Sat Jan 25 16:52:11 UTC 2025 I: starting to build bifrost/trixie/armhf on jenkins on '2025-01-25 16:51' Sat Jan 25 16:52:11 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/armhf_10/6926/console.log Sat Jan 25 16:52:11 UTC 2025 I: Downloading source for trixie/bifrost=1.3.1-1 --2025-01-25 16:52:11-- 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% 268M=0s 2025-01-25 16:52:11 (268 MB/s) - ‘bifrost_1.3.1-1.dsc’ saved [2099/2099] Sat Jan 25 16:52:11 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----- Sat Jan 25 16:52:11 UTC 2025 I: Checking whether the package is not for us Sat Jan 25 16:52:11 UTC 2025 I: Starting 1st build on remote node wbq0-armhf-rb.debian.net. Sat Jan 25 16:52:11 UTC 2025 I: Preparing to do remote build '1' on wbq0-armhf-rb.debian.net. Sat Jan 25 16:58:09 UTC 2025 I: Deleting $TMPDIR on wbq0-armhf-rb.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Sat Jan 25 04:52:23 -12 2025 I: pbuilder-time-stamp: 1737823943 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: 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 dpkg-source: warning: cannot verify inline signature for ./bifrost_1.3.1-1.dsc: unsupported subcommand 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/13400/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='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3 ' DISTRIBUTION='trixie' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='7e7a63c38259438fb13b541650a94f0c' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' 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='13400' 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.0aFc6LL4/pbuilderrc_KlIa --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.0aFc6LL4/b1 --logfile b1/build.log bifrost_1.3.1-1.dsc' SUDO_GID='113' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:3142/' I: uname -a Linux wbq0 6.1.0-30-armmp #1 SMP Debian 6.1.124-1 (2025-01-12) armv7l GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 14:40 /bin -> usr/bin I: user script /srv/workspace/pbuilder/13400/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: armhf 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 ... 19569 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} libffi8{a} libfile-stripnondeterminism-perl{a} libgnutls30t64{a} libgssapi-krb5-2{a} libicu72{a} libidn2-0{a} libjsoncpp26{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} libldap2{a} libmagic-mgc{a} libmagic1t64{a} libnghttp2-14{a} libp11-kit0{a} libpipeline1{a} libproc2-0{a} libpsl5t64{a} librhash1{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libssh2-1t64{a} libtasn1-6{a} libtool{a} libuchardet0{a} libunistring5{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, 61 newly installed, 0 to remove and 0 not upgraded. Need to get 34.0 MB of archives. After unpacking 124 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian trixie/main armhf libproc2-0 armhf 2:4.0.4-6 [56.0 kB] Get: 2 http://deb.debian.org/debian trixie/main armhf procps armhf 2:4.0.4-6 [864 kB] Get: 3 http://deb.debian.org/debian trixie/main armhf sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian trixie/main armhf libmagic-mgc armhf 1:5.45-3+b1 [314 kB] Get: 5 http://deb.debian.org/debian trixie/main armhf libmagic1t64 armhf 1:5.45-3+b1 [98.5 kB] Get: 6 http://deb.debian.org/debian trixie/main armhf file armhf 1:5.45-3+b1 [42.3 kB] Get: 7 http://deb.debian.org/debian trixie/main armhf gettext-base armhf 0.22.5-4 [196 kB] Get: 8 http://deb.debian.org/debian trixie/main armhf libuchardet0 armhf 0.0.8-1+b2 [65.6 kB] Get: 9 http://deb.debian.org/debian trixie/main armhf groff-base armhf 1.23.0-7 [1095 kB] Get: 10 http://deb.debian.org/debian trixie/main armhf bsdextrautils armhf 2.40.4-1 [84.6 kB] Get: 11 http://deb.debian.org/debian trixie/main armhf libpipeline1 armhf 1.5.8-1 [35.0 kB] Get: 12 http://deb.debian.org/debian trixie/main armhf man-db armhf 2.13.0-1 [1382 kB] Get: 13 http://deb.debian.org/debian trixie/main armhf m4 armhf 1.4.19-5 [272 kB] Get: 14 http://deb.debian.org/debian trixie/main armhf autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian trixie/main armhf autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian trixie/main armhf automake all 1:1.16.5-1.3 [823 kB] Get: 17 http://deb.debian.org/debian trixie/main armhf autopoint all 0.22.5-4 [723 kB] Get: 18 http://deb.debian.org/debian trixie/main armhf cmake-data all 3.31.4-2 [2267 kB] Get: 19 http://deb.debian.org/debian trixie/main armhf libicu72 armhf 72.1-6 [9086 kB] Get: 20 http://deb.debian.org/debian trixie/main armhf libxml2 armhf 2.12.7+dfsg+really2.9.14-0.2+b1 [605 kB] Get: 21 http://deb.debian.org/debian trixie/main armhf libarchive13t64 armhf 3.7.4-1.1 [306 kB] Get: 22 http://deb.debian.org/debian trixie/main armhf libbrotli1 armhf 1.1.0-2+b6 [282 kB] Get: 23 http://deb.debian.org/debian trixie/main armhf libkrb5support0 armhf 1.21.3-3 [30.0 kB] Get: 24 http://deb.debian.org/debian trixie/main armhf libcom-err2 armhf 1.47.2-1 [23.3 kB] Get: 25 http://deb.debian.org/debian trixie/main armhf libk5crypto3 armhf 1.21.3-3 [75.8 kB] Get: 26 http://deb.debian.org/debian trixie/main armhf libkeyutils1 armhf 1.6.3-4 [8096 B] Get: 27 http://deb.debian.org/debian trixie/main armhf libkrb5-3 armhf 1.21.3-3 [283 kB] Get: 28 http://deb.debian.org/debian trixie/main armhf libgssapi-krb5-2 armhf 1.21.3-3 [114 kB] Get: 29 http://deb.debian.org/debian trixie/main armhf libunistring5 armhf 1.3-1 [444 kB] Get: 30 http://deb.debian.org/debian trixie/main armhf libidn2-0 armhf 2.3.7-2+b1 [125 kB] Get: 31 http://deb.debian.org/debian trixie/main armhf libsasl2-modules-db armhf 2.1.28+dfsg1-8+b1 [18.6 kB] Get: 32 http://deb.debian.org/debian trixie/main armhf libsasl2-2 armhf 2.1.28+dfsg1-8+b1 [50.6 kB] Get: 33 http://deb.debian.org/debian trixie/main armhf libldap2 armhf 2.6.9+dfsg-1 [167 kB] Get: 34 http://deb.debian.org/debian trixie/main armhf libnghttp2-14 armhf 1.64.0-1 [62.9 kB] Get: 35 http://deb.debian.org/debian trixie/main armhf libpsl5t64 armhf 0.21.2-1.1+b1 [55.8 kB] Get: 36 http://deb.debian.org/debian trixie/main armhf libffi8 armhf 3.4.6-1 [20.0 kB] Get: 37 http://deb.debian.org/debian trixie/main armhf libp11-kit0 armhf 0.25.5-3 [385 kB] Get: 38 http://deb.debian.org/debian trixie/main armhf libtasn1-6 armhf 4.19.0-3+b3 [43.9 kB] Get: 39 http://deb.debian.org/debian trixie/main armhf libgnutls30t64 armhf 3.8.8-2 [1370 kB] Get: 40 http://deb.debian.org/debian trixie/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b5 [53.2 kB] Get: 41 http://deb.debian.org/debian trixie/main armhf libssh2-1t64 armhf 1.11.1-1 [227 kB] Get: 42 http://deb.debian.org/debian trixie/main armhf libcurl4t64 armhf 8.11.1-1+b1 [304 kB] Get: 43 http://deb.debian.org/debian trixie/main armhf libexpat1 armhf 2.6.4-1 [83.5 kB] Get: 44 http://deb.debian.org/debian trixie/main armhf libjsoncpp26 armhf 1.9.6-3 [69.9 kB] Get: 45 http://deb.debian.org/debian trixie/main armhf librhash1 armhf 1.4.5-1 [143 kB] Get: 46 http://deb.debian.org/debian trixie/main armhf libuv1t64 armhf 1.48.0-7 [134 kB] Get: 47 http://deb.debian.org/debian trixie/main armhf cmake armhf 3.31.4-2 [5912 kB] Get: 48 http://deb.debian.org/debian trixie/main armhf d-shlibs all 0.109 [11.1 kB] Get: 49 http://deb.debian.org/debian trixie/main armhf libdebhelper-perl all 13.23 [90.6 kB] Get: 50 http://deb.debian.org/debian trixie/main armhf libtool all 2.5.4-2 [539 kB] Get: 51 http://deb.debian.org/debian trixie/main armhf dh-autoreconf all 20 [17.1 kB] Get: 52 http://deb.debian.org/debian trixie/main armhf libarchive-zip-perl all 1.68-1 [104 kB] Get: 53 http://deb.debian.org/debian trixie/main armhf libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 54 http://deb.debian.org/debian trixie/main armhf dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 55 http://deb.debian.org/debian trixie/main armhf libelf1t64 armhf 0.192-4 [184 kB] Get: 56 http://deb.debian.org/debian trixie/main armhf dwz armhf 0.15-1+b2 [106 kB] Get: 57 http://deb.debian.org/debian trixie/main armhf gettext armhf 0.22.5-4 [1489 kB] Get: 58 http://deb.debian.org/debian trixie/main armhf intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 59 http://deb.debian.org/debian trixie/main armhf po-debconf all 1.0.21+nmu1 [248 kB] Get: 60 http://deb.debian.org/debian trixie/main armhf debhelper all 13.23 [919 kB] Get: 61 http://deb.debian.org/debian trixie/main armhf zlib1g-dev armhf 1:1.3.dfsg+really1.3.1-1+b1 [905 kB] Fetched 34.0 MB in 4s (8579 kB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:armhf. (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 ... 19569 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-6_armhf.deb ... Unpacking libproc2-0:armhf (2:4.0.4-6) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.4-6_armhf.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_armhf.deb ... Unpacking libmagic-mgc (1:5.45-3+b1) ... Selecting previously unselected package libmagic1t64:armhf. Preparing to unpack .../04-libmagic1t64_1%3a5.45-3+b1_armhf.deb ... Unpacking libmagic1t64:armhf (1:5.45-3+b1) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.45-3+b1_armhf.deb ... Unpacking file (1:5.45-3+b1) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.22.5-4_armhf.deb ... Unpacking gettext-base (0.22.5-4) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../07-libuchardet0_0.0.8-1+b2_armhf.deb ... Unpacking libuchardet0:armhf (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-7_armhf.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.4-1_armhf.deb ... Unpacking bsdextrautils (2.40.4-1) ... Selecting previously unselected package libpipeline1:armhf. Preparing to unpack .../10-libpipeline1_1.5.8-1_armhf.deb ... Unpacking libpipeline1:armhf (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.0-1_armhf.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-5_armhf.deb ... Unpacking m4 (1.4.19-5) ... 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_0.22.5-4_all.deb ... Unpacking autopoint (0.22.5-4) ... Selecting previously unselected package cmake-data. Preparing to unpack .../17-cmake-data_3.31.4-2_all.deb ... Unpacking cmake-data (3.31.4-2) ... Selecting previously unselected package libicu72:armhf. Preparing to unpack .../18-libicu72_72.1-6_armhf.deb ... Unpacking libicu72:armhf (72.1-6) ... Selecting previously unselected package libxml2:armhf. Preparing to unpack .../19-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_armhf.deb ... Unpacking libxml2:armhf (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package libarchive13t64:armhf. Preparing to unpack .../20-libarchive13t64_3.7.4-1.1_armhf.deb ... Unpacking libarchive13t64:armhf (3.7.4-1.1) ... 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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 armhf 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-arm-linux-gnueabihf && 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/arm-linux-gnueabihf -DCOMPILATION_ARCH=OFF .. CMake Deprecation Warning at CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 3.10 will be removed from a future version of CMake. Update the VERSION argument value. Or, use the ... syntax to tell CMake that the project requires at least but has been updated to work with policies introduced by or earlier. -- 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/arm-linux-gnueabihf/libz.so (found version "1.3.1") -- Configuring done (10.7s) -- Generating done (0.2s) 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-arm-linux-gnueabihf make[1]: Leaving directory '/build/reproducible-path/bifrost-1.3.1' dh_auto_build cd obj-arm-linux-gnueabihf && make -j3 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf' /usr/bin/cmake -S/build/reproducible-path/bifrost-1.3.1 -B/build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf/CMakeFiles 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Entering directory '/build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf' [ 3%] Building CXX object src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf/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 -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 [ 6%] Building CXX object src/CMakeFiles/bifrost_static.dir/BitContainer.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf/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 -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 [ 9%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf/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 -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 /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/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; | ~ ^~~~~~~ | ) 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: 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: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: 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: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: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: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/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/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: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 /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/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); | ^~~~~~~~~ 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/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/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: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 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=(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::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& 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::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& 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 '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: 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: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 /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 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: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 '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 '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 '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 '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 '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 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::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 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: 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/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; | ^~~~~~~~~~~~~~~~~~~~~ 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: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/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; | ^~~~~~~~~~~~~~~~~~~~~ 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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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; | ~~~~~~~~~~~~~~^~~~~ 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/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; | ~~~~~~~~~~~~~~^~~~~ 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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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 '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 '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 '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; | ~~~~~~~~~~~~~^~~~~ /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 '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: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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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; | ~~~~~~^~~~~ 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); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~^~~~~ /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); | ~~~^~~~~~~~~~~~~~~~~~~~~~~~ /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); | ~~~~~~~~~~~~~~~~^~~~~ /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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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: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: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:5706:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>)' 5706 | max(initializer_list<_Tp> __l) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5706:5: note: candidate expects 1 argument, 2 provided /usr/include/c++/14/bits/stl_algo.h:5716:5: note: candidate: 'template _Tp std::max(initializer_list<_Tp>, _Compare)' 5716 | max(initializer_list<_Tp> __l, _Compare __comp) | ^~~ /usr/include/c++/14/bits/stl_algo.h:5716:5: 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 '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/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/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; | ^~~~~~~~~~~~~~~~~~ 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/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_() [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_::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/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/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/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/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/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 = 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_& 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/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_::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/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/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/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/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/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 '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/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/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/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 '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 '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/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/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/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_() [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/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 '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 = 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/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/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/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 '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::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: 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: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 '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 '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/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/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/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_() [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_() [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 '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_() [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: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) {} | ^~~~~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf/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 -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 /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/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/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/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_(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/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 = 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 '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) {} | ^~~~~~~~~~~~~~~~~~~~~ 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/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.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 '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 '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/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: 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 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 '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 make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:110: src/CMakeFiles/bifrost_static.dir/BlockedBloomFilter.cpp.o] Error 1 make[3]: *** Waiting for unfinished jobs.... [ 15%] Building CXX object src/CMakeFiles/bifrost_dynamic.dir/BitContainer.cpp.o cd /build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf/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 -fstack-clash-protection -Wformat -Werror=format-security -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_TIME_BITS=64 -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 make[3]: *** [src/CMakeFiles/bifrost_dynamic.dir/build.make:82: src/CMakeFiles/bifrost_dynamic.dir/Bifrost.cpp.o] Error 1 make[3]: *** Waiting for unfinished jobs.... make[3]: *** [src/CMakeFiles/bifrost_static.dir/build.make:82: src/CMakeFiles/bifrost_static.dir/Bifrost.cpp.o] Error 1 make[3]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf' make[2]: *** [CMakeFiles/Makefile2:115: src/CMakeFiles/bifrost_static.dir/all] Error 2 make[2]: *** Waiting for unfinished jobs.... /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; | ^~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf' make[2]: *** [CMakeFiles/Makefile2:147: src/CMakeFiles/bifrost_dynamic.dir/all] Error 2 make[2]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf' make[1]: *** [Makefile:139: all] Error 2 make[1]: Leaving directory '/build/reproducible-path/bifrost-1.3.1/obj-arm-linux-gnueabihf' dh_auto_build: error: cd obj-arm-linux-gnueabihf && make -j3 "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/13400 and its subdirectories Sat Jan 25 16:58:12 UTC 2025 W: No second build log, what happened?