uint128_t)lowbits * d) >> 64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:24: error: expected ')' before 'lowbits' 46 | return ((__uint128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_s32(uint64_t, int32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:12: error: '__int128_t' was not declared in this scope; did you mean '__int128__'? 50 | return ((__int128_t)lowbits * d) >> 64; | ^~~~~~~~~~ | __int128__ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:23: error: expected ')' before 'lowbits' 50 | return ((__int128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:23:21: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 23 | #define FASTMOD_API inline | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:1: note: in expansion of macro 'FASTMOD_API' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:33: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:63: error: expected primary-expression before 'd' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:64: error: expression list treated as compound expression in initializer [-fpermissive] 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:139:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 139 | FASTMOD_API __uint128_t computeM_u64(uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:149:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 149 | FASTMOD_API __uint128_t computeM_s64(int64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:161:46: error: '__uint128_t' has not been declared 161 | FASTMOD_API uint64_t fastmod_u64(uint64_t a, __uint128_t M, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastmod_u64(uint64_t, int, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:162:3: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 162 | __uint128_t lowbits = M * a; | ^~~~~~~~~~~ | __uint8_t In file included from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:13, from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:21: error: 'lowbits' was not declared in this scope 163 | return mul128_u64(lowbits, d); | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:20: error: 'fastmod::mul128_u64' cannot be used as a function 163 | return mul128_u64(lowbits, d); | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:166:46: error: '__uint128_t' has not been declared 166 | FASTMOD_API uint64_t fastdiv_u64(uint64_t a, __uint128_t M) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastdiv_u64(uint64_t, int)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:167:20: error: 'fastmod::mul128_u64' cannot be used as a function 167 | return mul128_u64(M, a); | ~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:17: /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:130:33: note: in expansion of macro 'kroundup64' 130 | kroundup64(str->m); \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:157:9: note: in expansion of macro '__KS_GETUNTIL' 157 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:234:9: note: in expansion of macro 'KSTREAM_INIT' 234 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t kseq_read(kseq_t*)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:207:25: note: in expansion of macro 'kroundup64' 207 | kroundup64(seq->seq.m); /* rounded to the next closest 2^k */ \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:237:9: note: in expansion of macro '__KSEQ_READ' 237 | __KSEQ_READ(SCOPE) | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:149: src/CMakeFiles/bifrost_dynamic.dir/CompressedSequence.cpp.o] Error 1 make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:163: src/CMakeFiles/bifrost_static.dir/FASTX_Parser.cpp.o] Error 1 /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp: In constructor 'BitContainer::BitContainer_const_iterator::BitContainer_const_iterator(const BitContainer*, bool)': /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp:959:164: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 959 | BitContainer::BitContainer_const_iterator::BitContainer_const_iterator( const BitContainer* cs_, const bool beg) : cs(cs_), ck_id(0xffffffffffffffff), it_setBits(0xffffffffffffffff), | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp:1092:45: warning: conversion from 'long long unsigned int' to 'uintptr_t' {aka 'unsigned int'} changes value from '18446744073709551608' to '4294967288' [-Woverflow] 1092 | const uintptr_t BitContainer::pointerMask = 0xFFFFFFFFFFFFFFF8; | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:13, from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:17: /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:130:33: note: in expansion of macro 'kroundup64' 130 | kroundup64(str->m); \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:157:9: note: in expansion of macro '__KS_GETUNTIL' 157 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:234:9: note: in expansion of macro 'KSTREAM_INIT' 234 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp: In constructor 'BitContainer::BitContainer_const_iterator::BitContainer_const_iterator(const BitContainer*, bool)': /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp:959:164: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 959 | BitContainer::BitContainer_const_iterator::BitContainer_const_iterator( const BitContainer* cs_, const bool beg) : cs(cs_), ck_id(0xffffffffffffffff), it_setBits(0xffffffffffffffff), | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t kseq_read(kseq_t*)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:207:25: note: in expansion of macro 'kroundup64' 207 | kroundup64(seq->seq.m); /* rounded to the next closest 2^k */ \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:237:9: note: in expansion of macro '__KSEQ_READ' 237 | __KSEQ_READ(SCOPE) | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/BitContainer.cpp:1092:45: warning: conversion from 'long long unsigned int' to 'uintptr_t' {aka 'unsigned int'} changes value from '18446744073709551608' to '4294967288' [-Woverflow] 1092 | const uintptr_t BitContainer::pointerMask = 0xFFFFFFFFFFFFFFF8; | ^~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/Kmer.hpp:21, from /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:14: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:220:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 220 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In copy constructor 'MinimizerIndex::MinimizerIndex(const MinimizerIndex&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:23:61: error: class 'MinimizerIndex' does not have any field named 'M_u64' 23 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:23:69: error: 'const class MinimizerIndex' has no member named 'M_u64' 23 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In constructor 'MinimizerIndex::MinimizerIndex(MinimizerIndex&&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:40:57: error: class 'MinimizerIndex' does not have any field named 'M_u64' 40 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:40:65: error: 'class MinimizerIndex' has no member named 'M_u64' 40 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'MinimizerIndex& MinimizerIndex::operator=(const MinimizerIndex&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:60:9: error: 'M_u64' was not declared in this scope 60 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:60:19: error: 'const class MinimizerIndex' has no member named 'M_u64' 60 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'MinimizerIndex& MinimizerIndex::operator=(MinimizerIndex&&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:89:9: error: 'M_u64' was not declared in this scope 89 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:89:19: error: 'class MinimizerIndex' has no member named 'M_u64' 89 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'MinimizerIndex::iterator MinimizerIndex::find(const Minimizer&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:128:53: error: 'M_u64' was not declared in this scope 128 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'MinimizerIndex::const_iterator MinimizerIndex::find(const Minimizer&) const': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:193:53: error: 'M_u64' was not declared in this scope 193 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:8: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'size_t MinimizerIndex::erase(const_iterator)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:280:76: error: 'M_u64' was not declared in this scope 280 | const size_t h = fastmod::fastmod_u64(table_keys[it.h].hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:299:106: error: 'M_u64' was not declared in this scope 299 | while ((i != size_) && !table_keys[j2].isEmpty() && (fastmod::fastmod_u64(table_keys[j2].hash(), M_u64, size_) != j2)) { | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:8: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'std::pair, bool> MinimizerIndex::insert(const Minimizer&, const packed_tiny_vector&, const uint8_t&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:331:49: error: 'M_u64' was not declared in this scope 331 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: In member function 'void CompressedCoverage::initialize(size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:89:39: warning: left shift count >= width of type [-Wshift-count-overflow] 89 | if (full) asBits = fullMask | (sz << 32); | ~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: In member function 'void CompressedCoverage::releasePointer()': /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:131:37: warning: left shift count >= width of type [-Wshift-count-overflow] 131 | asBits = fullMask | (size() << 32); | ~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'void MinimizerIndex::recomputeMaxPSL(size_t)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:423:81: error: 'M_u64' was not declared in this scope 423 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: In member function 'size_t CompressedCoverage::size() const': /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:143:56: warning: right shift count >= width of type [-Wshift-count-overflow] 143 | if ((asBits & fullMask) == fullMask) return asBits >> 32; | ~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: In member function 'void CompressedCoverage::initialize(size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:89:39: warning: left shift count >= width of type [-Wshift-count-overflow] 89 | if (full) asBits = fullMask | (sz << 32); | ~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: In member function 'void CompressedCoverage::releasePointer()': /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:131:37: warning: left shift count >= width of type [-Wshift-count-overflow] 131 | asBits = fullMask | (size() << 32); | ~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: In member function 'size_t CompressedCoverage::size() const': /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:143:56: warning: right shift count >= width of type [-Wshift-count-overflow] 143 | if ((asBits & fullMask) == fullMask) return asBits >> 32; | ~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:453:93: error: 'M_u64' was not declared in this scope 453 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: In member function 'bool CompressedCoverage::cover(size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:247:41: warning: left shift count >= width of type [-Wshift-count-overflow] 247 | asBits = fullMask | (size() << 32); | ~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: In member function 'bool CompressedCoverage::cover(size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:247:41: warning: left shift count >= width of type [-Wshift-count-overflow] 247 | asBits = fullMask | (size() << 32); | ~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'void MinimizerIndex::clear_tables()': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:526:5: error: 'M_u64' was not declared in this scope 526 | M_u64 = 0; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'void MinimizerIndex::init_tables(size_t)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:538:5: error: 'M_u64' was not declared in this scope 538 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:538:22: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 538 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: In member function 'void CompressedCoverage::setFull()': /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:434:72: warning: left shift count >= width of type [-Wshift-count-overflow] 434 | if ((asBits & tagMask) == tagMask) asBits = fullMask | (size() << 32); | ~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:443:51: warning: unsigned conversion from 'long long int' to 'uintptr_t' {aka 'unsigned int'} changes value from '48038396025285290' to '2863311530' [-Woverflow] 443 | uintptr_t CompressedCoverage::localCoverageMask = 0xAAAAAAAAAAAAAA; // 0b10101010101010101010101010101010101010101010101010101010 | ^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'void MinimizerIndex::reserve(size_t)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:570:9: error: 'M_u64' was not declared in this scope 570 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:570:26: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 570 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: In member function 'void CompressedCoverage::setFull()': /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:434:72: warning: left shift count >= width of type [-Wshift-count-overflow] 434 | if ((asBits & tagMask) == tagMask) asBits = fullMask | (size() << 32); | ~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/CompressedCoverage.cpp:443:51: warning: unsigned conversion from 'long long int' to 'uintptr_t' {aka 'unsigned int'} changes value from '48038396025285290' to '2863311530' [-Woverflow] 443 | uintptr_t CompressedCoverage::localCoverageMask = 0xAAAAAAAAAAAAAA; // 0b10101010101010101010101010101010101010101010101010101010 | ^~~~~~~~~~~~~~~~ make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:163: src/CMakeFiles/bifrost_dynamic.dir/FASTX_Parser.cpp.o] Error 1 /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_(MI_ptr_t) [with bool is_const = false; MI_ptr_t = MinimizerIndex*]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:183:25: required from here 183 | return iterator(this); | ^ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:35:50: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_(MI_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:35:78: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_(MI_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_(MI_ptr_t) [with bool is_const = true; MI_ptr_t = const MinimizerIndex*]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:251:31: required from here 251 | return const_iterator(this); | ^ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:35:50: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_(MI_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:35:78: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_(MI_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_(MI_ptr_t, size_t) [with bool is_const = false; MI_ptr_t = MinimizerIndex*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:256:73: required from here 256 | if ((h < size_) && !table_keys[h].isEmpty()) return iterator(this, h); | ^ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:36:71: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(MI_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_(MI_ptr_t, size_t) [with bool is_const = true; MI_ptr_t = const MinimizerIndex*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:263:79: required from here 263 | if ((h < size_) && !table_keys[h].isEmpty()) return const_iterator(this, h); | ^ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:36:71: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(MI_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_() [with bool is_const = false]': /usr/include/c++/14/bits/stl_pair.h:726:9: required from 'constexpr std::pair<_T1, _T2>::pair() [with _U1 = MinimizerIndex::iterator_; _U2 = bool; typename std::enable_if, std::__is_implicitly_default_constructible<_U2> >::value, bool>::type = true; _T1 = MinimizerIndex::iterator_; _T2 = bool]' 726 | : first(), second() { } | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:335:42: required from here 335 | pair it_ret; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:34:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 34 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:34:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 34 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'void MinimizerIndex::iterator_::get_to_first() [with bool is_const = false]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:478:20: required from here 478 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:118:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 118 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:119:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 119 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'void MinimizerIndex::iterator_::get_to_first() [with bool is_const = true]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:487:20: required from here 487 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:118:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 118 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:119:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 119 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.hpp:5, from /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/Kmer.hpp:21, from /build/reproducible-path/bifrost-1.3.1/src/KmerIterator.cpp:3: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:135: src/CMakeFiles/bifrost_dynamic.dir/CompressedCoverage.cpp.o] Error 1 /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:135: src/CMakeFiles/bifrost_static.dir/CompressedCoverage.cpp.o] Error 1 In file included from /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:12, from /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_u32(uint64_t, uint32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:12: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 46 | return ((__uint128_t)lowbits * d) >> 64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:24: error: expected ')' before 'lowbits' 46 | return ((__uint128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_s32(uint64_t, int32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:12: error: '__int128_t' was not declared in this scope; did you mean '__int128__'? 50 | return ((__int128_t)lowbits * d) >> 64; | ^~~~~~~~~~ | __int128__ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:23: error: expected ')' before 'lowbits' 50 | return ((__int128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:23:21: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 23 | #define FASTMOD_API inline | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:1: note: in expansion of macro 'FASTMOD_API' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:33: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:63: error: expected primary-expression before 'd' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:64: error: expression list treated as compound expression in initializer [-fpermissive] 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:139:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 139 | FASTMOD_API __uint128_t computeM_u64(uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:149:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 149 | FASTMOD_API __uint128_t computeM_s64(int64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:161:46: error: '__uint128_t' has not been declared 161 | FASTMOD_API uint64_t fastmod_u64(uint64_t a, __uint128_t M, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastmod_u64(uint64_t, int, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:162:3: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 162 | __uint128_t lowbits = M * a; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:21: error: 'lowbits' was not declared in this scope 163 | return mul128_u64(lowbits, d); | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:20: error: 'fastmod::mul128_u64' cannot be used as a function 163 | return mul128_u64(lowbits, d); | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:166:46: error: '__uint128_t' has not been declared 166 | FASTMOD_API uint64_t fastdiv_u64(uint64_t a, __uint128_t M) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastdiv_u64(uint64_t, int)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:167:20: error: 'fastmod::mul128_u64' cannot be used as a function 167 | return mul128_u64(M, a); | ~~~~~~~~~~^~~~~~ make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:205: src/CMakeFiles/bifrost_dynamic.dir/KmerIterator.cpp.o] Error 1 make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:219: src/CMakeFiles/bifrost_static.dir/MinimizerIndex.cpp.o] Error 1 In file included from /build/reproducible-path/bifrost-1.3.1/src/Kmer.hpp:21, from /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:14: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:220:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 220 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In copy constructor 'MinimizerIndex::MinimizerIndex(const MinimizerIndex&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:23:61: error: class 'MinimizerIndex' does not have any field named 'M_u64' 23 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:23:69: error: 'const class MinimizerIndex' has no member named 'M_u64' 23 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In constructor 'MinimizerIndex::MinimizerIndex(MinimizerIndex&&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:40:57: error: class 'MinimizerIndex' does not have any field named 'M_u64' 40 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:40:65: error: 'class MinimizerIndex' has no member named 'M_u64' 40 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'MinimizerIndex& MinimizerIndex::operator=(const MinimizerIndex&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:60:9: error: 'M_u64' was not declared in this scope 60 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:60:19: error: 'const class MinimizerIndex' has no member named 'M_u64' 60 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'MinimizerIndex& MinimizerIndex::operator=(MinimizerIndex&&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:89:9: error: 'M_u64' was not declared in this scope 89 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:89:19: error: 'class MinimizerIndex' has no member named 'M_u64' 89 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'MinimizerIndex::iterator MinimizerIndex::find(const Minimizer&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:128:53: error: 'M_u64' was not declared in this scope 128 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'MinimizerIndex::const_iterator MinimizerIndex::find(const Minimizer&) const': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:193:53: error: 'M_u64' was not declared in this scope 193 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'size_t MinimizerIndex::erase(const_iterator)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:280:76: error: 'M_u64' was not declared in this scope 280 | const size_t h = fastmod::fastmod_u64(table_keys[it.h].hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:299:106: error: 'M_u64' was not declared in this scope 299 | while ((i != size_) && !table_keys[j2].isEmpty() && (fastmod::fastmod_u64(table_keys[j2].hash(), M_u64, size_) != j2)) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'std::pair, bool> MinimizerIndex::insert(const Minimizer&, const packed_tiny_vector&, const uint8_t&)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:331:49: error: 'M_u64' was not declared in this scope 331 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'void MinimizerIndex::recomputeMaxPSL(size_t)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:423:81: error: 'M_u64' was not declared in this scope 423 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:453:93: error: 'M_u64' was not declared in this scope 453 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'void MinimizerIndex::clear_tables()': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:526:5: error: 'M_u64' was not declared in this scope 526 | M_u64 = 0; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'void MinimizerIndex::init_tables(size_t)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:538:5: error: 'M_u64' was not declared in this scope 538 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:538:22: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 538 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp: In member function 'void MinimizerIndex::reserve(size_t)': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:570:9: error: 'M_u64' was not declared in this scope 570 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:570:26: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 570 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 In file included from /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:14, from /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_u32(uint64_t, uint32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:12: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 46 | return ((__uint128_t)lowbits * d) >> 64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:24: error: expected ')' before 'lowbits' 46 | return ((__uint128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_s32(uint64_t, int32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:12: error: '__int128_t' was not declared in this scope; did you mean '__int128__'? 50 | return ((__int128_t)lowbits * d) >> 64; | ^~~~~~~~~~ | __int128__ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:23: error: expected ')' before 'lowbits' 50 | return ((__int128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:23:21: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 23 | #define FASTMOD_API inline | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:1: note: in expansion of macro 'FASTMOD_API' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:33: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:63: error: expected primary-expression before 'd' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:64: error: expression list treated as compound expression in initializer [-fpermissive] 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:139:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 139 | FASTMOD_API __uint128_t computeM_u64(uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:149:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 149 | FASTMOD_API __uint128_t computeM_s64(int64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:161:46: error: '__uint128_t' has not been declared 161 | FASTMOD_API uint64_t fastmod_u64(uint64_t a, __uint128_t M, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastmod_u64(uint64_t, int, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:162:3: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 162 | __uint128_t lowbits = M * a; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:21: error: 'lowbits' was not declared in this scope 163 | return mul128_u64(lowbits, d); | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:20: error: 'fastmod::mul128_u64' cannot be used as a function 163 | return mul128_u64(lowbits, d); | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:166:46: error: '__uint128_t' has not been declared 166 | FASTMOD_API uint64_t fastdiv_u64(uint64_t a, __uint128_t M) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastdiv_u64(uint64_t, int)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:167:20: error: 'fastmod::mul128_u64' cannot be used as a function 167 | return mul128_u64(M, a); | ~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_(MI_ptr_t) [with bool is_const = false; MI_ptr_t = MinimizerIndex*]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:183:25: required from here 183 | return iterator(this); | ^ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:35:50: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_(MI_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:35:78: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_(MI_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_(MI_ptr_t) [with bool is_const = true; MI_ptr_t = const MinimizerIndex*]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:251:31: required from here 251 | return const_iterator(this); | ^ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:35:50: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_(MI_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:35:78: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_(MI_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_(MI_ptr_t, size_t) [with bool is_const = false; MI_ptr_t = MinimizerIndex*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:256:73: required from here 256 | if ((h < size_) && !table_keys[h].isEmpty()) return iterator(this, h); | ^ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:36:71: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(MI_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_(MI_ptr_t, size_t) [with bool is_const = true; MI_ptr_t = const MinimizerIndex*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:263:79: required from here 263 | if ((h < size_) && !table_keys[h].isEmpty()) return const_iterator(this, h); | ^ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:36:71: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(MI_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_() [with bool is_const = false]': /usr/include/c++/14/bits/stl_pair.h:726:9: required from 'constexpr std::pair<_T1, _T2>::pair() [with _U1 = MinimizerIndex::iterator_; _U2 = bool; typename std::enable_if, std::__is_implicitly_default_constructible<_U2> >::value, bool>::type = true; _T1 = MinimizerIndex::iterator_; _T2 = bool]' 726 | : first(), second() { } | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:335:42: required from here 335 | pair it_ret; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:34:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 34 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:34:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 34 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:14, from /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_u32(uint64_t, uint32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:12: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 46 | return ((__uint128_t)lowbits * d) >> 64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:24: error: expected ')' before 'lowbits' 46 | return ((__uint128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'void MinimizerIndex::iterator_::get_to_first() [with bool is_const = false]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:478:20: required from here 478 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:118:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 118 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:119:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 119 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'void MinimizerIndex::iterator_::get_to_first() [with bool is_const = true]': /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.cpp:487:20: required from here 487 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:118:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 118 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:119:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 119 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_s32(uint64_t, int32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:12: error: '__int128_t' was not declared in this scope; did you mean '__int128__'? 50 | return ((__int128_t)lowbits * d) >> 64; | ^~~~~~~~~~ | __int128__ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:23: error: expected ')' before 'lowbits' 50 | return ((__int128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:23:21: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 23 | #define FASTMOD_API inline | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:1: note: in expansion of macro 'FASTMOD_API' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:33: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:63: error: expected primary-expression before 'd' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:64: error: expression list treated as compound expression in initializer [-fpermissive] 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:139:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 139 | FASTMOD_API __uint128_t computeM_u64(uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:149:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 149 | FASTMOD_API __uint128_t computeM_s64(int64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:161:46: error: '__uint128_t' has not been declared 161 | FASTMOD_API uint64_t fastmod_u64(uint64_t a, __uint128_t M, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastmod_u64(uint64_t, int, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:162:3: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 162 | __uint128_t lowbits = M * a; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:21: error: 'lowbits' was not declared in this scope 163 | return mul128_u64(lowbits, d); | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:20: error: 'fastmod::mul128_u64' cannot be used as a function 163 | return mul128_u64(lowbits, d); | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:166:46: error: '__uint128_t' has not been declared 166 | FASTMOD_API uint64_t fastdiv_u64(uint64_t a, __uint128_t M) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastdiv_u64(uint64_t, int)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:167:20: error: 'fastmod::mul128_u64' cannot be used as a function 167 | return mul128_u64(M, a); | ~~~~~~~~~~^~~~~~ make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:219: src/CMakeFiles/bifrost_dynamic.dir/MinimizerIndex.cpp.o] Error 1 In file included from /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:14, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:27, from /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_u32(uint64_t, uint32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:12: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 46 | return ((__uint128_t)lowbits * d) >> 64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:24: error: expected ')' before 'lowbits' 46 | return ((__uint128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_s32(uint64_t, int32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:12: error: '__int128_t' was not declared in this scope; did you mean '__int128__'? 50 | return ((__int128_t)lowbits * d) >> 64; | ^~~~~~~~~~ | __int128__ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:23: error: expected ')' before 'lowbits' 50 | return ((__int128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:23:21: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 23 | #define FASTMOD_API inline | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:1: note: in expansion of macro 'FASTMOD_API' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:33: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:63: error: expected primary-expression before 'd' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:64: error: expression list treated as compound expression in initializer [-fpermissive] 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:139:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 139 | FASTMOD_API __uint128_t computeM_u64(uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:149:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 149 | FASTMOD_API __uint128_t computeM_s64(int64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:161:46: error: '__uint128_t' has not been declared 161 | FASTMOD_API uint64_t fastmod_u64(uint64_t a, __uint128_t M, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastmod_u64(uint64_t, int, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:162:3: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 162 | __uint128_t lowbits = M * a; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:21: error: 'lowbits' was not declared in this scope 163 | return mul128_u64(lowbits, d); | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:20: error: 'fastmod::mul128_u64' cannot be used as a function 163 | return mul128_u64(lowbits, d); | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:166:46: error: '__uint128_t' has not been declared 166 | FASTMOD_API uint64_t fastdiv_u64(uint64_t a, __uint128_t M) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastdiv_u64(uint64_t, int)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:167:20: error: 'fastmod::mul128_u64' cannot be used as a function 167 | return mul128_u64(M, a); | ~~~~~~~~~~^~~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:14, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:27, from /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:4, from /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.hpp:324: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_u32(uint64_t, uint32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:12: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 46 | return ((__uint128_t)lowbits * d) >> 64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:24: error: expected ')' before 'lowbits' 46 | return ((__uint128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) In file included from /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:14, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:27, from /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:1: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_u32(uint64_t, uint32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:12: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 46 | return ((__uint128_t)lowbits * d) >> 64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:24: error: expected ')' before 'lowbits' 46 | return ((__uint128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_s32(uint64_t, int32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:12: error: '__int128_t' was not declared in this scope; did you mean '__int128__'? 50 | return ((__int128_t)lowbits * d) >> 64; | ^~~~~~~~~~ | __int128__ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:23: error: expected ')' before 'lowbits' 50 | return ((__int128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_s32(uint64_t, int32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:12: error: '__int128_t' was not declared in this scope; did you mean '__int128__'? 50 | return ((__int128_t)lowbits * d) >> 64; | ^~~~~~~~~~ | __int128__ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:23: error: expected ')' before 'lowbits' 50 | return ((__int128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:23:21: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 23 | #define FASTMOD_API inline | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:1: note: in expansion of macro 'FASTMOD_API' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:33: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:63: error: expected primary-expression before 'd' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:64: error: expression list treated as compound expression in initializer [-fpermissive] 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:139:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 139 | FASTMOD_API __uint128_t computeM_u64(uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:149:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 149 | FASTMOD_API __uint128_t computeM_s64(int64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:161:46: error: '__uint128_t' has not been declared 161 | FASTMOD_API uint64_t fastmod_u64(uint64_t a, __uint128_t M, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastmod_u64(uint64_t, int, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:162:3: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 162 | __uint128_t lowbits = M * a; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:23:21: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 23 | #define FASTMOD_API inline | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:1: note: in expansion of macro 'FASTMOD_API' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:21: error: 'lowbits' was not declared in this scope 163 | return mul128_u64(lowbits, d); | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:20: error: 'fastmod::mul128_u64' cannot be used as a function 163 | return mul128_u64(lowbits, d); | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:166:46: error: '__uint128_t' has not been declared 166 | FASTMOD_API uint64_t fastdiv_u64(uint64_t a, __uint128_t M) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastdiv_u64(uint64_t, int)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:167:20: error: 'fastmod::mul128_u64' cannot be used as a function 167 | return mul128_u64(M, a); | ~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:33: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:63: error: expected primary-expression before 'd' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:64: error: expression list treated as compound expression in initializer [-fpermissive] 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:139:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 139 | FASTMOD_API __uint128_t computeM_u64(uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:149:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 149 | FASTMOD_API __uint128_t computeM_s64(int64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:161:46: error: '__uint128_t' has not been declared 161 | FASTMOD_API uint64_t fastmod_u64(uint64_t a, __uint128_t M, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastmod_u64(uint64_t, int, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:162:3: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 162 | __uint128_t lowbits = M * a; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:21: error: 'lowbits' was not declared in this scope 163 | return mul128_u64(lowbits, d); | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:20: error: 'fastmod::mul128_u64' cannot be used as a function 163 | return mul128_u64(lowbits, d); | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:166:46: error: '__uint128_t' has not been declared 166 | FASTMOD_API uint64_t fastdiv_u64(uint64_t a, __uint128_t M) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastdiv_u64(uint64_t, int)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:167:20: error: 'fastmod::mul128_u64' cannot be used as a function 167 | return mul128_u64(M, a); | ~~~~~~~~~~^~~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:14, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:27, from /build/reproducible-path/bifrost-1.3.1/src/ColorSet.hpp:6, from /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp:5: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_u32(uint64_t, uint32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:12: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 46 | return ((__uint128_t)lowbits * d) >> 64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:24: error: expected ')' before 'lowbits' 46 | return ((__uint128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_s32(uint64_t, int32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:12: error: '__int128_t' was not declared in this scope; did you mean '__int128__'? 50 | return ((__int128_t)lowbits * d) >> 64; | ^~~~~~~~~~ | __int128__ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:23: error: expected ')' before 'lowbits' 50 | return ((__int128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:23:21: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 23 | #define FASTMOD_API inline | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:1: note: in expansion of macro 'FASTMOD_API' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:33: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:63: error: expected primary-expression before 'd' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:64: error: expression list treated as compound expression in initializer [-fpermissive] 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:139:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 139 | FASTMOD_API __uint128_t computeM_u64(uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:149:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 149 | FASTMOD_API __uint128_t computeM_s64(int64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:161:46: error: '__uint128_t' has not been declared 161 | FASTMOD_API uint64_t fastmod_u64(uint64_t a, __uint128_t M, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastmod_u64(uint64_t, int, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:162:3: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 162 | __uint128_t lowbits = M * a; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:21: error: 'lowbits' was not declared in this scope 163 | return mul128_u64(lowbits, d); | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:20: error: 'fastmod::mul128_u64' cannot be used as a function 163 | return mul128_u64(lowbits, d); | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:166:46: error: '__uint128_t' has not been declared 166 | FASTMOD_API uint64_t fastdiv_u64(uint64_t a, __uint128_t M) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastdiv_u64(uint64_t, int)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:167:20: error: 'fastmod::mul128_u64' cannot be used as a function 167 | return mul128_u64(M, a); | ~~~~~~~~~~^~~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:14, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:27, from /build/reproducible-path/bifrost-1.3.1/src/ColorSet.hpp:6, from /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp:5: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_u32(uint64_t, uint32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:12: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 46 | return ((__uint128_t)lowbits * d) >> 64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:46:24: error: expected ')' before 'lowbits' 46 | return ((__uint128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::mul128_s32(uint64_t, int32_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:12: error: '__int128_t' was not declared in this scope; did you mean '__int128__'? 50 | return ((__int128_t)lowbits * d) >> 64; | ^~~~~~~~~~ | __int128__ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:50:23: error: expected ')' before 'lowbits' 50 | return ((__int128_t)lowbits * d) >> 64; | ~ ^~~~~~~ | ) /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:23:21: warning: inline variables are only available with '-std=c++17' or '-std=gnu++17' [-Wc++17-extensions] 23 | #define FASTMOD_API inline | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:1: note: in expansion of macro 'FASTMOD_API' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:33: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:63: error: expected primary-expression before 'd' 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:54:64: error: expression list treated as compound expression in initializer [-fpermissive] 54 | FASTMOD_API uint64_t mul128_u64(__uint128_t lowbits, uint64_t d) { | ^ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:139:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 139 | FASTMOD_API __uint128_t computeM_u64(uint64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:149:13: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 149 | FASTMOD_API __uint128_t computeM_s64(int64_t d) { | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:161:46: error: '__uint128_t' has not been declared 161 | FASTMOD_API uint64_t fastmod_u64(uint64_t a, __uint128_t M, uint64_t d) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastmod_u64(uint64_t, int, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:162:3: error: '__uint128_t' was not declared in this scope; did you mean '__uint8_t'? 162 | __uint128_t lowbits = M * a; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:21: error: 'lowbits' was not declared in this scope 163 | return mul128_u64(lowbits, d); | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:163:20: error: 'fastmod::mul128_u64' cannot be used as a function 163 | return mul128_u64(lowbits, d); | ~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: At global scope: /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:166:46: error: '__uint128_t' has not been declared 166 | FASTMOD_API uint64_t fastdiv_u64(uint64_t a, __uint128_t M) { | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/fastmod.h: In function 'uint64_t fastmod::fastdiv_u64(uint64_t, int)': /build/reproducible-path/bifrost-1.3.1/src/fastmod.h:167:20: error: 'fastmod::mul128_u64' cannot be used as a function 167 | return mul128_u64(M, a); | ~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:145:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 145 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:289:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 289 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:145:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 145 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:28: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:145:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 145 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t In file included from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:17, from /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:29: /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:130:33: note: in expansion of macro 'kroundup64' 130 | kroundup64(str->m); \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:157:9: note: in expansion of macro '__KS_GETUNTIL' 157 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:234:9: note: in expansion of macro 'KSTREAM_INIT' 234 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t kseq_read(kseq_t*)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:207:25: note: in expansion of macro 'kroundup64' 207 | kroundup64(seq->seq.m); /* rounded to the next closest 2^k */ \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:237:9: note: in expansion of macro '__KSEQ_READ' 237 | __KSEQ_READ(SCOPE) | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:289:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 289 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:289:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 289 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In copy constructor 'BlockedBloomFilter::BlockedBloomFilter(const BlockedBloomFilter&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:14:83: error: class 'BlockedBloomFilter' does not have any field named 'M_u64' 14 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush(o.ush) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:14:91: error: 'const class BlockedBloomFilter' has no member named 'M_u64' 14 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush(o.ush) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In constructor 'BlockedBloomFilter::BlockedBloomFilter(BlockedBloomFilter&&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:30:79: error: class 'BlockedBloomFilter' does not have any field named 'M_u64' 30 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush(move(o.ush)) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:30:87: error: 'class BlockedBloomFilter' has no member named 'M_u64' 30 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush(move(o.ush)) { | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:28: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'BlockedBloomFilter& BlockedBloomFilter::operator=(const BlockedBloomFilter&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:49:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 49 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:49:15: error: 'const class BlockedBloomFilter' has no member named 'M_u64' 49 | M_u64 = o.M_u64; | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:17, from /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:29: /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:130:33: note: in expansion of macro 'kroundup64' 130 | kroundup64(str->m); \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:157:9: note: in expansion of macro '__KS_GETUNTIL' 157 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:234:9: note: in expansion of macro 'KSTREAM_INIT' 234 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t kseq_read(kseq_t*)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:207:25: note: in expansion of macro 'kroundup64' 207 | kroundup64(seq->seq.m); /* rounded to the next closest 2^k */ \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:237:9: note: in expansion of macro '__KSEQ_READ' 237 | __KSEQ_READ(SCOPE) | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'BlockedBloomFilter& BlockedBloomFilter::operator=(BlockedBloomFilter&&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:79:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 79 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:79:19: error: 'class BlockedBloomFilter' has no member named 'M_u64' 79 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'void BlockedBloomFilter::clear()': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:129:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 129 | M_u64 = 0; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'void BlockedBloomFilter::init_arrays()': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:146:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 146 | M_u64 = fastmod::computeM_u64(blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:146:22: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 146 | M_u64 = fastmod::computeM_u64(blocks_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'DualBlockedBloomFilter BlockedBloomFilter::transferToDBBF(uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:159:10: error: 'class DualBlockedBloomFilter' has no member named 'M_u64' 159 | dbbf.M_u64 = M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:159:18: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 159 | dbbf.M_u64 = M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'std::array BlockedBloomFilter::contains_bids(const uint64_t (&)[4], uint64_t, int) const': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:213:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 213 | uint64_t bid1 = fastmod::fastmod_u64(minh1, M_u64, blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp: In static member function 'static int FileParser::getFileFormat(const char*)': /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:230:64: warning: right shift count >= width of type [-Wshift-count-overflow] 230 | else if ((reinterpret_cast(buffer)[0] >> 32) == BFG_GRAPHBIN_FORMAT_HEADER) ret_v = 3; // BFG | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:231:64: warning: right shift count >= width of type [-Wshift-count-overflow] 231 | else if ((reinterpret_cast(buffer)[0] >> 32) == BFG_METABIN_FORMAT_HEADER) ret_v = 4; // BFI | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'int64_t BlockedBloomFilter::contains_bids(uint64_t, uint64_t) const': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:299:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 299 | uint64_t bid1 = fastmod::fastmod_u64(minh1, M_u64, blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:145:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 145 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'uint64_t BlockedBloomFilter::insert_par(uint64_t, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:419:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 419 | uint64_t bid1 = fastmod::fastmod_u64(minh1, M_u64, blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp: In static member function 'static int FileParser::getFileFormat(const char*)': /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:230:64: warning: right shift count >= width of type [-Wshift-count-overflow] 230 | else if ((reinterpret_cast(buffer)[0] >> 32) == BFG_GRAPHBIN_FORMAT_HEADER) ret_v = 3; // BFG | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:231:64: warning: right shift count >= width of type [-Wshift-count-overflow] 231 | else if ((reinterpret_cast(buffer)[0] >> 32) == BFG_METABIN_FORMAT_HEADER) ret_v = 4; // BFI | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'uint64_t BlockedBloomFilter::insert_unpar(uint64_t, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:530:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 530 | uint64_t bid1 = fastmod::fastmod_u64(minh1, M_u64, blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:289:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 289 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In copy constructor 'DualBlockedBloomFilter::DualBlockedBloomFilter(const DualBlockedBloomFilter&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:609:95: error: class 'DualBlockedBloomFilter' does not have any field named 'M_u64' 609 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush{o.ush[0], o.ush[1]} { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:609:103: error: 'const class DualBlockedBloomFilter' has no member named 'M_u64' 609 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush{o.ush[0], o.ush[1]} { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In constructor 'DualBlockedBloomFilter::DualBlockedBloomFilter(DualBlockedBloomFilter&&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:625:91: error: class 'DualBlockedBloomFilter' does not have any field named 'M_u64' 625 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush{move(o.ush[0]), move(o.ush[1])} { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:625:99: error: 'class DualBlockedBloomFilter' has no member named 'M_u64' 625 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush{move(o.ush[0]), move(o.ush[1])} { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In copy constructor 'BlockedBloomFilter::BlockedBloomFilter(const BlockedBloomFilter&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:14:83: error: class 'BlockedBloomFilter' does not have any field named 'M_u64' 14 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush(o.ush) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:14:91: error: 'const class BlockedBloomFilter' has no member named 'M_u64' 14 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush(o.ush) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In constructor 'BlockedBloomFilter::BlockedBloomFilter(BlockedBloomFilter&&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:30:79: error: class 'BlockedBloomFilter' does not have any field named 'M_u64' 30 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush(move(o.ush)) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:30:87: error: 'class BlockedBloomFilter' has no member named 'M_u64' 30 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush(move(o.ush)) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'DualBlockedBloomFilter& DualBlockedBloomFilter::operator=(const DualBlockedBloomFilter&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:644:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 644 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:644:15: error: 'const class DualBlockedBloomFilter' has no member named 'M_u64' 644 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'BlockedBloomFilter& BlockedBloomFilter::operator=(const BlockedBloomFilter&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:49:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 49 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:49:15: error: 'const class BlockedBloomFilter' has no member named 'M_u64' 49 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'DualBlockedBloomFilter& DualBlockedBloomFilter::operator=(DualBlockedBloomFilter&&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:676:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 676 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:676:19: error: 'class DualBlockedBloomFilter' has no member named 'M_u64' 676 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'BlockedBloomFilter& BlockedBloomFilter::operator=(BlockedBloomFilter&&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:79:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 79 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:79:19: error: 'class BlockedBloomFilter' has no member named 'M_u64' 79 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'void DualBlockedBloomFilter::clear()': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:727:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 727 | M_u64 = 0; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'void DualBlockedBloomFilter::init_arrays()': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:749:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 749 | M_u64 = fastmod::computeM_u64(blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:749:22: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 749 | M_u64 = fastmod::computeM_u64(blocks_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'void BlockedBloomFilter::clear()': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:129:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 129 | M_u64 = 0; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'std::array DualBlockedBloomFilter::contains_bids(const uint64_t (&)[4], uint64_t, int, uint64_t) const': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:789:54: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 789 | uint64_t bid1 = (fastmod::fastmod_u64(minh1, M_u64, blocks_) << 1) + idx_bbf_norm; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'void BlockedBloomFilter::init_arrays()': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:146:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 146 | M_u64 = fastmod::computeM_u64(blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:146:22: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 146 | M_u64 = fastmod::computeM_u64(blocks_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'int64_t DualBlockedBloomFilter::contains_bids(uint64_t, uint64_t, uint64_t) const': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:876:54: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 876 | uint64_t bid1 = (fastmod::fastmod_u64(minh1, M_u64, blocks_) << 1) + idx_bbf_norm; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'DualBlockedBloomFilter BlockedBloomFilter::transferToDBBF(uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:159:10: error: 'class DualBlockedBloomFilter' has no member named 'M_u64' 159 | dbbf.M_u64 = M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:159:18: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 159 | dbbf.M_u64 = M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'std::array BlockedBloomFilter::contains_bids(const uint64_t (&)[4], uint64_t, int) const': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:213:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 213 | uint64_t bid1 = fastmod::fastmod_u64(minh1, M_u64, blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'BlockedBloomFilter DualBlockedBloomFilter::transferToBBF(uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:928:9: error: 'class BlockedBloomFilter' has no member named 'M_u64' 928 | bbf.M_u64 = M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'int64_t BlockedBloomFilter::contains_bids(uint64_t, uint64_t) const': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:299:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 299 | uint64_t bid1 = fastmod::fastmod_u64(minh1, M_u64, blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:928:17: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 928 | bbf.M_u64 = M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'uint64_t BlockedBloomFilter::insert_par(uint64_t, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:419:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 419 | uint64_t bid1 = fastmod::fastmod_u64(minh1, M_u64, blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'uint64_t DualBlockedBloomFilter::insert_par(uint64_t, uint64_t, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:1092:54: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 1092 | uint64_t bid1 = (fastmod::fastmod_u64(minh1, M_u64, blocks_) << 1) + idx_bbf_norm; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'uint64_t BlockedBloomFilter::insert_unpar(uint64_t, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:530:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 530 | uint64_t bid1 = fastmod::fastmod_u64(minh1, M_u64, blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In copy constructor 'DualBlockedBloomFilter::DualBlockedBloomFilter(const DualBlockedBloomFilter&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:609:95: error: class 'DualBlockedBloomFilter' does not have any field named 'M_u64' 609 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush{o.ush[0], o.ush[1]} { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:609:103: error: 'const class DualBlockedBloomFilter' has no member named 'M_u64' 609 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush{o.ush[0], o.ush[1]} { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In constructor 'DualBlockedBloomFilter::DualBlockedBloomFilter(DualBlockedBloomFilter&&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:625:91: error: class 'DualBlockedBloomFilter' does not have any field named 'M_u64' 625 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush{move(o.ush[0]), move(o.ush[1])} { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:625:99: error: 'class DualBlockedBloomFilter' has no member named 'M_u64' 625 | k_(o.k_), M_u64(o.M_u64), seed1(o.seed1), seed2(o.seed2), ush{move(o.ush[0]), move(o.ush[1])} { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'DualBlockedBloomFilter& DualBlockedBloomFilter::operator=(const DualBlockedBloomFilter&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:644:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 644 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:644:15: error: 'const class DualBlockedBloomFilter' has no member named 'M_u64' 644 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'DualBlockedBloomFilter& DualBlockedBloomFilter::operator=(DualBlockedBloomFilter&&)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:676:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 676 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:676:19: error: 'class DualBlockedBloomFilter' has no member named 'M_u64' 676 | M_u64 = o.M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'uint64_t DualBlockedBloomFilter::insert_unpar(uint64_t, uint64_t, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:1204:54: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 1204 | uint64_t bid1 = (fastmod::fastmod_u64(minh1, M_u64, blocks_) << 1) + idx_bbf_norm; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'void DualBlockedBloomFilter::clear()': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:727:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 727 | M_u64 = 0; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'void DualBlockedBloomFilter::init_arrays()': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:749:5: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 749 | M_u64 = fastmod::computeM_u64(blocks_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:749:22: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 749 | M_u64 = fastmod::computeM_u64(blocks_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'std::array DualBlockedBloomFilter::contains_bids(const uint64_t (&)[4], uint64_t, int, uint64_t) const': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:789:54: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 789 | uint64_t bid1 = (fastmod::fastmod_u64(minh1, M_u64, blocks_) << 1) + idx_bbf_norm; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'int64_t DualBlockedBloomFilter::contains_bids(uint64_t, uint64_t, uint64_t) const': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:876:54: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 876 | uint64_t bid1 = (fastmod::fastmod_u64(minh1, M_u64, blocks_) << 1) + idx_bbf_norm; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'BlockedBloomFilter DualBlockedBloomFilter::transferToBBF(uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:928:9: error: 'class BlockedBloomFilter' has no member named 'M_u64' 928 | bbf.M_u64 = M_u64; | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:928:17: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 928 | bbf.M_u64 = M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'uint64_t DualBlockedBloomFilter::insert_par(uint64_t, uint64_t, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:1092:54: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 1092 | uint64_t bid1 = (fastmod::fastmod_u64(minh1, M_u64, blocks_) << 1) + idx_bbf_norm; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp: In member function 'uint64_t DualBlockedBloomFilter::insert_unpar(uint64_t, uint64_t, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.cpp:1204:54: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 1204 | uint64_t bid1 = (fastmod::fastmod_u64(minh1, M_u64, blocks_) << 1) + idx_bbf_norm; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:145:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 145 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:289:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 289 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t In file included from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:17, from /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:29: /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:130:33: note: in expansion of macro 'kroundup64' 130 | kroundup64(str->m); \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:157:9: note: in expansion of macro '__KS_GETUNTIL' 157 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:234:9: note: in expansion of macro 'KSTREAM_INIT' 234 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t kseq_read(kseq_t*)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:207:25: note: in expansion of macro 'kroundup64' 207 | kroundup64(seq->seq.m); /* rounded to the next closest 2^k */ \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:237:9: note: in expansion of macro '__KSEQ_READ' 237 | __KSEQ_READ(SCOPE) | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:34: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:19:5: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 19 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In copy constructor 'KmerHashTable::KmerHashTable(const KmerHashTable&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:153:113: error: class 'KmerHashTable' does not have any field named 'M_u64' 153 | size_(o.size_), pop(o.pop), sum_psl(o.sum_psl), max_psl(o.max_psl), M_u64(o.M_u64) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In constructor 'KmerHashTable::KmerHashTable(KmerHashTable&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:167:41: error: class 'KmerHashTable' does not have any field named 'M_u64' 167 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable& KmerHashTable::operator=(const KmerHashTable&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:186:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 186 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:145:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 145 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable& KmerHashTable::operator=(KmerHashTable&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:212:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 212 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:289:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 289 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:107: src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o] Error 1 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:28: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:17, from /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:29: /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:130:33: note: in expansion of macro 'kroundup64' 130 | kroundup64(str->m); \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:157:9: note: in expansion of macro '__KS_GETUNTIL' 157 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:234:9: note: in expansion of macro 'KSTREAM_INIT' 234 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::clear()': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:249:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 249 | M_u64 = 0; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t kseq_read(kseq_t*)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:207:25: note: in expansion of macro 'kroundup64' 207 | kroundup64(seq->seq.m); /* rounded to the next closest 2^k */ \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:237:9: note: in expansion of macro '__KSEQ_READ' 237 | __KSEQ_READ(SCOPE) | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:107: src/CMakeFiles/bifrost_dynamic.dir/BlockedBloomFilter.cpp.o] Error 1 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable::iterator KmerHashTable::find(const Kmer&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:261:57: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 261 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable::const_iterator KmerHashTable::find(const Kmer&) const': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:326:57: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 326 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'size_t KmerHashTable::erase(const_iterator)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:412:80: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 412 | const size_t h = fastmod::fastmod_u64(table_keys[it.h].hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:430:110: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 430 | while ((i != size_) && !table_keys[j2].isEmpty() && (fastmod::fastmod_u64(table_keys[j2].hash(), M_u64, size_) != j2)) { | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp: In static member function 'static int FileParser::getFileFormat(const char*)': /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:230:64: warning: right shift count >= width of type [-Wshift-count-overflow] 230 | else if ((reinterpret_cast(buffer)[0] >> 32) == BFG_GRAPHBIN_FORMAT_HEADER) ret_v = 3; // BFG | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:231:64: warning: right shift count >= width of type [-Wshift-count-overflow] 231 | else if ((reinterpret_cast(buffer)[0] >> 32) == BFG_METABIN_FORMAT_HEADER) ret_v = 4; // BFI | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'std::pair::iterator_, bool> KmerHashTable::insert(const Kmer&, const T&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:469:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 469 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp: In static member function 'static int FileParser::getFileFormat(const char*)': /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:230:64: warning: right shift count >= width of type [-Wshift-count-overflow] 230 | else if ((reinterpret_cast(buffer)[0] >> 32) == BFG_GRAPHBIN_FORMAT_HEADER) ret_v = 3; // BFG | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:231:64: warning: right shift count >= width of type [-Wshift-count-overflow] 231 | else if ((reinterpret_cast(buffer)[0] >> 32) == BFG_METABIN_FORMAT_HEADER) ret_v = 4; // BFI | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:569:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 569 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:34: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:19:5: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 19 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In copy constructor 'KmerHashTable::KmerHashTable(const KmerHashTable&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:153:113: error: class 'KmerHashTable' does not have any field named 'M_u64' 153 | size_(o.size_), pop(o.pop), sum_psl(o.sum_psl), max_psl(o.max_psl), M_u64(o.M_u64) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In constructor 'KmerHashTable::KmerHashTable(KmerHashTable&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:167:41: error: class 'KmerHashTable' does not have any field named 'M_u64' 167 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::recomputeMaxPSL(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:664:85: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 664 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable& KmerHashTable::operator=(const KmerHashTable&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:186:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 186 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable& KmerHashTable::operator=(KmerHashTable&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:212:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 212 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:694:97: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 694 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::clear()': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:249:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 249 | M_u64 = 0; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::init_tables(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:776:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 776 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:776:26: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 776 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable::iterator KmerHashTable::find(const Kmer&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:261:57: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 261 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::reserve(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:804:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 804 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:804:30: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 804 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable::const_iterator KmerHashTable::find(const Kmer&) const': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:326:57: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 326 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:34: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:19:5: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 19 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'size_t KmerHashTable::erase(const_iterator)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:412:80: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 412 | const size_t h = fastmod::fastmod_u64(table_keys[it.h].hash(), M_u64, size_); | ^~~~~ | M_Ef64 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:36: /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:119:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 119 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:430:110: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 430 | while ((i != size_) && !table_keys[j2].isEmpty() && (fastmod::fastmod_u64(table_keys[j2].hash(), M_u64, size_) != j2)) { | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In copy constructor 'KmerHashTable::KmerHashTable(const KmerHashTable&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:153:113: error: class 'KmerHashTable' does not have any field named 'M_u64' 153 | size_(o.size_), pop(o.pop), sum_psl(o.sum_psl), max_psl(o.max_psl), M_u64(o.M_u64) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In constructor 'KmerHashTable::KmerHashTable(KmerHashTable&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:167:41: error: class 'KmerHashTable' does not have any field named 'M_u64' 167 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update(const char*, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:201:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 201 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update_p(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:270:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 270 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update_p(const char*, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:366:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 366 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:577:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 577 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update(const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:654:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 654 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update_p(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:722:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 722 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update_p(const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:817:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 817 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'std::pair::iterator_, bool> KmerHashTable::insert(const Kmer&, const T&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:469:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 469 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable& KmerHashTable::operator=(const KmerHashTable&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:186:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 186 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:145:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 145 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:39: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:220:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 220 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable& KmerHashTable::operator=(KmerHashTable&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:212:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 212 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:569:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 569 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:34: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:19:5: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 19 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/BlockedBloomFilter.hpp:289:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 289 | __uint128_t M_u64; // for fast division/modulo | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::clear()': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:249:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 249 | M_u64 = 0; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In copy constructor 'KmerHashTable::KmerHashTable(const KmerHashTable&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:153:113: error: class 'KmerHashTable' does not have any field named 'M_u64' 153 | size_(o.size_), pop(o.pop), sum_psl(o.sum_psl), max_psl(o.max_psl), M_u64(o.M_u64) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In constructor 'KmerHashTable::KmerHashTable(KmerHashTable&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:167:41: error: class 'KmerHashTable' does not have any field named 'M_u64' 167 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::recomputeMaxPSL(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:664:85: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 664 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ | M_Ef64 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:28: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'bool isDNA(char)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:48:47: error: narrowing conversion of '4504192333906058' from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} [-Wnarrowing] 48 | static const size_t DNAbits[4] = {0x0ULL, 0x10008A0010008AULL, 0x0ULL, 0x0ULL}; | ^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: In function 'size_t rndup(size_t)': /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:192:12: warning: right shift count >= width of type [-Wshift-count-overflow] 192 | v |= v >> 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:198:21: error: redefinition of 'uint32_t rndup(uint32_t)' 198 | BFG_INLINE uint32_t rndup(uint32_t v) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:184:19: note: 'size_t rndup(size_t)' previously defined here 184 | BFG_INLINE size_t rndup(size_t v) { | ^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:17, from /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:29: /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t ks_getuntil2(kstream_t*, int, kstring_t*, int*, int)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:130:33: note: in expansion of macro 'kroundup64' 130 | kroundup64(str->m); \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:157:9: note: in expansion of macro '__KS_GETUNTIL' 157 | __KS_GETUNTIL(__read, __bufsize) | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:234:9: note: in expansion of macro 'KSTREAM_INIT' 234 | KSTREAM_INIT(type_t, __read, 16384) \ | ^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp: In function 'int64_t kseq_read(kseq_t*)': /build/reproducible-path/bifrost-1.3.1/src/kseq.h:95:105: warning: right shift count >= width of type [-Wshift-count-overflow] 95 | #define kroundup64(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, (x)|=(x)>>32, ++(x)) | ~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:207:25: note: in expansion of macro 'kroundup64' 207 | kroundup64(seq->seq.m); /* rounded to the next closest 2^k */ \ | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:237:9: note: in expansion of macro '__KSEQ_READ' 237 | __KSEQ_READ(SCOPE) | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/kseq.h:239:35: note: in expansion of macro 'KSEQ_INIT2' 239 | #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read) | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/FASTX_Parser.hpp:18:1: note: in expansion of macro 'KSEQ_INIT' 18 | KSEQ_INIT(gzFile, gzread); | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable::iterator KmerHashTable::find(const Kmer&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:261:57: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 261 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:826: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::build(CDBG_Build_opt&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: error: no matching function for call to 'max(long unsigned int, size_t)' 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:12: /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable& KmerHashTable::operator=(const KmerHashTable&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:186:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 186 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 In file included from /usr/include/c++/14/algorithm:61, from /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:5: /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: error: no matching function for call to 'max(long unsigned int, size_t)' 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: error: no matching function for call to 'max(long unsigned int, size_t)' 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: error: no matching function for call to 'max(long unsigned int, size_t)' 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:694:97: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 694 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'const_UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:768:43: warning: right shift count >= width of type [-Wshift-count-overflow] 768 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:892:43: warning: right shift count >= width of type [-Wshift-count-overflow] 892 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable::const_iterator KmerHashTable::find(const Kmer&) const': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:326:57: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 326 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'const_UnitigMap CompactedDBG::find(const Kmer&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1016:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1016 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const Kmer&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1219:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1219 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1342:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1342 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1498:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1498 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable& KmerHashTable::operator=(KmerHashTable&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:212:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 212 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1658:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1658 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1848:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1848 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::init_tables(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:776:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 776 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:776:26: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 776 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'size_t KmerHashTable::erase(const_iterator)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:412:80: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 412 | const size_t h = fastmod::fastmod_u64(table_keys[it.h].hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::clear()': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:249:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 249 | M_u64 = 0; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::reserve(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:804:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 804 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:804:30: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 804 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:430:110: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 430 | while ((i != size_) && !table_keys[j2].isEmpty() && (fastmod::fastmod_u64(table_keys[j2].hash(), M_u64, size_) != j2)) { | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable::iterator KmerHashTable::find(const Kmer&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:261:57: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 261 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'std::pair::iterator_, bool> KmerHashTable::insert(const Kmer&, const T&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:469:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 469 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable::const_iterator KmerHashTable::find(const Kmer&) const': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:326:57: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 326 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:569:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 569 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'size_t KmerHashTable::erase(const_iterator)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:412:80: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 412 | const size_t h = fastmod::fastmod_u64(table_keys[it.h].hash(), M_u64, size_); | ^~~~~ | M_Ef64 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:36: /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:119:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 119 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::recomputeMaxPSL(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:664:85: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 664 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update(const char*, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:201:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 201 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update_p(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:270:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 270 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update_p(const char*, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:366:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 366 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:430:110: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 430 | while ((i != size_) && !table_keys[j2].isEmpty() && (fastmod::fastmod_u64(table_keys[j2].hash(), M_u64, size_) != j2)) { | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:577:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 577 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update(const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:654:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 654 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update_p(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:722:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 722 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::addUnitig(const std::string&, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4725:38: warning: left shift count >= width of type [-Wshift-count-overflow] 4725 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4727:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 4727 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update_p(const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:817:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 817 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::moveToAbundant()': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4912:92: warning: right shift count >= width of type [-Wshift-count-overflow] 4912 | if (static_cast(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4912:148: warning: right shift count >= width of type [-Wshift-count-overflow] 4912 | if (static_cast(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::addUnitig(const std::string&, size_t, size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5119:49: warning: left shift count >= width of type [-Wshift-count-overflow] 5119 | const size_t pos_id_unitig_r = (id_unitig_r << 32) | ((static_cast(!is_short_r) - 1) & MASK_CONTIG_TYPE); | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5122:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 5122 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5124:38: warning: left shift count >= width of type [-Wshift-count-overflow] 5124 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:694:97: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 694 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::swapUnitigs(bool, size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5315:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 5315 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5317:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5317 | size_t shift_id_unitig_a = id_a << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5318:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5318 | size_t shift_id_unitig_b = id_b << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'std::pair::iterator_, bool> KmerHashTable::insert(const Kmer&, const T&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:469:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 469 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp: In static member function 'static int FileParser::getFileFormat(const char*)': /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:230:64: warning: right shift count >= width of type [-Wshift-count-overflow] 230 | else if ((reinterpret_cast(buffer)[0] >> 32) == BFG_GRAPHBIN_FORMAT_HEADER) ret_v = 3; // BFG | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/File_Parser.hpp:231:64: warning: right shift count >= width of type [-Wshift-count-overflow] 231 | else if ((reinterpret_cast(buffer)[0] >> 32) == BFG_METABIN_FORMAT_HEADER) ret_v = 4; // BFI | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:39: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:220:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 220 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::init_tables(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:776:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 776 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:776:26: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 776 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:569:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 569 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'typename std::enable_if<(! is_void), void>::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6010:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6010 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6011:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6011 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'typename std::enable_if::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6170:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6170 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6171:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6171 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::deleteUnitig_(bool, bool, size_t, const std::string&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6315:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6315 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6316:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6316 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::reserve(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:804:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 804 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:804:30: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 804 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const Kmer&, const preAllocMinHashIterator&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6594:42: warning: right shift count >= width of type [-Wshift-count-overflow] 6594 | unitig_id = v(i, flag_v) >> 32; | ~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::recomputeMaxPSL(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:664:85: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 664 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ | M_Ef64 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:34: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:19:5: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 19 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:826: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::build(CDBG_Build_opt&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: error: no matching function for call to 'max(long unsigned int, size_t)' 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51, from /usr/include/c++/14/bits/locale_classes.h:40, from /usr/include/c++/14/bits/ios_base.h:41, from /usr/include/c++/14/ios:44, from /usr/include/c++/14/ostream:40, from /usr/include/c++/14/iostream:41, from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:12: /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided In file included from /usr/include/c++/14/algorithm:61, from /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:5: /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: error: no matching function for call to 'max(long unsigned int, size_t)' 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: error: no matching function for call to 'max(long unsigned int, size_t)' 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In copy constructor 'KmerHashTable::KmerHashTable(const KmerHashTable&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:153:113: error: class 'KmerHashTable' does not have any field named 'M_u64' 153 | size_(o.size_), pop(o.pop), sum_psl(o.sum_psl), max_psl(o.max_psl), M_u64(o.M_u64) { | ^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: error: no matching function for call to 'max(long unsigned int, size_t)' 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In constructor 'KmerHashTable::KmerHashTable(KmerHashTable&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:167:41: error: class 'KmerHashTable' does not have any field named 'M_u64' 167 | M_u64(o.M_u64), max_ratio_occupancy(o.max_ratio_occupancy) { | ^~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:694:97: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 694 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'const_UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:768:43: warning: right shift count >= width of type [-Wshift-count-overflow] 768 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:892:43: warning: right shift count >= width of type [-Wshift-count-overflow] 892 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'const_UnitigMap CompactedDBG::find(const Kmer&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1016:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1016 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const Kmer&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1219:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1219 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1342:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1342 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1498:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1498 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable& KmerHashTable::operator=(const KmerHashTable&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:186:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 186 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1658:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1658 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1848:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1848 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::init_tables(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:776:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 776 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:776:26: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 776 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable& KmerHashTable::operator=(KmerHashTable&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:212:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 212 | M_u64 = o.M_u64; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::reserve(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:804:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 804 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:804:30: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 804 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::clear()': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:249:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 249 | M_u64 = 0; | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable::iterator KmerHashTable::find(const Kmer&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:261:57: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 261 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'KmerHashTable::const_iterator KmerHashTable::find(const Kmer&) const': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:326:57: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 326 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'size_t KmerHashTable::erase(const_iterator)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:412:80: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 412 | const size_t h = fastmod::fastmod_u64(table_keys[it.h].hash(), M_u64, size_); | ^~~~~ | M_Ef64 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:828: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::read(const std::string&, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: error: no matching function for call to 'max(long unsigned int, size_t)' 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: error: no matching function for call to 'max(long unsigned int, size_t)' 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:36: /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:119:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 119 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update(const char*, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:201:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 201 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update_p(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:270:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 270 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update_p(const char*, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:366:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 366 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:577:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 577 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update(const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:654:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 654 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:430:110: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 430 | while ((i != size_) && !table_keys[j2].isEmpty() && (fastmod::fastmod_u64(table_keys[j2].hash(), M_u64, size_) != j2)) { | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::readBinaryIndex(std::istream&, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:993:55: warning: right shift count >= width of type [-Wshift-count-overflow] 993 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'std::pair::iterator_, bool> KmerHashTable::insert(const Kmer&, const T&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:469:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 469 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update_p(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:722:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 722 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update_p(const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:817:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 817 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:569:53: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 569 | size_t h = fastmod::fastmod_u64(key.hash(), M_u64, size_); | ^~~~~ | M_Ef64 In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:39: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:220:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 220 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1037:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1037 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::recomputeMaxPSL(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:664:85: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 664 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1052:61: warning: left shift count >= width of type [-Wshift-count-overflow] 1052 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1085:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1085 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1094:57: warning: left shift count >= width of type [-Wshift-count-overflow] 1094 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos; | ~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1121:66: warning: right shift count >= width of type [-Wshift-count-overflow] 1121 | vector v_bmp_abundant((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1122:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1122 | vector v_bmp_overcrowded((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1131:58: warning: right shift count >= width of type [-Wshift-count-overflow] 1131 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1132:64: warning: right shift count >= width of type [-Wshift-count-overflow] 1132 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'std::pair CompactedDBG::readBinaryGraph(std::istream&)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1230:55: warning: right shift count >= width of type [-Wshift-count-overflow] 1230 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryGraph(std::ostream&, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1431:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1431 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::addUnitig(const std::string&, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4725:38: warning: left shift count >= width of type [-Wshift-count-overflow] 4725 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4727:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 4727 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1471:67: warning: right shift count >= width of type [-Wshift-count-overflow] 1471 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1494:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1494 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1501:45: warning: right shift count >= width of type [-Wshift-count-overflow] 1501 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1512:49: warning: right shift count >= width of type [-Wshift-count-overflow] 1512 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1516:53: warning: right shift count >= width of type [-Wshift-count-overflow] 1516 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1531:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1531 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1535:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1535 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1681:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1681 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1; | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1695:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1695 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1706:73: warning: right shift count >= width of type [-Wshift-count-overflow] 1706 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1713:70: warning: right shift count >= width of type [-Wshift-count-overflow] 1713 | const size_t id_bmp = id_special >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::moveToAbundant()': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4912:92: warning: right shift count >= width of type [-Wshift-count-overflow] 4912 | if (static_cast(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1762:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1762 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1773:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1773 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4912:148: warning: right shift count >= width of type [-Wshift-count-overflow] 4912 | if (static_cast(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); | ~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:36: /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:119:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 119 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::addUnitig(const std::string&, size_t, size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5119:49: warning: left shift count >= width of type [-Wshift-count-overflow] 5119 | const size_t pos_id_unitig_r = (id_unitig_r << 32) | ((static_cast(!is_short_r) - 1) & MASK_CONTIG_TYPE); | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5122:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 5122 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5124:38: warning: left shift count >= width of type [-Wshift-count-overflow] 5124 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update(const char*, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:201:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 201 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::swapUnitigs(bool, size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5315:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 5315 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5317:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5317 | size_t shift_id_unitig_a = id_a << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5318:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5318 | size_t shift_id_unitig_b = id_b << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update_p(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:270:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 270 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update_p(const char*, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:366:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 366 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:694:97: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 694 | const size_t h = fastmod::fastmod_u64(table_keys[i].hash(), M_u64, size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:577:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 577 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update(const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:654:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 654 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update_p(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:722:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 722 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update_p(const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:817:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 817 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'typename std::enable_if<(! is_void), void>::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6010:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6010 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6011:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6011 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::init_tables(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:776:9: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 776 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:776:26: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 776 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'typename std::enable_if::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6170:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6170 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6171:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6171 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::deleteUnitig_(bool, bool, size_t, const std::string&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6315:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6315 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6316:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6316 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const Kmer&, const preAllocMinHashIterator&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6594:42: warning: right shift count >= width of type [-Wshift-count-overflow] 6594 | unitig_id = v(i, flag_v) >> 32; | ~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:39: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:220:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 220 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:826: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::build(CDBG_Build_opt&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: error: no matching function for call to 'max(long unsigned int, size_t)' 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:60, from /build/reproducible-path/bifrost-1.3.1/src/roaring.hh:10, from /build/reproducible-path/bifrost-1.3.1/src/ColorSet.hpp:4: /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In member function 'void KmerHashTable::reserve(size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:804:13: error: 'M_u64' was not declared in this scope; did you mean 'M_Ef64'? 804 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~ | M_Ef64 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:804:30: error: 'computeM_u64' is not a member of 'fastmod'; did you mean 'computeM_u32'? 804 | M_u64 = fastmod::computeM_u64(size_); | ^~~~~~~~~~~~ | computeM_u32 In file included from /usr/include/c++/14/algorithm:61: /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: error: no matching function for call to 'max(long unsigned int, size_t)' 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: error: no matching function for call to 'max(long unsigned int, size_t)' 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: error: no matching function for call to 'max(long unsigned int, size_t)' 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'const_UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:768:43: warning: right shift count >= width of type [-Wshift-count-overflow] 768 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:892:43: warning: right shift count >= width of type [-Wshift-count-overflow] 892 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'const_UnitigMap CompactedDBG::find(const Kmer&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1016:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1016 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const Kmer&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1219:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1219 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1342:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1342 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1498:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1498 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1658:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1658 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ In file included from /usr/include/c++/14/string:42, from /build/reproducible-path/bifrost-1.3.1/src/GFA_Parser.hpp:4, from /build/reproducible-path/bifrost-1.3.1/src/GFA_Parser.cpp:1: In static member function 'static std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:435:21, inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:430:7, inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy_chars(_CharT*, const _CharT*, const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:489:16, inlined from 'void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::forward_iterator_tag) [with _FwdIterator = const char*; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.tcc:247:21, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, size_type, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:632:14, inlined from 'GFA_Parser::GFA_line GFA_Parser::read(size_t&, bool&, bool)' at /build/reproducible-path/bifrost-1.3.1/src/GFA_Parser.cpp:553:122: /usr/include/c++/14/bits/char_traits.h:427:56: warning: argument 2 null where non-null expected [-Wnonnull] 427 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/char_traits.h:427:56: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, unsigned int)' In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:826: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::build(CDBG_Build_opt&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: error: no matching function for call to 'max(long unsigned int, size_t)' 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/string:51, from /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.hpp:4: /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided In file included from /usr/include/c++/14/algorithm:61, from /build/reproducible-path/bifrost-1.3.1/src/Common.hpp:5: /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: error: no matching function for call to 'max(long unsigned int, size_t)' 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: error: no matching function for call to 'max(long unsigned int, size_t)' 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: error: no matching function for call to 'max(long unsigned int, size_t)' 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1848:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1848 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'const_UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:768:43: warning: right shift count >= width of type [-Wshift-count-overflow] 768 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:892:43: warning: right shift count >= width of type [-Wshift-count-overflow] 892 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'const_UnitigMap CompactedDBG::find(const Kmer&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1016:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1016 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:36: /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:119:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 119 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update(const char*, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:201:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 201 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const Kmer&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1219:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1219 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update_p(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:270:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 270 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadQualityHasherMinimizer::update_p(const char*, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:366:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 366 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1342:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1342 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:828: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::read(const std::string&, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: error: no matching function for call to 'max(long unsigned int, size_t)' 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:577:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 577 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: error: no matching function for call to 'max(long unsigned int, size_t)' 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update(const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:654:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 654 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update_p(const char*, size_t, const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:722:49: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 722 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1498:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1498 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp: In member function 'std::pair ReadHasherMinimizer::update_p(const char*, size_t)': /build/reproducible-path/bifrost-1.3.1/src/KmerStream.hpp:817:57: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 817 | size_t i = 0, j = 0, prev_pos_min = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1658:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1658 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1848:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1848 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:39: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:220:9: error: '__uint128_t' does not name a type; did you mean '__uint8_t'? 220 | __uint128_t M_u64; | ^~~~~~~~~~~ | __uint8_t /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::readBinaryIndex(std::istream&, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:993:55: warning: right shift count >= width of type [-Wshift-count-overflow] 993 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1037:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1037 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1052:61: warning: left shift count >= width of type [-Wshift-count-overflow] 1052 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1085:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1085 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1094:57: warning: left shift count >= width of type [-Wshift-count-overflow] 1094 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos; | ~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1121:66: warning: right shift count >= width of type [-Wshift-count-overflow] 1121 | vector v_bmp_abundant((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1122:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1122 | vector v_bmp_overcrowded((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1131:58: warning: right shift count >= width of type [-Wshift-count-overflow] 1131 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1132:64: warning: right shift count >= width of type [-Wshift-count-overflow] 1132 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'std::pair CompactedDBG::readBinaryGraph(std::istream&)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1230:55: warning: right shift count >= width of type [-Wshift-count-overflow] 1230 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryGraph(std::ostream&, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1431:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1431 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1471:67: warning: right shift count >= width of type [-Wshift-count-overflow] 1471 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1494:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1494 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1501:45: warning: right shift count >= width of type [-Wshift-count-overflow] 1501 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1512:49: warning: right shift count >= width of type [-Wshift-count-overflow] 1512 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1516:53: warning: right shift count >= width of type [-Wshift-count-overflow] 1516 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1531:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1531 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1535:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1535 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1681:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1681 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1; | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1695:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1695 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1706:73: warning: right shift count >= width of type [-Wshift-count-overflow] 1706 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1713:70: warning: right shift count >= width of type [-Wshift-count-overflow] 1713 | const size_t id_bmp = id_special >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1762:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1762 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1773:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1773 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:826: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::build(CDBG_Build_opt&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: error: no matching function for call to 'max(long unsigned int, size_t)' 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/14/algorithm:60, from /build/reproducible-path/bifrost-1.3.1/src/roaring.hh:10, from /build/reproducible-path/bifrost-1.3.1/src/ColorSet.hpp:4: /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided In file included from /usr/include/c++/14/algorithm:61: /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:653:38: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 653 | nb_unique_kmers = max(1UL, kms.KmerF0()); | ~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: error: no matching function for call to 'max(long unsigned int, size_t)' 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:654:43: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 654 | nb_unique_minimizers = max(1UL, kms.MinimizerF0()); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: error: no matching function for call to 'max(long unsigned int, size_t)' 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:655:63: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 655 | nb_non_unique_kmers = reference_mode ? 0 : max(1UL, nb_unique_kmers - min(nb_unique_kmers, kms.Kmerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: error: no matching function for call to 'max(long unsigned int, size_t)' 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:656:68: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 656 | nb_non_unique_minimizers = reference_mode ? 0 : max(1UL, nb_unique_minimizers - min(nb_unique_minimizers, kms.Minimizerf1())); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'const_UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:768:43: warning: right shift count >= width of type [-Wshift-count-overflow] 768 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:892:43: warning: right shift count >= width of type [-Wshift-count-overflow] 892 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'const_UnitigMap CompactedDBG::find(const Kmer&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1016:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1016 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const Kmer&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1219:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1219 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1342:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1342 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1498:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1498 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) const': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1658:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1658 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1848:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1848 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::addUnitig(const std::string&, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4725:38: warning: left shift count >= width of type [-Wshift-count-overflow] 4725 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4727:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 4727 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::moveToAbundant()': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4912:92: warning: right shift count >= width of type [-Wshift-count-overflow] 4912 | if (static_cast(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4912:148: warning: right shift count >= width of type [-Wshift-count-overflow] 4912 | if (static_cast(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::addUnitig(const std::string&, size_t, size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5119:49: warning: left shift count >= width of type [-Wshift-count-overflow] 5119 | const size_t pos_id_unitig_r = (id_unitig_r << 32) | ((static_cast(!is_short_r) - 1) & MASK_CONTIG_TYPE); | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5122:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 5122 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5124:38: warning: left shift count >= width of type [-Wshift-count-overflow] 5124 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::swapUnitigs(bool, size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5315:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 5315 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5317:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5317 | size_t shift_id_unitig_a = id_a << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5318:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5318 | size_t shift_id_unitig_b = id_b << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'typename std::enable_if<(! is_void), void>::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6010:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6010 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6011:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6011 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::addUnitig(const std::string&, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4725:38: warning: left shift count >= width of type [-Wshift-count-overflow] 4725 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4727:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 4727 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'typename std::enable_if::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6170:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6170 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6171:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6171 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::addUnitig(const std::string&, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4725:38: warning: left shift count >= width of type [-Wshift-count-overflow] 4725 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4727:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 4727 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::deleteUnitig_(bool, bool, size_t, const std::string&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6315:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6315 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6316:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6316 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::moveToAbundant()': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4912:92: warning: right shift count >= width of type [-Wshift-count-overflow] 4912 | if (static_cast(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4912:148: warning: right shift count >= width of type [-Wshift-count-overflow] 4912 | if (static_cast(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::addUnitig(const std::string&, size_t, size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5119:49: warning: left shift count >= width of type [-Wshift-count-overflow] 5119 | const size_t pos_id_unitig_r = (id_unitig_r << 32) | ((static_cast(!is_short_r) - 1) & MASK_CONTIG_TYPE); | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5122:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 5122 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5124:38: warning: left shift count >= width of type [-Wshift-count-overflow] 5124 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::moveToAbundant()': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4912:92: warning: right shift count >= width of type [-Wshift-count-overflow] 4912 | if (static_cast(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4912:148: warning: right shift count >= width of type [-Wshift-count-overflow] 4912 | if (static_cast(unitig_id_pos & MASK_CONTIG_TYPE) && ((unitig_id_pos >> 32) != RESERVED_ID)) v_km_rm.push_back(unitig_id_pos >> 32); | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const Kmer&, const preAllocMinHashIterator&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6594:42: warning: right shift count >= width of type [-Wshift-count-overflow] 6594 | unitig_id = v(i, flag_v) >> 32; | ~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'bool CompactedDBG::addUnitig(const std::string&, size_t, size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5119:49: warning: left shift count >= width of type [-Wshift-count-overflow] 5119 | const size_t pos_id_unitig_r = (id_unitig_r << 32) | ((static_cast(!is_short_r) - 1) & MASK_CONTIG_TYPE); | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5122:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 5122 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5124:38: warning: left shift count >= width of type [-Wshift-count-overflow] 5124 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::swapUnitigs(bool, size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5315:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 5315 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5317:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5317 | size_t shift_id_unitig_a = id_a << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5318:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5318 | size_t shift_id_unitig_b = id_b << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::swapUnitigs(bool, size_t, size_t)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5315:40: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 5315 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5317:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5317 | size_t shift_id_unitig_a = id_a << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5318:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5318 | size_t shift_id_unitig_b = id_b << 32; | ~~~~~^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/DataManager.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:2: /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc: In instantiation of 'std::pair, UnitigColors*> DataStorage::insert_(Kmer, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1763:60: required from here 1763 | const pair, UnitigColors*> p(insert_(head, unitig_sz, force_overflow)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1741:45: warning: narrowing conversion of 'pos' from 'uint64_t' {aka 'long long unsigned int'} to 'unsigned int' [-Wnarrowing] 1741 | overflow.insert({{head, unitig_sz}, pos}); // Insertion | ^~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc: In instantiation of 'UnitigColors DataStorage::joinUnitigColors(const_UnitigColorMap&, const_UnitigColorMap&) const [with Unitig_data_t = void; const_UnitigColorMap = UnitigMap, DataStorage, true>]': /build/reproducible-path/bifrost-1.3.1/src/DataAccessor.tcc:174:48: required from here 174 | UnitigColors uc_ = ds->joinUnitigColors(um_dest, um_src); // Join the UnitigColors of the two reference unitigs | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1444:36: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 1444 | size_t prev_color_id = 0xffffffffffffffff; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1445:35: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 1445 | size_t prev_km_dist = 0xffffffffffffffff; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'typename std::enable_if<(! is_void), void>::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6010:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6010 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6011:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6011 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'typename std::enable_if::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6170:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6170 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6171:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6171 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::deleteUnitig_(bool, bool, size_t, const std::string&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6315:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6315 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6316:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6316 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'typename std::enable_if<(! is_void), void>::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6010:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6010 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6011:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6011 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const Kmer&, const preAllocMinHashIterator&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6594:42: warning: right shift count >= width of type [-Wshift-count-overflow] 6594 | unitig_id = v(i, flag_v) >> 32; | ~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'typename std::enable_if::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6170:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6170 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6171:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6171 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'void CompactedDBG::deleteUnitig_(bool, bool, size_t, const std::string&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6315:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6315 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6316:44: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744071562067968' to '2147483648' [-Woverflow] 6316 | const size_t mask = MASK_CONTIG_ID | MASK_CONTIG_TYPE; /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In member function 'UnitigMap CompactedDBG::find(const Kmer&, const preAllocMinHashIterator&)': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6594:42: warning: right shift count >= width of type [-Wshift-count-overflow] 6594 | unitig_id = v(i, flag_v) >> 32; | ~~~~~~~~~~~~~^~~~~ In file included from /usr/include/c++/14/string:42, from /build/reproducible-path/bifrost-1.3.1/src/GFA_Parser.hpp:4, from /build/reproducible-path/bifrost-1.3.1/src/GFA_Parser.cpp:1: In static member function 'static std::char_traits::char_type* std::char_traits::copy(char_type*, const char_type*, std::size_t)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:435:21, inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:430:7, inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy_chars(_CharT*, const _CharT*, const _CharT*) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:489:16, inlined from 'void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_M_construct(_InIterator, _InIterator, std::forward_iterator_tag) [with _FwdIterator = const char*; _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.tcc:247:21, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, size_type, const _Alloc&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/14/bits/basic_string.h:632:14, inlined from 'GFA_Parser::GFA_line GFA_Parser::read(size_t&, bool&, bool)' at /build/reproducible-path/bifrost-1.3.1/src/GFA_Parser.cpp:553:122: /usr/include/c++/14/bits/char_traits.h:427:56: warning: argument 2 null where non-null expected [-Wnonnull] 427 | return static_cast(__builtin_memcpy(__s1, __s2, __n)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/char_traits.h:427:56: note: in a call to built-in function 'void* __builtin_memcpy(void*, const void*, unsigned int)' In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:828: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::read(const std::string&, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: error: no matching function for call to 'max(long unsigned int, size_t)' 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: error: no matching function for call to 'max(long unsigned int, size_t)' 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:828: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::read(const std::string&, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: error: no matching function for call to 'max(long unsigned int, size_t)' 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: error: no matching function for call to 'max(long unsigned int, size_t)' 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::readBinaryIndex(std::istream&, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:993:55: warning: right shift count >= width of type [-Wshift-count-overflow] 993 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1037:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1037 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1052:61: warning: left shift count >= width of type [-Wshift-count-overflow] 1052 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1085:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1085 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1094:57: warning: left shift count >= width of type [-Wshift-count-overflow] 1094 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos; | ~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1121:66: warning: right shift count >= width of type [-Wshift-count-overflow] 1121 | vector v_bmp_abundant((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1122:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1122 | vector v_bmp_overcrowded((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1131:58: warning: right shift count >= width of type [-Wshift-count-overflow] 1131 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1132:64: warning: right shift count >= width of type [-Wshift-count-overflow] 1132 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'std::pair CompactedDBG::readBinaryGraph(std::istream&)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1230:55: warning: right shift count >= width of type [-Wshift-count-overflow] 1230 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = true; T = CompressedCoverage_t >]': /build/reproducible-path/bifrost-1.3.1/src/UnitigIterator.tcc:7:145: required from 'unitigIterator::unitigIterator() [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = false]' 7 | unitigIterator::unitigIterator() : i(0), v_unitigs_sz(0), v_kmers_sz(0), h_kmers_ccov_sz(0), sz(0), invalid(true), cdbg(nullptr) {} | ^ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:979:54: required from here 979 | typename ColoredCDBG::iterator l_a, l_b; | ^~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = true; T = CompressedCoverage_t >]': /build/reproducible-path/bifrost-1.3.1/src/UnitigIterator.tcc:55:9: required from 'unitigIterator& unitigIterator::operator++() [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = false]' 55 | ++it_h_kmers_ccov; | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:991:86: required from here 991 | for (size_t cpt = 0; (cpt < chunk) && (l_b != g_b); ++cpt, ++l_b){} | ^~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::readBinaryIndex(std::istream&, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:993:55: warning: right shift count >= width of type [-Wshift-count-overflow] 993 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryGraph(std::ostream&, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1431:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1431 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1471:67: warning: right shift count >= width of type [-Wshift-count-overflow] 1471 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1037:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1037 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1494:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1494 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1052:61: warning: left shift count >= width of type [-Wshift-count-overflow] 1052 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1501:45: warning: right shift count >= width of type [-Wshift-count-overflow] 1501 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1512:49: warning: right shift count >= width of type [-Wshift-count-overflow] 1512 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1516:53: warning: right shift count >= width of type [-Wshift-count-overflow] 1516 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1085:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1085 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1094:57: warning: left shift count >= width of type [-Wshift-count-overflow] 1094 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos; | ~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1531:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1531 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1535:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1535 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1121:66: warning: right shift count >= width of type [-Wshift-count-overflow] 1121 | vector v_bmp_abundant((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1122:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1122 | vector v_bmp_overcrowded((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1131:58: warning: right shift count >= width of type [-Wshift-count-overflow] 1131 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1132:64: warning: right shift count >= width of type [-Wshift-count-overflow] 1132 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1681:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1681 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1; | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1695:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1695 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'std::pair CompactedDBG::readBinaryGraph(std::istream&)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1230:55: warning: right shift count >= width of type [-Wshift-count-overflow] 1230 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1706:73: warning: right shift count >= width of type [-Wshift-count-overflow] 1706 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1713:70: warning: right shift count >= width of type [-Wshift-count-overflow] 1713 | const size_t id_bmp = id_special >> 32; | ~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.hpp:828: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::read(const std::string&, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: error: no matching function for call to 'max(long unsigned int, size_t)' 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1762:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1762 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:191:60: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 191 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1773:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1773 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: error: no matching function for call to 'max(long unsigned int, size_t)' 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&)' 257 | max(const _Tp& __a, const _Tp& __b) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:257:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: note: deduced conflicting types for parameter 'const _Tp' ('long unsigned int' and 'size_t' {aka 'unsigned int'}) 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate: 'template const _Tp& std::max(const _Tp&, const _Tp&, _Compare)' 303 | max(const _Tp& __a, const _Tp& __b, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algobase.h:303:5: note: candidate expects 3 arguments, 2 provided /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5705 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5705:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5715:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5715 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5715:5: note: template argument deduction/substitution failed: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:261:60: note: mismatched types 'std::initializer_list<_Tp>' and 'long unsigned int' 261 | MinimizerIndex hmap_min_unitigs_tmp(max(1UL, kms.MinimizerF0()) * 1.05); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryGraph(std::ostream&, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1431:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1431 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1471:67: warning: right shift count >= width of type [-Wshift-count-overflow] 1471 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1494:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1494 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1501:45: warning: right shift count >= width of type [-Wshift-count-overflow] 1501 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1512:49: warning: right shift count >= width of type [-Wshift-count-overflow] 1512 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1516:53: warning: right shift count >= width of type [-Wshift-count-overflow] 1516 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1531:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1531 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1535:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1535 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1681:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1681 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1; | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1695:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1695 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1706:73: warning: right shift count >= width of type [-Wshift-count-overflow] 1706 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1713:70: warning: right shift count >= width of type [-Wshift-count-overflow] 1713 | const size_t id_bmp = id_special >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1762:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1762 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1773:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1773 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ In file included from /build/reproducible-path/bifrost-1.3.1/src/DataManager.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.hpp:10, from /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:2: /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc: In instantiation of 'std::pair, UnitigColors*> DataStorage::insert_(Kmer, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1763:60: required from here 1763 | const pair, UnitigColors*> p(insert_(head, unitig_sz, force_overflow)); | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1741:45: warning: narrowing conversion of 'pos' from 'uint64_t' {aka 'long long unsigned int'} to 'unsigned int' [-Wnarrowing] 1741 | overflow.insert({{head, unitig_sz}, pos}); // Insertion | ^~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc: In instantiation of 'UnitigColors DataStorage::joinUnitigColors(const_UnitigColorMap&, const_UnitigColorMap&) const [with Unitig_data_t = void; const_UnitigColorMap = UnitigMap, DataStorage, true>]': /build/reproducible-path/bifrost-1.3.1/src/DataAccessor.tcc:174:48: required from here 174 | UnitigColors uc_ = ds->joinUnitigColors(um_dest, um_src); // Join the UnitigColors of the two reference unitigs | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1444:36: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 1444 | size_t prev_color_id = 0xffffffffffffffff; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1445:35: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 1445 | size_t prev_km_dist = 0xffffffffffffffff; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp: In member function 'UnitigColors UnitigColors::getFullColors(const UnitigMapBase&) const': /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp:1154:28: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 1154 | size_t prev_color_ID = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp: In constructor 'UnitigColors::UnitigColors_const_iterator::UnitigColors_const_iterator(const UnitigColors*, size_t, size_t, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp:1350:123: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 1350 | end_pos(0), ck_id(0xffffffffffffffff), it_setBits(0xffffffffffffffff), | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp:1617:45: warning: conversion from 'long long unsigned int' to 'uintptr_t' {aka 'unsigned int'} changes value from '18446744073709551608' to '4294967288' [-Woverflow] 1617 | const uintptr_t UnitigColors::pointerMask = 0xFFFFFFFFFFFFFFF8; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp: In member function 'UnitigColors UnitigColors::getFullColors(const UnitigMapBase&) const': /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp:1154:28: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 1154 | size_t prev_color_ID = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp: In constructor 'UnitigColors::UnitigColors_const_iterator::UnitigColors_const_iterator(const UnitigColors*, size_t, size_t, size_t, bool)': /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp:1350:123: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 1350 | end_pos(0), ck_id(0xffffffffffffffff), it_setBits(0xffffffffffffffff), | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp: At global scope: /build/reproducible-path/bifrost-1.3.1/src/ColorSet.cpp:1617:45: warning: conversion from 'long long unsigned int' to 'uintptr_t' {aka 'unsigned int'} changes value from '18446744073709551608' to '4294967288' [-Woverflow] 1617 | const uintptr_t UnitigColors::pointerMask = 0xFFFFFFFFFFFFFFF8; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::readBinaryIndex(std::istream&, uint64_t)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:993:55: warning: right shift count >= width of type [-Wshift-count-overflow] 993 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1037:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1037 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1052:61: warning: left shift count >= width of type [-Wshift-count-overflow] 1052 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1085:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1085 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1094:57: warning: left shift count >= width of type [-Wshift-count-overflow] 1094 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos; | ~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1121:66: warning: right shift count >= width of type [-Wshift-count-overflow] 1121 | vector v_bmp_abundant((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1122:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1122 | vector v_bmp_overcrowded((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1131:58: warning: right shift count >= width of type [-Wshift-count-overflow] 1131 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1132:64: warning: right shift count >= width of type [-Wshift-count-overflow] 1132 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'std::pair CompactedDBG::readBinaryGraph(std::istream&)': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1230:55: warning: right shift count >= width of type [-Wshift-count-overflow] 1230 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryGraph(std::ostream&, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1431:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1431 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1471:67: warning: right shift count >= width of type [-Wshift-count-overflow] 1471 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In lambda function: /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1494:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1494 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1501:45: warning: right shift count >= width of type [-Wshift-count-overflow] 1501 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1512:49: warning: right shift count >= width of type [-Wshift-count-overflow] 1512 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1516:53: warning: right shift count >= width of type [-Wshift-count-overflow] 1516 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1531:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1531 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1535:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1535 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In member function 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1681:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1681 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1; | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1695:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1695 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1706:73: warning: right shift count >= width of type [-Wshift-count-overflow] 1706 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1713:70: warning: right shift count >= width of type [-Wshift-count-overflow] 1713 | const size_t id_bmp = id_special >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1762:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1762 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1773:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1773 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = true; T = CompressedCoverage_t >]': /build/reproducible-path/bifrost-1.3.1/src/UnitigIterator.tcc:7:145: required from 'unitigIterator::unitigIterator() [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = false]' 7 | unitigIterator::unitigIterator() : i(0), v_unitigs_sz(0), v_kmers_sz(0), h_kmers_ccov_sz(0), sz(0), invalid(true), cdbg(nullptr) {} | ^ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:979:54: required from here 979 | typename ColoredCDBG::iterator l_a, l_b; | ^~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = true; T = CompressedCoverage_t >]': /build/reproducible-path/bifrost-1.3.1/src/UnitigIterator.tcc:55:9: required from 'unitigIterator& unitigIterator::operator++() [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = false]' 55 | ++it_h_kmers_ccov; | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:991:86: required from here 991 | for (size_t cpt = 0; (cpt < chunk) && (l_b != g_b); ++cpt, ++l_b){} | ^~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t, size_t) [with bool is_const = false; T = CompressedCoverage_t >; KHT_ptr_t = KmerHashTable > >*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:389:61: required from 'KmerHashTable::iterator KmerHashTable::find(size_t) [with T = CompressedCoverage_t >; iterator = KmerHashTable > >::iterator_; size_t = unsigned int]' 389 | if ((h < size_) && !table_keys[h].isEmpty()) return iterator(this, h); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:96:55: required from 'Kmer UnitigMap::getUnitigHead() const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = false]' 96 | if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig).getKey(); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1600:43: required from here 1600 | const Kmer head = um.getUnitigHead(); | ~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:37:72: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 37 | iterator_(KHT_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = false; T = CompressedCoverage_t >; KHT_ptr_t = KmerHashTable > >*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:391:16: required from 'KmerHashTable::iterator KmerHashTable::find(size_t) [with T = CompressedCoverage_t >; iterator = KmerHashTable > >::iterator_; size_t = unsigned int]' 391 | return iterator(this); | ^~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:96:55: required from 'Kmer UnitigMap::getUnitigHead() const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = false]' 96 | if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig).getKey(); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1600:43: required from here 1600 | const Kmer head = um.getUnitigHead(); | ~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'UnitigMap CompactedDBG::find(const Kmer&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8075:26: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 8075 | if (!find(head.backwardBase(alpha[i]), true).isEmpty){ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1219:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1219 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'void CompactedDBG::swapUnitigs(bool, size_t, size_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8104:25: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 8104 | swapUnitigs(false, j, v_unitigs_sz), | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5317:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5317 | size_t shift_id_unitig_a = id_a << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5318:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5318 | size_t shift_id_unitig_b = id_b << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = false; T = CompressedCoverage_t >]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8160:97: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 8160 | for (typename h_kmers_ccov_t::iterator it = h_kmers_ccov.begin(); it != h_kmers_ccov.end(); ++it) { | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'typename std::enable_if<(! is_void), void>::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), void>::type = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8197:87: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 8197 | for (j = v_unitigs_sz; j < v_unitigs.size(); ++j) deleteUnitig_::value>(false, false, j); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6010:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6010 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = false; T = char]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7469:79: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7469 | for (KmerHashTable::iterator it = joins.begin(); it != joins.end(); ++it) { | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::addUnitig(const std::string&, size_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7577:30: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7577 | addUnitig(joinSeq, v_unitigs_size); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4725:38: warning: left shift count >= width of type [-Wshift-count-overflow] 4725 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4865:62: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow] 4865 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v); /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = true; T = CompressedCoverage_t]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:130:9: required from 'CompactedDBG& CompactedDBG::toDataGraph(CompactedDBG&&, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 130 | ++it_s; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:611:45: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 611 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = false; T = CompressedCoverage_t]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:3516:125: required from 'bool CompactedDBG::construct(const CDBG_Build_opt&, DualBlockedBloomFilter&, Roaring&, size_t, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 3516 | for (typename h_kmers_ccov_t::iterator it = dbg_extra.h_kmers_ccov.begin(); it != dbg_extra.h_kmers_ccov.end(); ++it) { | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:679:62: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 679 | if (construct_finished) construct_finished = construct(opt, dbbf, r, nb_unique_minimizers, nb_non_unique_minimizers, nb_unique_kmers, nb_non_unique_kmers); // Construction step | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'UnitigMap CompactedDBG::find(const Kmer&, bool) [with Unitig_data_t = void; Graph_data_t = void]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:3524:53: required from 'bool CompactedDBG::construct(const CDBG_Build_opt&, DualBlockedBloomFilter&, Roaring&, size_t, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 3524 | const UnitigMap um2 = find(km, true); | ~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:679:62: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 679 | if (construct_finished) construct_finished = construct(opt, dbbf, r, nb_unique_minimizers, nb_non_unique_minimizers, nb_unique_kmers, nb_non_unique_kmers); // Construction step | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1219:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1219 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t, size_t) [with bool is_const = false; T = CompressedCoverage_t >; KHT_ptr_t = KmerHashTable > >*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:389:61: required from 'KmerHashTable::iterator KmerHashTable::find(size_t) [with T = CompressedCoverage_t >; iterator = KmerHashTable > >::iterator_; size_t = unsigned int]' 389 | if ((h < size_) && !table_keys[h].isEmpty()) return iterator(this, h); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:96:55: required from 'Kmer UnitigMap::getUnitigHead() const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = false]' 96 | if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig).getKey(); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1600:43: required from here 1600 | const Kmer head = um.getUnitigHead(); | ~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:37:72: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 37 | iterator_(KHT_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = false; T = CompressedCoverage_t >; KHT_ptr_t = KmerHashTable > >*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:391:16: required from 'KmerHashTable::iterator KmerHashTable::find(size_t) [with T = CompressedCoverage_t >; iterator = KmerHashTable > >::iterator_; size_t = unsigned int]' 391 | return iterator(this); | ^~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:96:55: required from 'Kmer UnitigMap::getUnitigHead() const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = false]' 96 | if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig).getKey(); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/DataStorage.tcc:1600:43: required from here 1600 | const Kmer head = um.getUnitigHead(); | ~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:121: src/CMakeFiles/bifrost_static.dir/ColorSet.cpp.o] Error 1 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'void CompactedDBG::swapUnitigs(bool, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8104:25: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 8104 | swapUnitigs(false, j, v_unitigs_sz), | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5317:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5317 | size_t shift_id_unitig_a = id_a << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5318:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5318 | size_t shift_id_unitig_b = id_b << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'typename std::enable_if::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8197:87: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 8197 | for (j = v_unitigs_sz; j < v_unitigs.size(); ++j) deleteUnitig_::value>(false, false, j); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6170:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6170 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::addUnitig(const std::string&, size_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7735:30: required from 'typename std::enable_if::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = unsigned int; size_t = unsigned int]' 7735 | addUnitig(joinSeq, v_unitigs_size); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4725:38: warning: left shift count >= width of type [-Wshift-count-overflow] 4725 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'UnitigMap CompactedDBG::find(const Kmer&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8075:26: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 8075 | if (!find(head.backwardBase(alpha[i]), true).isEmpty){ | ~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1219:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1219 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4865:62: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow] 4865 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v); /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'void CompactedDBG::swapUnitigs(bool, size_t, size_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8104:25: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 8104 | swapUnitigs(false, j, v_unitigs_sz), | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5317:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5317 | size_t shift_id_unitig_a = id_a << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5318:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5318 | size_t shift_id_unitig_b = id_b << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = false; T = CompressedCoverage_t >]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8160:97: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 8160 | for (typename h_kmers_ccov_t::iterator it = h_kmers_ccov.begin(); it != h_kmers_ccov.end(); ++it) { | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) const [with Unitig_data_t = void; Graph_data_t = void]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:468:72: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 468 | const vector> pred = findPredecessors(head, true); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1342:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1342 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'typename std::enable_if<(! is_void), void>::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), void>::type = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8197:87: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 8197 | for (j = v_unitigs_sz; j < v_unitigs.size(); ++j) deleteUnitig_::value>(false, false, j); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6010:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6010 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:469:70: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 469 | const vector> succ = findSuccessors(tail, 4, true); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1658:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1658 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = false; T = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:667:78: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 667 | for (size_t i = 0; (it != idmap.end()) && (i < chunk_size); ++i, ++it) { | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = false; T = char]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7469:79: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7469 | for (KmerHashTable::iterator it = joins.begin(); it != joins.end(); ++it) { | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = false; T = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:804:57: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 804 | KmerHashTable::iterator l_it; | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::addUnitig(const std::string&, size_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7577:30: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7577 | addUnitig(joinSeq, v_unitigs_size); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4725:38: warning: left shift count >= width of type [-Wshift-count-overflow] 4725 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::writeBinaryGraph(std::ostream&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1362:28: required from 'bool CompactedDBG::writeBinaryGraph(const std::string&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 1362 | return writeBinaryGraph(out, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:84:62: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 84 | else if (BFG_output) write_success = writeBinaryGraph(fn, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4865:62: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow] 4865 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v); /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream; uint64_t = long long unsigned int; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1423:28: required from 'bool CompactedDBG::writeBinaryIndex(const std::string&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int; size_t = unsigned int]' 1423 | return writeBinaryIndex(out, checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:117:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 117 | write_success = writeBinaryIndex(fn, graph_checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1431:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1431 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1471:67: warning: right shift count >= width of type [-Wshift-count-overflow] 1471 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1472:77: warning: right shift count >= width of type [-Wshift-count-overflow] 1472 | const size_t nb_bmp_km_short = ((km_unitigs.size() * (k_ - g_ + 1)) >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1494:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1494 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1501:45: warning: right shift count >= width of type [-Wshift-count-overflow] 1501 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1512:49: warning: right shift count >= width of type [-Wshift-count-overflow] 1512 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1516:53: warning: right shift count >= width of type [-Wshift-count-overflow] 1516 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1531:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1531 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1535:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1535 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1681:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1681 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1; | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1695:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1695 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1706:73: warning: right shift count >= width of type [-Wshift-count-overflow] 1706 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1713:70: warning: right shift count >= width of type [-Wshift-count-overflow] 1713 | const size_t id_bmp = id_special >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1762:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1762 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1773:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1773 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG::merge(ColoredCDBG&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]' 203 | ret = CompactedDBG, DataStorage>::annotateSplitUnitigs(o, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:673:65: required from here 673 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5655:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5655 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5656:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5656 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::annotateSplitUnitig(const std::string&, LockGraph&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2284:52: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 2284 | annotateSplitUnitig(it_unitig->referenceUnitigToString(), lck_g/*, t*/, false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG::merge(ColoredCDBG&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]' 203 | ret = CompactedDBG, DataStorage>::annotateSplitUnitigs(o, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:673:65: required from here 673 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5806:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5806 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5807:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5807 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = true; T = CompressedCoverage_t]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:130:9: required from 'CompactedDBG& CompactedDBG::toDataGraph(CompactedDBG&&, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 130 | ++it_s; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:611:45: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 611 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'std::pair CompactedDBG::readBinaryGraph(std::istream&) [with Unitig_data_t = void; Graph_data_t = void; std::istream = std::basic_istream]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1198:27: required from 'std::pair CompactedDBG::readBinaryGraph(const std::string&) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 1198 | return readBinaryGraph(in); | ~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:382:46: required from 'bool CompactedDBG::read(const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 382 | p_readSuccess_checksum = readBinaryGraph(input_graph_fn); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:685:46: required from here 685 | else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1230:55: warning: right shift count >= width of type [-Wshift-count-overflow] 1230 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::readBinaryIndex(std::istream&, uint64_t) [with Unitig_data_t = void; Graph_data_t = void; std::istream = std::basic_istream; uint64_t = long long unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:945:27: required from 'bool CompactedDBG::readBinaryIndex(const std::string&, uint64_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int]' 945 | return readBinaryIndex(in, checksum); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:392:32: required from 'bool CompactedDBG::read(const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 392 | invalid = !readBinaryIndex(input_index_fn, p_readSuccess_checksum.first); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:685:46: required from here 685 | else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:993:55: warning: right shift count >= width of type [-Wshift-count-overflow] 993 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1037:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1037 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1052:61: warning: left shift count >= width of type [-Wshift-count-overflow] 1052 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; | ~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1085:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1085 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1094:57: warning: left shift count >= width of type [-Wshift-count-overflow] 1094 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos; | ~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1121:66: warning: right shift count >= width of type [-Wshift-count-overflow] 1121 | vector v_bmp_abundant((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1122:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1122 | vector v_bmp_overcrowded((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1131:58: warning: right shift count >= width of type [-Wshift-count-overflow] 1131 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1132:64: warning: right shift count >= width of type [-Wshift-count-overflow] 1132 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2129:13: required from 'bool CompactedDBG::merge(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2129 | if (annotateSplitUnitigs(o, nb_threads, verbose)){ | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:705:55: required from here 705 | success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5655:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5655 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5656:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5656 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = false; T = CompressedCoverage_t]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:3516:125: required from 'bool CompactedDBG::construct(const CDBG_Build_opt&, DualBlockedBloomFilter&, Roaring&, size_t, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 3516 | for (typename h_kmers_ccov_t::iterator it = dbg_extra.h_kmers_ccov.begin(); it != dbg_extra.h_kmers_ccov.end(); ++it) { | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:679:62: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 679 | if (construct_finished) construct_finished = construct(opt, dbbf, r, nb_unique_minimizers, nb_non_unique_minimizers, nb_unique_kmers, nb_non_unique_kmers); // Construction step | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::annotateSplitUnitig(const std::string&, LockGraph&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2284:52: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2284 | annotateSplitUnitig(it_unitig->referenceUnitigToString(), lck_g/*, t*/, false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2129:13: required from 'bool CompactedDBG::merge(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2129 | if (annotateSplitUnitigs(o, nb_threads, verbose)){ | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:705:55: required from here 705 | success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5806:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5806 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5807:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5807 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'UnitigMap CompactedDBG::find(const Kmer&, bool) [with Unitig_data_t = void; Graph_data_t = void]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:3524:53: required from 'bool CompactedDBG::construct(const CDBG_Build_opt&, DualBlockedBloomFilter&, Roaring&, size_t, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 3524 | const UnitigMap um2 = find(km, true); | ~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:679:62: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 679 | if (construct_finished) construct_finished = construct(opt, dbbf, r, nb_unique_minimizers, nb_non_unique_minimizers, nb_unique_kmers, nb_non_unique_kmers); // Construction step | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1219:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1219 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'void CompactedDBG::swapUnitigs(bool, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8104:25: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 8104 | swapUnitigs(false, j, v_unitigs_sz), | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5317:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5317 | size_t shift_id_unitig_a = id_a << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5318:37: warning: left shift count >= width of type [-Wshift-count-overflow] 5318 | size_t shift_id_unitig_b = id_b << 32; | ~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'typename std::enable_if::type CompactedDBG::deleteUnitig_(bool, bool, size_t, bool) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:8197:87: required from 'size_t CompactedDBG::removeUnitigs(bool, bool, std::vector&) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 8197 | for (j = v_unitigs_sz; j < v_unitigs.size(); ++j) deleteUnitig_::value>(false, false, j); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:706:26: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 706 | size_t removed = removeUnitigs(delete_short_isolated_unitigs, clip_short_tips, v_joins); | ^~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6170:42: warning: left shift count >= width of type [-Wshift-count-overflow] 6170 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::addUnitig(const std::string&, size_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7735:30: required from 'typename std::enable_if::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = unsigned int; size_t = unsigned int]' 7735 | addUnitig(joinSeq, v_unitigs_size); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4725:38: warning: left shift count >= width of type [-Wshift-count-overflow] 4725 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4865:62: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow] 4865 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v); /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) const [with Unitig_data_t = void; Graph_data_t = void]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:468:72: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 468 | const vector> pred = findPredecessors(head, true); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1342:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1342 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:469:70: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 469 | const vector> succ = findSuccessors(tail, 4, true); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1658:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1658 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_& KmerHashTable::iterator_::operator++() [with bool is_const = false; T = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:667:78: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 667 | for (size_t i = 0; (it != idmap.end()) && (i < chunk_size); ++i, ++it) { | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:88:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 88 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = false; T = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:804:57: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 804 | KmerHashTable::iterator l_it; | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::writeBinaryGraph(std::ostream&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1362:28: required from 'bool CompactedDBG::writeBinaryGraph(const std::string&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 1362 | return writeBinaryGraph(out, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:84:62: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 84 | else if (BFG_output) write_success = writeBinaryGraph(fn, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream; uint64_t = long long unsigned int; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1423:28: required from 'bool CompactedDBG::writeBinaryIndex(const std::string&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int; size_t = unsigned int]' 1423 | return writeBinaryIndex(out, checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:117:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 117 | write_success = writeBinaryIndex(fn, graph_checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1431:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1431 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1471:67: warning: right shift count >= width of type [-Wshift-count-overflow] 1471 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1472:77: warning: right shift count >= width of type [-Wshift-count-overflow] 1472 | const size_t nb_bmp_km_short = ((km_unitigs.size() * (k_ - g_ + 1)) >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1494:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1494 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1501:45: warning: right shift count >= width of type [-Wshift-count-overflow] 1501 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1512:49: warning: right shift count >= width of type [-Wshift-count-overflow] 1512 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1516:53: warning: right shift count >= width of type [-Wshift-count-overflow] 1516 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1531:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1531 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1535:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1535 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1681:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1681 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1; | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1695:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1695 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1706:73: warning: right shift count >= width of type [-Wshift-count-overflow] 1706 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1713:70: warning: right shift count >= width of type [-Wshift-count-overflow] 1713 | const size_t id_bmp = id_special >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1762:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1762 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1773:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1773 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG::merge(ColoredCDBG&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]' 203 | ret = CompactedDBG, DataStorage>::annotateSplitUnitigs(o, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:673:65: required from here 673 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5655:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5655 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5656:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5656 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t, size_t) [with bool is_const = true; T = CompressedCoverage_t >; KHT_ptr_t = const KmerHashTable > >*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:396:61: required from 'KmerHashTable::const_iterator KmerHashTable::find(size_t) const [with T = CompressedCoverage_t >; const_iterator = KmerHashTable > >::iterator_; size_t = unsigned int]' 396 | if ((h < size_) && !table_keys[h].isEmpty()) return const_iterator(this, h); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:274:51: required from 'typename std::enable_if<(! is_void), typename std::conditional::type>::type UnitigMap::getData_() const [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = true; typename std::enable_if<(! is_void), typename std::conditional::type>::type = const DataAccessor*; typename std::conditional::type = const DataAccessor*]' 274 | if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig)->getData(); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:253:39: required from 'UnitigMap::Unitig_data_ptr_t UnitigMap::getData() const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = true; Unitig_data_ptr_t = const DataAccessor*]' 253 | return getData_::value>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/DataAccessor.tcc:243:48: required from here 243 | const UnitigColors* uc_src = um_src.getData()->getUnitigColors(um_src); // Get UnitigColors associated with reference unitig of um_src | ~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:37:72: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 37 | iterator_(KHT_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = true; T = CompressedCoverage_t >; KHT_ptr_t = const KmerHashTable > >*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:398:16: required from 'KmerHashTable::const_iterator KmerHashTable::find(size_t) const [with T = CompressedCoverage_t >; const_iterator = KmerHashTable > >::iterator_; size_t = unsigned int]' 398 | return const_iterator(this); | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:274:51: required from 'typename std::enable_if<(! is_void), typename std::conditional::type>::type UnitigMap::getData_() const [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = true; typename std::enable_if<(! is_void), typename std::conditional::type>::type = const DataAccessor*; typename std::conditional::type = const DataAccessor*]' 274 | if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig)->getData(); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:253:39: required from 'UnitigMap::Unitig_data_ptr_t UnitigMap::getData() const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = true; Unitig_data_ptr_t = const DataAccessor*]' 253 | return getData_::value>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/DataAccessor.tcc:243:48: required from here 243 | const UnitigColors* uc_src = um_src.getData()->getUnitigColors(um_src); // Get UnitigColors associated with reference unitig of um_src | ~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = false; T = CompressedCoverage_t >]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:734:24: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = CompressedCoverage_t >; iterator = KmerHashTable > >::iterator_]' 734 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/UnitigIterator.tcc:12:165: required from 'unitigIterator::unitigIterator(CompactedDBG_ptr_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = false; CompactedDBG_ptr_t = CompactedDBG, DataStorage >*]' 12 | it_h_kmers_ccov((cdbg_ == nullptr) || cdbg_->invalid ? typename KmerHashTable>::const_iterator() : cdbg_->h_kmers_ccov.begin()){ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2509:14: required from 'CompactedDBG::iterator CompactedDBG::begin() [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; iterator = unitigIterator, DataStorage, false>]' 2509 | iterator it(this); | ^~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:968:59: required from here 968 | typename ColoredCDBG::iterator g_a = this->begin(); | ~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::annotateSplitUnitig(const std::string&, LockGraph&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2284:52: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 2284 | annotateSplitUnitig(it_unitig->referenceUnitigToString(), lck_g/*, t*/, false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG::merge(ColoredCDBG&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]' 203 | ret = CompactedDBG, DataStorage>::annotateSplitUnitigs(o, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:673:65: required from here 673 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5806:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5806 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5807:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5807 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'std::pair CompactedDBG::readBinaryGraph(std::istream&) [with Unitig_data_t = void; Graph_data_t = void; std::istream = std::basic_istream]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1198:27: required from 'std::pair CompactedDBG::readBinaryGraph(const std::string&) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 1198 | return readBinaryGraph(in); | ~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:382:46: required from 'bool CompactedDBG::read(const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 382 | p_readSuccess_checksum = readBinaryGraph(input_graph_fn); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:685:46: required from here 685 | else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1230:55: warning: right shift count >= width of type [-Wshift-count-overflow] 1230 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::readBinaryIndex(std::istream&, uint64_t) [with Unitig_data_t = void; Graph_data_t = void; std::istream = std::basic_istream; uint64_t = long long unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:945:27: required from 'bool CompactedDBG::readBinaryIndex(const std::string&, uint64_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int]' 945 | return readBinaryIndex(in, checksum); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:392:32: required from 'bool CompactedDBG::read(const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 392 | invalid = !readBinaryIndex(input_index_fn, p_readSuccess_checksum.first); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:685:46: required from here 685 | else success = cdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:993:55: warning: right shift count >= width of type [-Wshift-count-overflow] 993 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1037:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1037 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1052:61: warning: left shift count >= width of type [-Wshift-count-overflow] 1052 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; | ~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1085:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1085 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1094:57: warning: left shift count >= width of type [-Wshift-count-overflow] 1094 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos; | ~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1121:66: warning: right shift count >= width of type [-Wshift-count-overflow] 1121 | vector v_bmp_abundant((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1122:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1122 | vector v_bmp_overcrowded((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1131:58: warning: right shift count >= width of type [-Wshift-count-overflow] 1131 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1132:64: warning: right shift count >= width of type [-Wshift-count-overflow] 1132 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2129:13: required from 'bool CompactedDBG::merge(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2129 | if (annotateSplitUnitigs(o, nb_threads, verbose)){ | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:705:55: required from here 705 | success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5655:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5655 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5656:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5656 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::annotateSplitUnitig(const std::string&, LockGraph&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2284:52: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2284 | annotateSplitUnitig(it_unitig->referenceUnitigToString(), lck_g/*, t*/, false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2129:13: required from 'bool CompactedDBG::merge(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2129 | if (annotateSplitUnitigs(o, nb_threads, verbose)){ | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:705:55: required from here 705 | success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5806:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5806 | size_t nb_prev_pred = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5807:27: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 5807 | size_t nb_prev_succ = 0xFFFFFFFFFFFFFFFF; | ^~~~~~~~~~~~~~~~~~ make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:247: src/CMakeFiles/bifrost_static.dir/UnitigMap.cpp.o] Error 1 /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap CompactedDBG::find(const Kmer&, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; const_UnitigMap = UnitigMap, DataStorage, true>]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7428:50: required from 'void CompactedDBG::createJoinHT(std::vector*, KmerHashTable&, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 7428 | const const_UnitigMap cm = find(km, true); | ~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7465:17: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7465 | createJoinHT(v_joins, joins, nb_threads); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1016:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1016 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = false; T = char; KHT_ptr_t = KmerHashTable*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:732:18: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = char; iterator = KmerHashTable::iterator_]' 732 | iterator it(this); | ^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7469:56: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7469 | for (KmerHashTable::iterator it = joins.begin(); it != joins.end(); ++it) { | ~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = false; T = char]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:734:24: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = char; iterator = KmerHashTable::iterator_]' 734 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7469:56: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7469 | for (KmerHashTable::iterator it = joins.begin(); it != joins.end(); ++it) { | ~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:468:72: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 468 | const vector> pred = findPredecessors(head, true); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG::write(const std::string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 422 | if (!CompactedDBG, DataStorage>::write(prefix_output_fn, nb_threads, true, false, false, write_index_file, compress_output, verbose)) return false; // Write graph | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:632:55: required from here 632 | if (success) success = ccdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1342:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1342 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:469:70: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 469 | const vector> succ = findSuccessors(tail, 4, true); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG::write(const std::string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 422 | if (!CompactedDBG, DataStorage>::write(prefix_output_fn, nb_threads, true, false, false, write_index_file, compress_output, verbose)) return false; // Write graph | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:632:55: required from here 632 | if (success) success = ccdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1658:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1658 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::writeBinaryGraph(std::ostream&, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::ostream = std::basic_ostream; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1362:28: required from 'bool CompactedDBG::writeBinaryGraph(const std::string&, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 1362 | return writeBinaryGraph(out, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:84:62: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 84 | else if (BFG_output) write_success = writeBinaryGraph(fn, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG::write(const std::string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 422 | if (!CompactedDBG, DataStorage>::write(prefix_output_fn, nb_threads, true, false, false, write_index_file, compress_output, verbose)) return false; // Write graph | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:632:55: required from here 632 | if (success) success = ccdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::ostream = std::basic_ostream; uint64_t = long long unsigned int; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1423:28: required from 'bool CompactedDBG::writeBinaryIndex(const std::string&, uint64_t, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int; size_t = unsigned int]' 1423 | return writeBinaryIndex(out, checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:117:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 117 | write_success = writeBinaryIndex(fn, graph_checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG::write(const std::string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 422 | if (!CompactedDBG, DataStorage>::write(prefix_output_fn, nb_threads, true, false, false, write_index_file, compress_output, verbose)) return false; // Write graph | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:632:55: required from here 632 | if (success) success = ccdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1431:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1431 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1471:67: warning: right shift count >= width of type [-Wshift-count-overflow] 1471 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1472:77: warning: right shift count >= width of type [-Wshift-count-overflow] 1472 | const size_t nb_bmp_km_short = ((km_unitigs.size() * (k_ - g_ + 1)) >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1494:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1494 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1501:45: warning: right shift count >= width of type [-Wshift-count-overflow] 1501 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1512:49: warning: right shift count >= width of type [-Wshift-count-overflow] 1512 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1516:53: warning: right shift count >= width of type [-Wshift-count-overflow] 1516 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1531:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1531 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1535:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1535 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1681:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1681 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1; | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1695:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1695 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1706:73: warning: right shift count >= width of type [-Wshift-count-overflow] 1706 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1713:70: warning: right shift count >= width of type [-Wshift-count-overflow] 1713 | const size_t id_bmp = id_special >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1762:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1762 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1773:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1773 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = false; T = CompressedCoverage_t; KHT_ptr_t = KmerHashTable >*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:732:18: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = CompressedCoverage_t; iterator = KmerHashTable >::iterator_]' 732 | iterator it(this); | ^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:119:90: required from 'CompactedDBG& CompactedDBG::toDataGraph(CompactedDBG&&, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 119 | KmerHashTable>::const_iterator it_s = o.h_kmers_ccov.begin(); | ~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:611:45: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 611 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = false; T = CompressedCoverage_t]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:734:24: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = CompressedCoverage_t; iterator = KmerHashTable >::iterator_]' 734 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:119:90: required from 'CompactedDBG& CompactedDBG::toDataGraph(CompactedDBG&&, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 119 | KmerHashTable>::const_iterator it_s = o.h_kmers_ccov.begin(); | ~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:611:45: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 611 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = false; T = CompressedCoverage_t]': /usr/include/c++/14/bits/stl_pair.h:726:9: required from 'constexpr std::pair<_T1, _T2>::pair() [with _U1 = KmerHashTable >::iterator_; _U2 = bool; typename std::enable_if, std::__is_implicitly_default_constructible<_U2> >::value, bool>::type = true; _T1 = KmerHashTable >::iterator_; _T2 = bool]' 726 | : first(), second() { } | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:573:45: required from 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&) [with T = CompressedCoverage_t]' 573 | pair it_ret; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:128:28: required from 'CompactedDBG& CompactedDBG::toDataGraph(CompactedDBG&&, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 128 | h_kmers_ccov.insert(move(km), move(it_s->ccov)); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:611:45: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 611 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t, size_t) [with bool is_const = true; T = CompressedCoverage_t >; KHT_ptr_t = const KmerHashTable > >*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:396:61: required from 'KmerHashTable::const_iterator KmerHashTable::find(size_t) const [with T = CompressedCoverage_t >; const_iterator = KmerHashTable > >::iterator_; size_t = unsigned int]' 396 | if ((h < size_) && !table_keys[h].isEmpty()) return const_iterator(this, h); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:274:51: required from 'typename std::enable_if<(! is_void), typename std::conditional::type>::type UnitigMap::getData_() const [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = true; typename std::enable_if<(! is_void), typename std::conditional::type>::type = const DataAccessor*; typename std::conditional::type = const DataAccessor*]' 274 | if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig)->getData(); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:253:39: required from 'UnitigMap::Unitig_data_ptr_t UnitigMap::getData() const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = true; Unitig_data_ptr_t = const DataAccessor*]' 253 | return getData_::value>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/DataAccessor.tcc:243:48: required from here 243 | const UnitigColors* uc_src = um_src.getData()->getUnitigColors(um_src); // Get UnitigColors associated with reference unitig of um_src | ~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:37:72: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 37 | iterator_(KHT_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = true; T = CompressedCoverage_t >; KHT_ptr_t = const KmerHashTable > >*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:398:16: required from 'KmerHashTable::const_iterator KmerHashTable::find(size_t) const [with T = CompressedCoverage_t >; const_iterator = KmerHashTable > >::iterator_; size_t = unsigned int]' 398 | return const_iterator(this); | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:274:51: required from 'typename std::enable_if<(! is_void), typename std::conditional::type>::type UnitigMap::getData_() const [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = true; typename std::enable_if<(! is_void), typename std::conditional::type>::type = const DataAccessor*; typename std::conditional::type = const DataAccessor*]' 274 | if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig)->getData(); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:253:39: required from 'UnitigMap::Unitig_data_ptr_t UnitigMap::getData() const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = true; Unitig_data_ptr_t = const DataAccessor*]' 253 | return getData_::value>(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/DataAccessor.tcc:243:48: required from here 243 | const UnitigColors* uc_src = um_src.getData()->getUnitigColors(um_src); // Get UnitigColors associated with reference unitig of um_src | ~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = false; T = CompressedCoverage_t >]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:734:24: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = CompressedCoverage_t >; iterator = KmerHashTable > >::iterator_]' 734 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/UnitigIterator.tcc:12:165: required from 'unitigIterator::unitigIterator(CompactedDBG_ptr_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; bool is_const = false; CompactedDBG_ptr_t = CompactedDBG, DataStorage >*]' 12 | it_h_kmers_ccov((cdbg_ == nullptr) || cdbg_->invalid ? typename KmerHashTable>::const_iterator() : cdbg_->h_kmers_ccov.begin()){ | ~~~~~~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2509:14: required from 'CompactedDBG::iterator CompactedDBG::begin() [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; iterator = unitigIterator, DataStorage, false>]' 2509 | iterator it(this); | ^~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:968:59: required from here 968 | typename ColoredCDBG::iterator g_a = this->begin(); | ~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:121: src/CMakeFiles/bifrost_dynamic.dir/ColorSet.cpp.o] Error 1 /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = false; T = unsigned char]': /usr/include/c++/14/bits/stl_pair.h:726:9: required from 'constexpr std::pair<_T1, _T2>::pair() [with _U1 = KmerHashTable::iterator_; _U2 = bool; typename std::enable_if, std::__is_implicitly_default_constructible<_U2> >::value, bool>::type = true; _T1 = KmerHashTable::iterator_; _T2 = bool]' 726 | : first(), second() { } | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:473:45: required from 'std::pair::iterator_, bool> KmerHashTable::insert(const Kmer&, const T&) [with T = unsigned char]' 473 | pair it_ret; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:3080:135: required from 'bool CompactedDBG::construct(const CDBG_Build_opt&, DualBlockedBloomFilter&, Roaring&, size_t, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 3080 | const pair::const_iterator, bool> p_insert_kmt_fp_cand = kmt_fp_cand.insert(km_rep, 0); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:679:62: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 679 | if (construct_finished) construct_finished = construct(opt, dbbf, r, nb_unique_minimizers, nb_non_unique_minimizers, nb_unique_kmers, nb_non_unique_kmers); // Construction step | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = true; T = CompressedCoverage_t]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7309:69: required from 'void CompactedDBG::createJoinHT(std::vector*, KmerHashTable&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 7309 | typename h_kmers_ccov_t::const_iterator l_it; | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7634:17: required from 'typename std::enable_if::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = unsigned int; size_t = unsigned int]' 7634 | createJoinHT(v_joins, joins, nb_threads); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap CompactedDBG::find(const Kmer&, bool) const [with Unitig_data_t = void; Graph_data_t = void; const_UnitigMap = UnitigMap]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7428:50: required from 'void CompactedDBG::createJoinHT(std::vector*, KmerHashTable&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 7428 | const const_UnitigMap cm = find(km, true); | ~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7634:17: required from 'typename std::enable_if::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = unsigned int; size_t = unsigned int]' 7634 | createJoinHT(v_joins, joins, nb_threads); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1016:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1016 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t, size_t) [with bool is_const = false; T = CompressedCoverage_t; KHT_ptr_t = KmerHashTable >*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:389:61: required from 'KmerHashTable::iterator KmerHashTable::find(size_t) [with T = CompressedCoverage_t; iterator = KmerHashTable >::iterator_; size_t = unsigned int]' 389 | if ((h < size_) && !table_keys[h].isEmpty()) return iterator(this, h); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7651:72: required from 'typename std::enable_if::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = unsigned int; size_t = unsigned int]' 7651 | else if (cmHead.isAbundant) cmHead_head = h_kmers_ccov.find(cmHead.pos_unitig).getKey(); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:37:72: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 37 | iterator_(KHT_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = false; T = unsigned int; KHT_ptr_t = KmerHashTable*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:316:16: required from 'KmerHashTable::iterator KmerHashTable::find(const Kmer&) [with T = unsigned int; iterator = KmerHashTable::iterator_]' 316 | return iterator(this); | ^~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:475:65: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 475 | if (unitig.isAbundant) labelB = *(idmap.find(unitig.getUnitigHead().rep())); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = false; T = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:734:24: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = unsigned int; iterator = KmerHashTable::iterator_]' 734 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:544:62: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 544 | for (KmerHashTable::iterator it = idmap.begin(); it != idmap.end(); it++) { | ~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap CompactedDBG::find(const Kmer&, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; const_UnitigMap = UnitigMap, DataStorage, true>]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7428:50: required from 'void CompactedDBG::createJoinHT(std::vector*, KmerHashTable&, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 7428 | const const_UnitigMap cm = find(km, true); | ~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7465:17: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7465 | createJoinHT(v_joins, joins, nb_threads); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1016:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1016 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = false; T = char; KHT_ptr_t = KmerHashTable*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:732:18: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = char; iterator = KmerHashTable::iterator_]' 732 | iterator it(this); | ^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7469:56: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7469 | for (KmerHashTable::iterator it = joins.begin(); it != joins.end(); ++it) { | ~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = false; T = char]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:734:24: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = char; iterator = KmerHashTable::iterator_]' 734 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7469:56: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7469 | for (KmerHashTable::iterator it = joins.begin(); it != joins.end(); ++it) { | ~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = true; T = CompressedCoverage_t; KHT_ptr_t = const KmerHashTable >*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:741:24: required from 'KmerHashTable::const_iterator KmerHashTable::begin() const [with T = CompressedCoverage_t; const_iterator = KmerHashTable >::iterator_]' 741 | const_iterator it(this); | ^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:876:74: required from 'bool CompactedDBG::writeFASTA(const std::string&, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 876 | for (typename h_kmers_ccov_t::const_iterator it = h_kmers_ccov.begin(); !gout.fail() && (it != h_kmers_ccov.end()); ++it, ++i) { | ~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:83:48: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 83 | else if (FASTA_output) write_success = writeFASTA(fn, compressed_output); | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = true; T = CompressedCoverage_t]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:743:24: required from 'KmerHashTable::const_iterator KmerHashTable::begin() const [with T = CompressedCoverage_t; const_iterator = KmerHashTable >::iterator_]' 743 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:876:74: required from 'bool CompactedDBG::writeFASTA(const std::string&, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 876 | for (typename h_kmers_ccov_t::const_iterator it = h_kmers_ccov.begin(); !gout.fail() && (it != h_kmers_ccov.end()); ++it, ++i) { | ~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:83:48: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 83 | else if (FASTA_output) write_success = writeFASTA(fn, compressed_output); | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_& MinimizerIndex::iterator_::operator++() [with bool is_const = true]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1542:17: required from 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream; uint64_t = long long unsigned int; size_t = unsigned int]' 1542 | ++it; | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1423:28: required from 'bool CompactedDBG::writeBinaryIndex(const std::string&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int; size_t = unsigned int]' 1423 | return writeBinaryIndex(out, checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:117:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 117 | write_success = writeBinaryIndex(fn, graph_checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:101:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 101 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_() [with bool is_const = true]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1621:48: required from 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream; uint64_t = long long unsigned int; size_t = unsigned int]' 1621 | MinimizerIndex::const_iterator lit; | ^~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1423:28: required from 'bool CompactedDBG::writeBinaryIndex(const std::string&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int; size_t = unsigned int]' 1423 | return writeBinaryIndex(out, checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:117:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 117 | write_success = writeBinaryIndex(fn, graph_checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:34:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 34 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:34:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 34 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'std::pair CompactedDBG::readBinaryGraph(std::istream&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::istream = std::basic_istream]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1198:27: required from 'std::pair CompactedDBG::readBinaryGraph(const std::string&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]' 1198 | return readBinaryGraph(in); | ~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:382:46: required from 'bool CompactedDBG::read(const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 382 | p_readSuccess_checksum = readBinaryGraph(input_graph_fn); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:709:71: required from 'bool ColoredCDBG::read(const std::string&, const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 709 | invalid = !CompactedDBG, DataStorage>::read(input_graph_fn, input_index_fn, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:653:47: required from here 653 | else success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1230:55: warning: right shift count >= width of type [-Wshift-count-overflow] 1230 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:468:72: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 468 | const vector> pred = findPredecessors(head, true); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG::write(const std::string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 422 | if (!CompactedDBG, DataStorage>::write(prefix_output_fn, nb_threads, true, false, false, write_index_file, compress_output, verbose)) return false; // Write graph | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:632:55: required from here 632 | if (success) success = ccdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1342:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1342 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::readBinaryIndex(std::istream&, uint64_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::istream = std::basic_istream; uint64_t = long long unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:945:27: required from 'bool CompactedDBG::readBinaryIndex(const std::string&, uint64_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int]' 945 | return readBinaryIndex(in, checksum); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:392:32: required from 'bool CompactedDBG::read(const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 392 | invalid = !readBinaryIndex(input_index_fn, p_readSuccess_checksum.first); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:709:71: required from 'bool ColoredCDBG::read(const std::string&, const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 709 | invalid = !CompactedDBG, DataStorage>::read(input_graph_fn, input_index_fn, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:653:47: required from here 653 | else success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:993:55: warning: right shift count >= width of type [-Wshift-count-overflow] 993 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1037:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1037 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1052:61: warning: left shift count >= width of type [-Wshift-count-overflow] 1052 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; | ~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1085:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1085 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1094:57: warning: left shift count >= width of type [-Wshift-count-overflow] 1094 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos; | ~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1121:66: warning: right shift count >= width of type [-Wshift-count-overflow] 1121 | vector v_bmp_abundant((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1122:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1122 | vector v_bmp_overcrowded((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1131:58: warning: right shift count >= width of type [-Wshift-count-overflow] 1131 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1132:64: warning: right shift count >= width of type [-Wshift-count-overflow] 1132 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:469:70: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 469 | const vector> succ = findSuccessors(tail, 4, true); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG::write(const std::string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 422 | if (!CompactedDBG, DataStorage>::write(prefix_output_fn, nb_threads, true, false, false, write_index_file, compress_output, verbose)) return false; // Write graph | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:632:55: required from here 632 | if (success) success = ccdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1658:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1658 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5692:59: required from 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]' 5692 | vector> um_bw(findPredecessors(p.first)); | ~~~~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG::merge(ColoredCDBG&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]' 203 | ret = CompactedDBG, DataStorage>::annotateSplitUnitigs(o, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:673:65: required from here 673 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1498:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1498 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5693:57: required from 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]' 5693 | vector> um_fw(findSuccessors(p.first)); | ~~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG::merge(ColoredCDBG&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]' 203 | ret = CompactedDBG, DataStorage>::annotateSplitUnitigs(o, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:673:65: required from here 673 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1848:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1848 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::writeBinaryGraph(std::ostream&, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::ostream = std::basic_ostream; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1362:28: required from 'bool CompactedDBG::writeBinaryGraph(const std::string&, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 1362 | return writeBinaryGraph(out, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:84:62: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 84 | else if (BFG_output) write_success = writeBinaryGraph(fn, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG::write(const std::string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 422 | if (!CompactedDBG, DataStorage>::write(prefix_output_fn, nb_threads, true, false, false, write_index_file, compress_output, verbose)) return false; // Write graph | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:632:55: required from here 632 | if (success) success = ccdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1373:92: warning: left shift count >= width of type [-Wshift-count-overflow] 1373 | const size_t fileformat_version = (static_cast(BFG_GRAPHBIN_FORMAT_HEADER) << 32) | static_cast(BFG_GRAPHBIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::ostream = std::basic_ostream; uint64_t = long long unsigned int; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1423:28: required from 'bool CompactedDBG::writeBinaryIndex(const std::string&, uint64_t, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int; size_t = unsigned int]' 1423 | return writeBinaryIndex(out, checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:117:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 117 | write_success = writeBinaryIndex(fn, graph_checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:422:62: required from 'bool ColoredCDBG::write(const std::string&, size_t, bool, bool, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 422 | if (!CompactedDBG, DataStorage>::write(prefix_output_fn, nb_threads, true, false, false, write_index_file, compress_output, verbose)) return false; // Write graph | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:632:55: required from here 632 | if (success) success = ccdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1431:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1431 | const size_t nb_bmp_minz = (hmap_min_unitigs.size() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1442:91: warning: left shift count >= width of type [-Wshift-count-overflow] 1442 | const size_t fileformat_version = (static_cast(BFG_METABIN_FORMAT_HEADER) << 32) | static_cast(BFG_METABIN_FORMAT_VERSION); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1471:67: warning: right shift count >= width of type [-Wshift-count-overflow] 1471 | const size_t nb_bmp_unitigs = (v_block_len_unitigs.back() >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1472:77: warning: right shift count >= width of type [-Wshift-count-overflow] 1472 | const size_t nb_bmp_km_short = ((km_unitigs.size() * (k_ - g_ + 1)) >> 32) + 1; | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1494:57: warning: right shift count >= width of type [-Wshift-count-overflow] 1494 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1501:45: warning: right shift count >= width of type [-Wshift-count-overflow] 1501 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1512:49: warning: right shift count >= width of type [-Wshift-count-overflow] 1512 | lv_bmp_km_short[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1516:53: warning: right shift count >= width of type [-Wshift-count-overflow] 1516 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1531:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1531 | lv_bmp_unitigs[pos >> 32].add(pos & 0x00000000ffffffffULL); | ~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1535:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1535 | lv_bmp_minz[id_minz >> 32].add(id_minz & 0x00000000ffffffffULL); | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1681:61: warning: right shift count >= width of type [-Wshift-count-overflow] 1681 | const size_t nb_bmp_special_minz = (nb_special_minz >> 32) + 1; | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1695:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1695 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1706:73: warning: right shift count >= width of type [-Wshift-count-overflow] 1706 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1713:70: warning: right shift count >= width of type [-Wshift-count-overflow] 1713 | const size_t id_bmp = id_special >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1762:48: warning: right shift count >= width of type [-Wshift-count-overflow] 1762 | if (v_bmp_minz[id_minz >> 32].contains(id_minz & 0x00000000ffffffffULL)) { | ~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1773:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1773 | const size_t unitig_id = unitig_idx >> 32; | ~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = false; T = CompressedCoverage_t; KHT_ptr_t = KmerHashTable >*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:732:18: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = CompressedCoverage_t; iterator = KmerHashTable >::iterator_]' 732 | iterator it(this); | ^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:119:90: required from 'CompactedDBG& CompactedDBG::toDataGraph(CompactedDBG&&, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 119 | KmerHashTable>::const_iterator it_s = o.h_kmers_ccov.begin(); | ~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:611:45: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 611 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = false; T = CompressedCoverage_t]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:734:24: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = CompressedCoverage_t; iterator = KmerHashTable >::iterator_]' 734 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:119:90: required from 'CompactedDBG& CompactedDBG::toDataGraph(CompactedDBG&&, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 119 | KmerHashTable>::const_iterator it_s = o.h_kmers_ccov.begin(); | ~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:611:45: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 611 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = false; T = CompressedCoverage_t]': /usr/include/c++/14/bits/stl_pair.h:726:9: required from 'constexpr std::pair<_T1, _T2>::pair() [with _U1 = KmerHashTable >::iterator_; _U2 = bool; typename std::enable_if, std::__is_implicitly_default_constructible<_U2> >::value, bool>::type = true; _T1 = KmerHashTable >::iterator_; _T2 = bool]' 726 | : first(), second() { } | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:573:45: required from 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&) [with T = CompressedCoverage_t]' 573 | pair it_ret; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:128:28: required from 'CompactedDBG& CompactedDBG::toDataGraph(CompactedDBG&&, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 128 | h_kmers_ccov.insert(move(km), move(it_s->ccov)); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:611:45: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 611 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) [with Unitig_data_t = void; Graph_data_t = void]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5692:59: required from 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 5692 | vector> um_bw(findPredecessors(p.first)); | ~~~~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2129:13: required from 'bool CompactedDBG::merge(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2129 | if (annotateSplitUnitigs(o, nb_threads, verbose)){ | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:705:55: required from here 705 | success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1498:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1498 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5693:57: required from 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 5693 | vector> um_fw(findSuccessors(p.first)); | ~~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2129:13: required from 'bool CompactedDBG::merge(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2129 | if (annotateSplitUnitigs(o, nb_threads, verbose)){ | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:705:55: required from here 705 | success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1848:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1848 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::addUnitig(const std::string&, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6523:30: required from 'typename std::enable_if::type CompactedDBG::extractUnitig_(size_t&, size_t&, size_t&, size_t&, const std::vector >&) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = bool; size_t = unsigned int]' 6523 | if (addUnitig(split_str, v_kmers_sz, pos_v_unitigs, false)) h_kmers_ccov.find(Kmer(split_str.c_str()).rep())->ccov.setFull(); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6768:46: required from 'std::pair CompactedDBG::splitAllUnitigs() [with Unitig_data_t = void; Graph_data_t = void]' 6768 | extractUnitig_::value>(i, nxt_pos_insert, v_unitigs_sz, v_kmers_sz, sp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2132:44: required from 'bool CompactedDBG::merge(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2132 | const pair p = splitAllUnitigs(); | ^~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:705:55: required from here 705 | success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5119:49: warning: left shift count >= width of type [-Wshift-count-overflow] 5119 | const size_t pos_id_unitig_r = (id_unitig_r << 32) | ((static_cast(!is_short_r) - 1) & MASK_CONTIG_TYPE); | ~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5124:38: warning: left shift count >= width of type [-Wshift-count-overflow] 5124 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5291:62: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow] 5291 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v); /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = false; T = unsigned char]': /usr/include/c++/14/bits/stl_pair.h:726:9: required from 'constexpr std::pair<_T1, _T2>::pair() [with _U1 = KmerHashTable::iterator_; _U2 = bool; typename std::enable_if, std::__is_implicitly_default_constructible<_U2> >::value, bool>::type = true; _T1 = KmerHashTable::iterator_; _T2 = bool]' 726 | : first(), second() { } | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:473:45: required from 'std::pair::iterator_, bool> KmerHashTable::insert(const Kmer&, const T&) [with T = unsigned char]' 473 | pair it_ret; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:3080:135: required from 'bool CompactedDBG::construct(const CDBG_Build_opt&, DualBlockedBloomFilter&, Roaring&, size_t, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 3080 | const pair::const_iterator, bool> p_insert_kmt_fp_cand = kmt_fp_cand.insert(km_rep, 0); | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:679:62: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 679 | if (construct_finished) construct_finished = construct(opt, dbbf, r, nb_unique_minimizers, nb_non_unique_minimizers, nb_unique_kmers, nb_non_unique_kmers); // Construction step | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; const_UnitigMap = UnitigMap, DataStorage, true>; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4691:36: required from 'const_UnitigMap CompactedDBG::findUnitig(const char*, size_t, size_t, const minHashIterator&) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; const_UnitigMap = UnitigMap, DataStorage, true>; size_t = unsigned int]' 4691 | const_UnitigMap um = find(s, pos, it_min); | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Search.tcc:668:72: required from 'std::vector > > CompactedDBG::searchSequence(const std::string&, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]' 668 | const const_UnitigMap um = findUnitig(s_inexact_str, pos_s, s_inexact_len, mhi); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:1700:90: required from 'bool ColoredCDBG::search(const std::vector >&, const std::string&, double, bool, bool, bool, size_t, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 1700 | const vector>> v_um_e = this->searchSequence(query, true, false, false, false, false); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:725:56: required from here 725 | if (success) success = ccdbg.search(opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.get_nb_found_km, opt.get_ratio_found_km, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 726 | opt.inexact_search, opt.nb_threads, opt.verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:768:43: warning: right shift count >= width of type [-Wshift-count-overflow] 768 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool) const [with Unitig_data_t = void; Graph_data_t = void; const_UnitigMap = UnitigMap; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4691:36: required from 'const_UnitigMap CompactedDBG::findUnitig(const char*, size_t, size_t, const minHashIterator&) const [with Unitig_data_t = void; Graph_data_t = void; const_UnitigMap = UnitigMap; size_t = unsigned int]' 4691 | const_UnitigMap um = find(s, pos, it_min); | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Search.tcc:937:72: required from 'std::vector > > CompactedDBG::searchSequence(const std::string&, bool, bool, bool, bool, double, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 937 | const const_UnitigMap um = findUnitig(s_inexact_str, pos_s, s_inexact_len, mhi); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Search.tcc:1152:89: required from 'bool CompactedDBG::search(const std::vector >&, const std::string&, double, bool, bool, bool, size_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 1152 | const vector>> v = dbg.searchSequence( s, true, inexact_search, inexact_search, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1153 | inexact_search, 1.0, true); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:735:55: required from here 735 | if (success) success = cdbg.search( opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.get_nb_found_km, opt.get_ratio_found_km, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 736 | opt.inexact_search, opt.nb_threads, opt.verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:768:43: warning: right shift count >= width of type [-Wshift-count-overflow] 768 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = true; T = CompressedCoverage_t]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7309:69: required from 'void CompactedDBG::createJoinHT(std::vector*, KmerHashTable&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 7309 | typename h_kmers_ccov_t::const_iterator l_it; | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7634:17: required from 'typename std::enable_if::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = unsigned int; size_t = unsigned int]' 7634 | createJoinHT(v_joins, joins, nb_threads); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap CompactedDBG::find(const Kmer&, bool) const [with Unitig_data_t = void; Graph_data_t = void; const_UnitigMap = UnitigMap]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7428:50: required from 'void CompactedDBG::createJoinHT(std::vector*, KmerHashTable&, size_t) const [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 7428 | const const_UnitigMap cm = find(km, true); | ~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7634:17: required from 'typename std::enable_if::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = unsigned int; size_t = unsigned int]' 7634 | createJoinHT(v_joins, joins, nb_threads); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1016:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1016 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t, size_t) [with bool is_const = false; T = CompressedCoverage_t; KHT_ptr_t = KmerHashTable >*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:389:61: required from 'KmerHashTable::iterator KmerHashTable::find(size_t) [with T = CompressedCoverage_t; iterator = KmerHashTable >::iterator_; size_t = unsigned int]' 389 | if ((h < size_) && !table_keys[h].isEmpty()) return iterator(this, h); | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7651:72: required from 'typename std::enable_if::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = unsigned int; size_t = unsigned int]' 7651 | else if (cmHead.isAbundant) cmHead_head = h_kmers_ccov.find(cmHead.pos_unitig).getKey(); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = void; Graph_data_t = void]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:640:57: required from here 640 | if (success) success = cdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:37:72: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 37 | iterator_(KHT_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = false; T = unsigned int; KHT_ptr_t = KmerHashTable*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:316:16: required from 'KmerHashTable::iterator KmerHashTable::find(const Kmer&) [with T = unsigned int; iterator = KmerHashTable::iterator_]' 316 | return iterator(this); | ^~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:475:65: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 475 | if (unitig.isAbundant) labelB = *(idmap.find(unitig.getUnitigHead().rep())); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = false; T = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:734:24: required from 'KmerHashTable::iterator KmerHashTable::begin() [with T = unsigned int; iterator = KmerHashTable::iterator_]' 734 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:544:62: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 544 | for (KmerHashTable::iterator it = idmap.begin(); it != idmap.end(); it++) { | ~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = true; T = CompressedCoverage_t; KHT_ptr_t = const KmerHashTable >*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:741:24: required from 'KmerHashTable::const_iterator KmerHashTable::begin() const [with T = CompressedCoverage_t; const_iterator = KmerHashTable >::iterator_]' 741 | const_iterator it(this); | ^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:876:74: required from 'bool CompactedDBG::writeFASTA(const std::string&, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 876 | for (typename h_kmers_ccov_t::const_iterator it = h_kmers_ccov.begin(); !gout.fail() && (it != h_kmers_ccov.end()); ++it, ++i) { | ~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:83:48: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 83 | else if (FASTA_output) write_success = writeFASTA(fn, compressed_output); | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = true; T = CompressedCoverage_t]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:743:24: required from 'KmerHashTable::const_iterator KmerHashTable::begin() const [with T = CompressedCoverage_t; const_iterator = KmerHashTable >::iterator_]' 743 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:876:74: required from 'bool CompactedDBG::writeFASTA(const std::string&, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 876 | for (typename h_kmers_ccov_t::const_iterator it = h_kmers_ccov.begin(); !gout.fail() && (it != h_kmers_ccov.end()); ++it, ++i) { | ~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:83:48: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 83 | else if (FASTA_output) write_success = writeFASTA(fn, compressed_output); | ^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = false; T = CompressedCoverage_t >]': /usr/include/c++/14/bits/stl_pair.h:726:9: required from 'constexpr std::pair<_T1, _T2>::pair() [with _U1 = KmerHashTable > >::iterator_; _U2 = bool; typename std::enable_if, std::__is_implicitly_default_constructible<_U2> >::value, bool>::type = true; _T1 = KmerHashTable > >::iterator_; _T2 = bool]' 726 | : first(), second() { } | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:573:45: required from 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&) [with T = CompressedCoverage_t >]' 573 | pair it_ret; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:128:28: required from 'CompactedDBG& CompactedDBG::toDataGraph(CompactedDBG&&, size_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 128 | h_kmers_ccov.insert(move(km), move(it_s->ccov)); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:611:45: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 611 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:399:31: required from 'bool ColoredCDBG::buildGraph(const CCDBG_Build_opt&) [with Unitig_data_t = void]' 399 | invalid = !this->build(opt_); | ~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:628:47: required from here 628 | success = ccdbg.buildGraph(opt); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_& MinimizerIndex::iterator_::operator++() [with bool is_const = true]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1542:17: required from 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream; uint64_t = long long unsigned int; size_t = unsigned int]' 1542 | ++it; | ^~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1423:28: required from 'bool CompactedDBG::writeBinaryIndex(const std::string&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int; size_t = unsigned int]' 1423 | return writeBinaryIndex(out, checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:117:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 117 | write_success = writeBinaryIndex(fn, graph_checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:101:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 101 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp: In instantiation of 'MinimizerIndex::iterator_::iterator_() [with bool is_const = true]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1621:48: required from 'bool CompactedDBG::writeBinaryIndex(std::ostream&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::ostream = std::basic_ostream; uint64_t = long long unsigned int; size_t = unsigned int]' 1621 | MinimizerIndex::const_iterator lit; | ^~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1423:28: required from 'bool CompactedDBG::writeBinaryIndex(const std::string&, uint64_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int; size_t = unsigned int]' 1423 | return writeBinaryIndex(out, checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:117:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 117 | write_success = writeBinaryIndex(fn, graph_checksum, nb_threads); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:34:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 34 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/MinimizerIndex.hpp:34:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 34 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'std::pair CompactedDBG::readBinaryGraph(std::istream&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::istream = std::basic_istream]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1198:27: required from 'std::pair CompactedDBG::readBinaryGraph(const std::string&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]' 1198 | return readBinaryGraph(in); | ~~~~~~~~~~~~~~~^~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:382:46: required from 'bool CompactedDBG::read(const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 382 | p_readSuccess_checksum = readBinaryGraph(input_graph_fn); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:709:71: required from 'bool ColoredCDBG::read(const std::string&, const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 709 | invalid = !CompactedDBG, DataStorage>::read(input_graph_fn, input_index_fn, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:653:47: required from here 653 | else success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1230:55: warning: right shift count >= width of type [-Wshift-count-overflow] 1230 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc: In instantiation of 'bool CompactedDBG::readBinaryIndex(std::istream&, uint64_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::istream = std::basic_istream; uint64_t = long long unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:945:27: required from 'bool CompactedDBG::readBinaryIndex(const std::string&, uint64_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; uint64_t = long long unsigned int]' 945 | return readBinaryIndex(in, checksum); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:392:32: required from 'bool CompactedDBG::read(const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 392 | invalid = !readBinaryIndex(input_index_fn, p_readSuccess_checksum.first); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:709:71: required from 'bool ColoredCDBG::read(const std::string&, const std::string&, const std::string&, size_t, bool) [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 709 | invalid = !CompactedDBG, DataStorage>::read(input_graph_fn, input_index_fn, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:653:47: required from here 653 | else success = ccdbg1.read(lopt.filename_graph_in, lopt.filename_index_in, lopt.filename_colors_in, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:993:55: warning: right shift count >= width of type [-Wshift-count-overflow] 993 | const size_t file_format_header = file_format >> 32; | ~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1037:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1037 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1052:61: warning: left shift count >= width of type [-Wshift-count-overflow] 1052 | const size_t pos_id_unitig = (unitig_id << 32) | relative_pos; | ~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1085:41: warning: left shift count >= width of type [-Wshift-count-overflow] 1085 | const size_t id_bmp = i << 32; | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1094:57: warning: left shift count >= width of type [-Wshift-count-overflow] 1094 | const size_t pos_id_unitig = (km_id << 32) | MASK_CONTIG_TYPE | km_pos; | ~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1121:66: warning: right shift count >= width of type [-Wshift-count-overflow] 1121 | vector v_bmp_abundant((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1122:69: warning: right shift count >= width of type [-Wshift-count-overflow] 1122 | vector v_bmp_overcrowded((nb_special_minz >> 32) + 1); | ~~~~~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1131:58: warning: right shift count >= width of type [-Wshift-count-overflow] 1131 | const bool isAbundant = v_bmp_abundant[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:1132:64: warning: right shift count >= width of type [-Wshift-count-overflow] 1132 | const bool isOvercrowded = v_bmp_overcrowded[i >> 32].contains(i & 0x00000000ffffffffULL); | ~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5692:59: required from 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]' 5692 | vector> um_bw(findPredecessors(p.first)); | ~~~~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG::merge(ColoredCDBG&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]' 203 | ret = CompactedDBG, DataStorage>::annotateSplitUnitigs(o, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:673:65: required from here 673 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1498:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1498 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5693:57: required from 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]' 5693 | vector> um_fw(findSuccessors(p.first)); | ~~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:203:82: required from 'bool ColoredCDBG::merge(ColoredCDBG&&, size_t, bool) [with Unitig_data_t = void; size_t = unsigned int]' 203 | ret = CompactedDBG, DataStorage>::annotateSplitUnitigs(o, nb_threads, verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:673:65: required from here 673 | if (success) success = ccdbg_a.merge(move(ccdbg_b), lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1848:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1848 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = true; T = CompressedCoverage_t >]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:743:24: required from 'KmerHashTable::const_iterator KmerHashTable::begin() const [with T = CompressedCoverage_t >; const_iterator = KmerHashTable > >::iterator_]' 743 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7143:86: required from 'void CompactedDBG::createJoinHT(std::vector*, KmerHashTable&, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 7143 | for (typename h_kmers_ccov_t::const_iterator it_ccov = h_kmers_ccov.begin(); it_ccov != h_kmers_ccov.end(); ++it_ccov) { | ~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7465:17: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7465 | createJoinHT(v_joins, joins, nb_threads); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findPredecessors(const Kmer&, bool) [with Unitig_data_t = void; Graph_data_t = void]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5692:59: required from 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 5692 | vector> um_bw(findPredecessors(p.first)); | ~~~~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2129:13: required from 'bool CompactedDBG::merge(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2129 | if (annotateSplitUnitigs(o, nb_threads, verbose)){ | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:705:55: required from here 705 | success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1498:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1498 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = false; T = char]': /usr/include/c++/14/bits/stl_pair.h:726:9: required from 'constexpr std::pair<_T1, _T2>::pair() [with _U1 = KmerHashTable::iterator_; _U2 = bool; typename std::enable_if, std::__is_implicitly_default_constructible<_U2> >::value, bool>::type = true; _T1 = KmerHashTable::iterator_; _T2 = bool]' 726 | : first(), second() { } | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:573:45: required from 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&) [with T = char]' 573 | pair it_ret; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7152:95: required from 'void CompactedDBG::createJoinHT(std::vector*, KmerHashTable&, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 7152 | if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7465:17: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7465 | createJoinHT(v_joins, joins, nb_threads); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'std::vector > CompactedDBG::findSuccessors(const Kmer&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5693:57: required from 'bool CompactedDBG::annotateSplitUnitig(const std::string&, bool) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 5693 | vector> um_fw(findSuccessors(p.first)); | ~~~~~~~~~~~~~~^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2243:61: required from 'bool CompactedDBG::annotateSplitUnitigs(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2243 | for (const auto& unitig : o) annotateSplitUnitig(unitig.referenceUnitigToString(), false); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2129:13: required from 'bool CompactedDBG::merge(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2129 | if (annotateSplitUnitigs(o, nb_threads, verbose)){ | ^~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:705:55: required from here 705 | success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:1848:43: warning: right shift count >= width of type [-Wshift-count-overflow] 1848 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'bool CompactedDBG::addUnitig(const std::string&, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6523:30: required from 'typename std::enable_if::type CompactedDBG::extractUnitig_(size_t&, size_t&, size_t&, size_t&, const std::vector >&) [with bool is_void = true; Unitig_data_t = void; Graph_data_t = void; typename std::enable_if::type = bool; size_t = unsigned int]' 6523 | if (addUnitig(split_str, v_kmers_sz, pos_v_unitigs, false)) h_kmers_ccov.find(Kmer(split_str.c_str()).rep())->ccov.setFull(); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:6768:46: required from 'std::pair CompactedDBG::splitAllUnitigs() [with Unitig_data_t = void; Graph_data_t = void]' 6768 | extractUnitig_::value>(i, nxt_pos_insert, v_unitigs_sz, v_kmers_sz, sp); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:2132:44: required from 'bool CompactedDBG::merge(const CompactedDBG&, size_t, bool) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 2132 | const pair p = splitAllUnitigs(); | ^~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:705:55: required from here 705 | success = cdbg_a.merge(cdbg_b, lopt.nb_threads, lopt.verbose); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5119:49: warning: left shift count >= width of type [-Wshift-count-overflow] 5119 | const size_t pos_id_unitig_r = (id_unitig_r << 32) | ((static_cast(!is_short_r) - 1) & MASK_CONTIG_TYPE); | ~~~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5124:38: warning: left shift count >= width of type [-Wshift-count-overflow] 5124 | size_t pos_id_unitig = id_unitig << 32; | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:5291:62: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744069414584321' to '1' [-Woverflow] 5291 | else flag_v = v.push_back(MASK_CONTIG_ID + 1, flag_v); /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; const_UnitigMap = UnitigMap, DataStorage, true>; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4691:36: required from 'const_UnitigMap CompactedDBG::findUnitig(const char*, size_t, size_t, const minHashIterator&) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; const_UnitigMap = UnitigMap, DataStorage, true>; size_t = unsigned int]' 4691 | const_UnitigMap um = find(s, pos, it_min); | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Search.tcc:668:72: required from 'std::vector > > CompactedDBG::searchSequence(const std::string&, bool, bool, bool, bool, bool) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; std::string = std::__cxx11::basic_string]' 668 | const const_UnitigMap um = findUnitig(s_inexact_str, pos_s, s_inexact_len, mhi); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:1700:90: required from 'bool ColoredCDBG::search(const std::vector >&, const std::string&, double, bool, bool, bool, size_t, bool) const [with Unitig_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 1700 | const vector>> v_um_e = this->searchSequence(query, true, false, false, false, false); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:725:56: required from here 725 | if (success) success = ccdbg.search(opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.get_nb_found_km, opt.get_ratio_found_km, | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 726 | opt.inexact_search, opt.nb_threads, opt.verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:768:43: warning: right shift count >= width of type [-Wshift-count-overflow] 768 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc: In instantiation of 'const_UnitigMap CompactedDBG::find(const char*, size_t, const minHashIterator&, bool) const [with Unitig_data_t = void; Graph_data_t = void; const_UnitigMap = UnitigMap; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:4691:36: required from 'const_UnitigMap CompactedDBG::findUnitig(const char*, size_t, size_t, const minHashIterator&) const [with Unitig_data_t = void; Graph_data_t = void; const_UnitigMap = UnitigMap; size_t = unsigned int]' 4691 | const_UnitigMap um = find(s, pos, it_min); | ~~~~^~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Search.tcc:937:72: required from 'std::vector > > CompactedDBG::searchSequence(const std::string&, bool, bool, bool, bool, double, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string]' 937 | const const_UnitigMap um = findUnitig(s_inexact_str, pos_s, s_inexact_len, mhi); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Search.tcc:1152:89: required from 'bool CompactedDBG::search(const std::vector >&, const std::string&, double, bool, bool, bool, size_t, size_t) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 1152 | const vector>> v = dbg.searchSequence( s, true, inexact_search, inexact_search, | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1153 | inexact_search, 1.0, true); | ~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:735:55: required from here 735 | if (success) success = cdbg.search( opt.filename_query_in, opt.prefixFilenameOut, opt.ratio_kmers, opt.get_nb_found_km, opt.get_ratio_found_km, | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 736 | opt.inexact_search, opt.nb_threads, opt.verbose); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:768:43: warning: right shift count >= width of type [-Wshift-count-overflow] 768 | unitig_id = unitig_id_pos >> 32; | ~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = false; T = unsigned char; KHT_ptr_t = KmerHashTable*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:750:16: required from 'KmerHashTable::iterator KmerHashTable::end() [with T = unsigned char; iterator = KmerHashTable::iterator_]' 750 | return iterator(this); | ^~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:403:39: required from 'size_t KmerHashTable::erase(const_iterator) [with T = unsigned char; size_t = unsigned int; const_iterator = KmerHashTable::iterator_]' 403 | if ((size_ == 0) || (it == end())) return 0; | ~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:3084:72: required from 'bool CompactedDBG::construct(const CDBG_Build_opt&, DualBlockedBloomFilter&, Roaring&, size_t, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 3084 | if (has_full_cov) kmt_fp_cand.erase(p_insert_kmt_fp_cand.first); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:679:62: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 679 | if (construct_finished) construct_finished = construct(opt, dbbf, r, nb_unique_minimizers, nb_non_unique_minimizers, nb_unique_kmers, nb_non_unique_kmers); // Construction step | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = false; T = CompressedCoverage_t >]': /usr/include/c++/14/bits/stl_pair.h:726:9: required from 'constexpr std::pair<_T1, _T2>::pair() [with _U1 = KmerHashTable > >::iterator_; _U2 = bool; typename std::enable_if, std::__is_implicitly_default_constructible<_U2> >::value, bool>::type = true; _T1 = KmerHashTable > >::iterator_; _T2 = bool]' 726 | : first(), second() { } | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:573:45: required from 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&) [with T = CompressedCoverage_t >]' 573 | pair it_ret; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:128:28: required from 'CompactedDBG& CompactedDBG::toDataGraph(CompactedDBG&&, size_t) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 128 | h_kmers_ccov.insert(move(km), move(it_s->ccov)); | ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:611:45: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 611 | if (construct_finished) toDataGraph(std::move(graph_seq), opt.nb_threads); | ^~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/ColoredCDBG.tcc:399:31: required from 'bool ColoredCDBG::buildGraph(const CCDBG_Build_opt&) [with Unitig_data_t = void]' 399 | invalid = !this->build(opt_); | ~~~~~~~~~~~^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:628:47: required from here 628 | success = ccdbg.buildGraph(opt); | ~~~~~~~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t, size_t) [with bool is_const = true; T = CompressedCoverage_t; KHT_ptr_t = const KmerHashTable >*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:396:61: required from 'KmerHashTable::const_iterator KmerHashTable::find(size_t) const [with T = CompressedCoverage_t; const_iterator = KmerHashTable >::iterator_; size_t = unsigned int]' 396 | if ((h < size_) && !table_keys[h].isEmpty()) return const_iterator(this, h); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:96:55: required from 'Kmer UnitigMap::getUnitigHead() const [with Unitig_data_t = void; Graph_data_t = void; bool is_const = true]' 96 | if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig).getKey(); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:475:86: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 475 | if (unitig.isAbundant) labelB = *(idmap.find(unitig.getUnitigHead().rep())); | ~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:37:72: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 37 | iterator_(KHT_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'void KmerHashTable::iterator_::get_to_first() [with bool is_const = true; T = CompressedCoverage_t >]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:743:24: required from 'KmerHashTable::const_iterator KmerHashTable::begin() const [with T = CompressedCoverage_t >; const_iterator = KmerHashTable > >::iterator_]' 743 | it.get_to_first(); | ~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7143:86: required from 'void CompactedDBG::createJoinHT(std::vector*, KmerHashTable&, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 7143 | for (typename h_kmers_ccov_t::const_iterator it_ccov = h_kmers_ccov.begin(); it_ccov != h_kmers_ccov.end(); ++it_ccov) { | ~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7465:17: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7465 | createJoinHT(v_joins, joins, nb_threads); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:109:21: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 109 | h = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:110:23: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 110 | psl = 0xffffffffffffffffULL; | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_() [with bool is_const = false; T = char]': /usr/include/c++/14/bits/stl_pair.h:726:9: required from 'constexpr std::pair<_T1, _T2>::pair() [with _U1 = KmerHashTable::iterator_; _U2 = bool; typename std::enable_if, std::__is_implicitly_default_constructible<_U2> >::value, bool>::type = true; _T1 = KmerHashTable::iterator_; _T2 = bool]' 726 | : first(), second() { } | ^~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:573:45: required from 'std::pair::iterator_, bool> KmerHashTable::insert(Kmer&&, T&&) [with T = char]' 573 | pair it_ret; | ^~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7152:95: required from 'void CompactedDBG::createJoinHT(std::vector*, KmerHashTable&, size_t) const [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; size_t = unsigned int]' 7152 | if ((joins.find(tail) == joins.end()) && checkJoin(tail, cm, fw)) joins.insert(fw.twin(), tail.getChar(0)); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:7465:17: required from 'typename std::enable_if<(! is_void), unsigned int>::type CompactedDBG::joinUnitigs_(std::vector*, size_t) [with bool is_void = false; Unitig_data_t = DataAccessor; Graph_data_t = DataStorage; typename std::enable_if<(! is_void), unsigned int>::type = unsigned int; size_t = unsigned int]' 7465 | createJoinHT(v_joins, joins, nb_threads); | ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:708:70: required from 'bool CompactedDBG::simplify(bool, bool, bool) [with Unitig_data_t = DataAccessor; Graph_data_t = DataStorage]' 708 | if (clip_short_tips) joined = joinUnitigs_::value>(&v_joins); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:630:58: required from here 630 | if (success) success = ccdbg.simplify(opt.deleteIsolated, opt.clipTips, opt.verbose); | ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:42: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:35:70: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 35 | iterator_() : ht(nullptr), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t) [with bool is_const = false; T = unsigned char; KHT_ptr_t = KmerHashTable*]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:750:16: required from 'KmerHashTable::iterator KmerHashTable::end() [with T = unsigned char; iterator = KmerHashTable::iterator_]' 750 | return iterator(this); | ^~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:403:39: required from 'size_t KmerHashTable::erase(const_iterator) [with T = unsigned char; size_t = unsigned int; const_iterator = KmerHashTable::iterator_]' 403 | if ((size_ == 0) || (it == end())) return 0; | ~~~^~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:3084:72: required from 'bool CompactedDBG::construct(const CDBG_Build_opt&, DualBlockedBloomFilter&, Roaring&, size_t, size_t, size_t, size_t) [with Unitig_data_t = void; Graph_data_t = void; size_t = unsigned int]' 3084 | if (has_full_cov) kmt_fp_cand.erase(p_insert_kmt_fp_cand.first); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/CompactedDBG.tcc:679:62: required from 'bool CompactedDBG::build(CDBG_Build_opt&) [with Unitig_data_t = void; Graph_data_t = void]' 679 | if (construct_finished) construct_finished = construct(opt, dbbf, r, nb_unique_minimizers, nb_non_unique_minimizers, nb_unique_kmers, nb_non_unique_kmers); // Construction step | ^~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:638:41: required from here 638 | success = cdbg.build(opt); | ~~~~~~~~~~^~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:51: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:36:79: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 36 | iterator_(KHT_ptr_t ht_) : ht(ht_), h(0xffffffffffffffffULL), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp: In instantiation of 'KmerHashTable::iterator_::iterator_(KHT_ptr_t, size_t) [with bool is_const = true; T = CompressedCoverage_t; KHT_ptr_t = const KmerHashTable >*; size_t = unsigned int]': /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:396:61: required from 'KmerHashTable::const_iterator KmerHashTable::find(size_t) const [with T = CompressedCoverage_t; const_iterator = KmerHashTable >::iterator_; size_t = unsigned int]' 396 | if ((h < size_) && !table_keys[h].isEmpty()) return const_iterator(this, h); | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/UnitigMap.tcc:96:55: required from 'Kmer UnitigMap::getUnitigHead() const [with Unitig_data_t = void; Graph_data_t = void; bool is_const = true]' 96 | if (isAbundant) return cdbg->h_kmers_ccov.find(pos_unitig).getKey(); | ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:475:86: required from 'bool CompactedDBG::writeGFA(const std::string&, size_t, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 475 | if (unitig.isAbundant) labelB = *(idmap.find(unitig.getUnitigHead().rep())); | ~~~~~~~~~~~~~~~~~~~~^~ /build/reproducible-path/bifrost-1.3.1/src/IO.tcc:82:41: required from 'bool CompactedDBG::write(const std::string&, size_t, bool, bool, bool, bool, bool, bool) const [with Unitig_data_t = void; Graph_data_t = void; std::string = std::__cxx11::basic_string; size_t = unsigned int]' 82 | if (GFA_output) write_success = writeGFA(fn, nb_threads, compressed_output); | ^~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/Bifrost.cpp:641:54: required from here 641 | if (success) success = cdbg.write(opt.prefixFilenameOut, opt.nb_threads, opt.outputGFA, opt.outputFASTA, opt.outputBFG, opt.writeIndexFile, opt.compressOutput, opt.verbose); | ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/bifrost-1.3.1/src/KmerHashTable.hpp:37:72: warning: conversion from 'long long unsigned int' to 'size_t' {aka 'unsigned int'} changes value from '18446744073709551615' to '4294967295' [-Woverflow] 37 | iterator_(KHT_ptr_t ht_, size_t h_) : ht(ht_), h(h_), psl(0xffffffffffffffffULL) {} | ^~~~~~~~~~~~~~~~~~~~~ make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:79: src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o] Error 1 make[3]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:131: src/CMakeFiles/bifrost_dynamic.dir/all] Error 2 make[2]: *** Waiting for unfinished jobs.... make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:79: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1 make[3]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:105: src/CMakeFiles/bifrost_static.dir/all] Error 2 make[2]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' make[1]: *** [Makefile:139: all] Error 2 make[1]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-i686-linux-gnu' dh_auto_build: error: cd obj-i686-linux-gnu && make -j22 "INSTALL=install --strip-program=true" VERBOSE=1 returned exit code 2 make: *** [debian/rules:8: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/6636 and its subdirectories Fri Jan 3 08:00:22 UTC 2025 W: No second build log, what happened?