Tue Mar 18 17:18:33 UTC 2025 I: starting to build libbpp-seq/unstable/arm64 on jenkins on '2025-03-18 17:18' Tue Mar 18 17:18:33 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/arm64_7/62564/console.log Tue Mar 18 17:18:33 UTC 2025 I: Downloading source for unstable/libbpp-seq=2.4.1-13 --2025-03-18 17:18:34-- http://deb.debian.org/debian/pool/main/libb/libbpp-seq/libbpp-seq_2.4.1-13.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2169 (2.1K) [text/prs.lines.tag] Saving to: ‘libbpp-seq_2.4.1-13.dsc’ 0K .. 100% 332M=0s 2025-03-18 17:18:34 (332 MB/s) - ‘libbpp-seq_2.4.1-13.dsc’ saved [2169/2169] Tue Mar 18 17:18:34 UTC 2025 I: libbpp-seq_2.4.1-13.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 3.0 (quilt) Source: libbpp-seq Binary: libbpp-seq-dev, libbpp-seq12t64 Architecture: any Version: 2.4.1-13 Maintainer: Debian Med Packaging Team Uploaders: Julien Dutheil , Andreas Tille Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/med-team/libbpp-seq Vcs-Git: https://salsa.debian.org/med-team/libbpp-seq.git Build-Depends: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), cmake, d-shlibs (>= 0.106~), libbpp-core-dev Package-List: libbpp-seq-dev deb libdevel optional arch=any libbpp-seq12t64 deb libs optional arch=any Checksums-Sha1: a79687bdf2ce4c5c2031cb5da8394a9420804f90 322620 libbpp-seq_2.4.1.orig.tar.gz d826033655a203f1e71505464901b96e073dbf1e 12244 libbpp-seq_2.4.1-13.debian.tar.xz Checksums-Sha256: dbfcb04803e4b7f08f9f159da8a947c91906c3ca8b20683ac193f6dc524d4655 322620 libbpp-seq_2.4.1.orig.tar.gz 3e0b877ccae3846f83e0ed86546c5c475fc6107729aa58e203c6f2792aeeb56d 12244 libbpp-seq_2.4.1-13.debian.tar.xz Files: bdafc80aab9591ff79556138d6555941 322620 libbpp-seq_2.4.1.orig.tar.gz 52dec0368bb77da4a9af7983e03ab13c 12244 libbpp-seq_2.4.1-13.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQJFBAEBCAAvFiEE8fAHMgoDVUHwpmPKV4oElNHGRtEFAmazN+ERHHRpbGxlQGRl Ymlhbi5vcmcACgkQV4oElNHGRtE7MhAAhwuIuD8ZvxSHwCRhnz7yKONGDxnhfqqe bVJZ7xaytV2OUqCil2AqtMJ8cjLwB6s8WSsOUrGZGh3a7ydHi/LWBf44DuCch1bg 4xcb5RZKgPkkTnKWBHaeuUXjoCmu4UI+JsMCb6CZsU19HrrZux2ENYkI8Y6RNDSV +B6ep3R1mbnmIEiiQQRNrtg4tpgJijPmWxnFeQYhSYkIaYocYhZSBjEwXCruBAsI NPKq8LrlYdtBQxxuQQyij1mIxjSTRa1zKXj/QNMuM6Z4d/hW8neimiOWYQdFcPqi z5hoAix/Q5HSbeMBKNw7PQBViYHOJtLyLLtBkPyxI3ML15MAPsU6NfbyAj5JqBbg i61uTSZWWx+NgGqjNXbo38FXeD+hDijt0qCnpRHTFBKqM59z9oXOQVQ83Hjr95rc sleGahi5zKbHsYMFCYCHWmk5o5eMAtbC3ESSbQmo5gymWOczZE9EUf2Gm1sQZROB T7qxEijZnEWdmMmTmBNqKD3b0ghNsO4bi/CidNb5/w8l/VYOJBKAnswz6uGQwQTz lU9Kl0pY/D9dS+Ft3vDH4ND1ZjVbcTJnIY2b6o0ICtKzPQNWPzvqNpxacuBT0rEt MJx8bt+Wk498ABxG3Pm3aLdbfsWLV+y9Bfo+s52ZmZIg8ZUlH/98/UqmGimFVUXB EfswTPNAAd0= =jZSB -----END PGP SIGNATURE----- Tue Mar 18 17:18:34 UTC 2025 I: Checking whether the package is not for us Tue Mar 18 17:18:34 UTC 2025 I: Starting 1st build on remote node codethink04-arm64.debian.net. Tue Mar 18 17:18:34 UTC 2025 I: Preparing to do remote build '1' on codethink04-arm64.debian.net. Tue Mar 18 17:21:38 UTC 2025 I: Deleting $TMPDIR on codethink04-arm64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Mar 18 05:18:37 -12 2025 I: pbuilder-time-stamp: 1742318317 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-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 [libbpp-seq_2.4.1-13.dsc] I: copying [./libbpp-seq_2.4.1.orig.tar.gz] I: copying [./libbpp-seq_2.4.1-13.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbpp-seq_2.4.1-13.dsc: unsupported subcommand dpkg-source: info: extracting libbpp-seq in libbpp-seq-2.4.1 dpkg-source: info: unpacking libbpp-seq_2.4.1.orig.tar.gz dpkg-source: info: unpacking libbpp-seq_2.4.1-13.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying unforce-cxxflags.patch dpkg-source: info: applying spelling I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/4068209/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='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='arm64' IFS=' ' INVOCATION_ID='33eaee960fcd44289dc0a4d06a2e4486' 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='4068209' 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.6T2sEiXC/pbuilderrc_mo4W --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.6T2sEiXC/b1 --logfile b1/build.log libbpp-seq_2.4.1-13.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.4:3128' I: uname -a Linux codethink04-arm64 6.1.0-32-cloud-arm64 #1 SMP Debian 6.1.129-1 (2025-03-06) aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Mar 4 11:20 /bin -> usr/bin I: user script /srv/workspace/pbuilder/4068209/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: arm64 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: dpkg-dev (>= 1.22.5), debhelper-compat (= 13), cmake, d-shlibs (>= 0.106~), libbpp-core-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 ... 19898 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 cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on d-shlibs (>= 0.106~); however: Package d-shlibs is not installed. pbuilder-satisfydepends-dummy depends on libbpp-core-dev; however: Package libbpp-core-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} libbpp-core-dev{a} libbpp-core4t64{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} libicu76{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} libnghttp3-9{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} 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, 63 newly installed, 0 to remove and 0 not upgraded. Need to get 39.7 MB of archives. After unpacking 162 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main arm64 libproc2-0 arm64 2:4.0.4-7 [62.4 kB] Get: 2 http://deb.debian.org/debian unstable/main arm64 procps arm64 2:4.0.4-7 [868 kB] Get: 3 http://deb.debian.org/debian unstable/main arm64 sensible-utils all 0.0.24 [24.8 kB] Get: 4 http://deb.debian.org/debian unstable/main arm64 libmagic-mgc arm64 1:5.46-2 [337 kB] Get: 5 http://deb.debian.org/debian unstable/main arm64 libmagic1t64 arm64 1:5.46-2 [103 kB] Get: 6 http://deb.debian.org/debian unstable/main arm64 file arm64 1:5.46-2 [43.6 kB] Get: 7 http://deb.debian.org/debian unstable/main arm64 gettext-base arm64 0.23.1-1 [241 kB] Get: 8 http://deb.debian.org/debian unstable/main arm64 libuchardet0 arm64 0.0.8-1+b2 [69.2 kB] Get: 9 http://deb.debian.org/debian unstable/main arm64 groff-base arm64 1.23.0-7 [1129 kB] Get: 10 http://deb.debian.org/debian unstable/main arm64 bsdextrautils arm64 2.40.4-5 [92.0 kB] Get: 11 http://deb.debian.org/debian unstable/main arm64 libpipeline1 arm64 1.5.8-1 [40.2 kB] Get: 12 http://deb.debian.org/debian unstable/main arm64 man-db arm64 2.13.0-1 [1404 kB] Get: 13 http://deb.debian.org/debian unstable/main arm64 m4 arm64 1.4.19-7 [285 kB] Get: 14 http://deb.debian.org/debian unstable/main arm64 autoconf all 2.72-3 [493 kB] Get: 15 http://deb.debian.org/debian unstable/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 16 http://deb.debian.org/debian unstable/main arm64 automake all 1:1.17-3 [862 kB] Get: 17 http://deb.debian.org/debian unstable/main arm64 autopoint all 0.23.1-1 [770 kB] Get: 18 http://deb.debian.org/debian unstable/main arm64 cmake-data all 3.31.6-1 [2268 kB] Get: 19 http://deb.debian.org/debian unstable/main arm64 libicu76 arm64 76.1-3 [9526 kB] Get: 20 http://deb.debian.org/debian unstable/main arm64 libxml2 arm64 2.12.7+dfsg+really2.9.14-0.3+b1 [630 kB] Get: 21 http://deb.debian.org/debian unstable/main arm64 libarchive13t64 arm64 3.7.4-1.1 [323 kB] Get: 22 http://deb.debian.org/debian unstable/main arm64 libbrotli1 arm64 1.1.0-2+b7 [308 kB] Get: 23 http://deb.debian.org/debian unstable/main arm64 libkrb5support0 arm64 1.21.3-5 [32.4 kB] Get: 24 http://deb.debian.org/debian unstable/main arm64 libcom-err2 arm64 1.47.2-1+b1 [24.2 kB] Get: 25 http://deb.debian.org/debian unstable/main arm64 libk5crypto3 arm64 1.21.3-5 [81.2 kB] Get: 26 http://deb.debian.org/debian unstable/main arm64 libkeyutils1 arm64 1.6.3-4 [9352 B] Get: 27 http://deb.debian.org/debian unstable/main arm64 libkrb5-3 arm64 1.21.3-5 [308 kB] Get: 28 http://deb.debian.org/debian unstable/main arm64 libgssapi-krb5-2 arm64 1.21.3-5 [127 kB] Get: 29 http://deb.debian.org/debian unstable/main arm64 libunistring5 arm64 1.3-1 [449 kB] Get: 30 http://deb.debian.org/debian unstable/main arm64 libidn2-0 arm64 2.3.8-2 [107 kB] Get: 31 http://deb.debian.org/debian unstable/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg1-9 [20.1 kB] Get: 32 http://deb.debian.org/debian unstable/main arm64 libsasl2-2 arm64 2.1.28+dfsg1-9 [55.6 kB] Get: 33 http://deb.debian.org/debian unstable/main arm64 libldap2 arm64 2.6.9+dfsg-2 [179 kB] Get: 34 http://deb.debian.org/debian unstable/main arm64 libnghttp2-14 arm64 1.64.0-1 [71.3 kB] Get: 35 http://deb.debian.org/debian unstable/main arm64 libnghttp3-9 arm64 1.8.0-1 [63.2 kB] Get: 36 http://deb.debian.org/debian unstable/main arm64 libpsl5t64 arm64 0.21.2-1.1+b1 [57.1 kB] Get: 37 http://deb.debian.org/debian unstable/main arm64 libffi8 arm64 3.4.7-1 [21.2 kB] Get: 38 http://deb.debian.org/debian unstable/main arm64 libp11-kit0 arm64 0.25.5-3 [409 kB] Get: 39 http://deb.debian.org/debian unstable/main arm64 libtasn1-6 arm64 4.20.0-2 [47.3 kB] Get: 40 http://deb.debian.org/debian unstable/main arm64 libgnutls30t64 arm64 3.8.9-2 [1374 kB] Get: 41 http://deb.debian.org/debian unstable/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b5 [56.8 kB] Get: 42 http://deb.debian.org/debian unstable/main arm64 libssh2-1t64 arm64 1.11.1-1 [235 kB] Get: 43 http://deb.debian.org/debian unstable/main arm64 libcurl4t64 arm64 8.13.0~rc2-1 [347 kB] Get: 44 http://deb.debian.org/debian unstable/main arm64 libexpat1 arm64 2.7.0-1 [92.8 kB] Get: 45 http://deb.debian.org/debian unstable/main arm64 libjsoncpp26 arm64 1.9.6-3 [72.9 kB] Get: 46 http://deb.debian.org/debian unstable/main arm64 librhash1 arm64 1.4.5-1 [129 kB] Get: 47 http://deb.debian.org/debian unstable/main arm64 libuv1t64 arm64 1.50.0-2 [148 kB] Get: 48 http://deb.debian.org/debian unstable/main arm64 cmake arm64 3.31.6-1 [9912 kB] Get: 49 http://deb.debian.org/debian unstable/main arm64 d-shlibs all 0.109 [11.1 kB] Get: 50 http://deb.debian.org/debian unstable/main arm64 libdebhelper-perl all 13.24.1 [90.9 kB] Get: 51 http://deb.debian.org/debian unstable/main arm64 libtool all 2.5.4-4 [539 kB] Get: 52 http://deb.debian.org/debian unstable/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 53 http://deb.debian.org/debian unstable/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 54 http://deb.debian.org/debian unstable/main arm64 libfile-stripnondeterminism-perl all 1.14.1-2 [19.7 kB] Get: 55 http://deb.debian.org/debian unstable/main arm64 dh-strip-nondeterminism all 1.14.1-2 [8620 B] Get: 56 http://deb.debian.org/debian unstable/main arm64 libelf1t64 arm64 0.192-4 [189 kB] Get: 57 http://deb.debian.org/debian unstable/main arm64 dwz arm64 0.15-1+b1 [102 kB] Get: 58 http://deb.debian.org/debian unstable/main arm64 gettext arm64 0.23.1-1 [1610 kB] Get: 59 http://deb.debian.org/debian unstable/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 60 http://deb.debian.org/debian unstable/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 61 http://deb.debian.org/debian unstable/main arm64 debhelper all 13.24.1 [920 kB] Get: 62 http://deb.debian.org/debian unstable/main arm64 libbpp-core4t64 arm64 2.4.1-13+b1 [549 kB] Get: 63 http://deb.debian.org/debian unstable/main arm64 libbpp-core-dev arm64 2.4.1-13+b1 [941 kB] Fetched 39.7 MB in 0s (162 MB/s) Preconfiguring packages ... Selecting previously unselected package libproc2-0:arm64. (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 ... 19898 files and directories currently installed.) Preparing to unpack .../00-libproc2-0_2%3a4.0.4-7_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.4-7) ... Selecting previously unselected package procps. Preparing to unpack .../01-procps_2%3a4.0.4-7_arm64.deb ... Unpacking procps (2:4.0.4-7) ... 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%3a5.46-2_arm64.deb ... Unpacking libmagic-mgc (1:5.46-2) ... Selecting previously unselected package libmagic1t64:arm64. Preparing to unpack .../04-libmagic1t64_1%3a5.46-2_arm64.deb ... Unpacking libmagic1t64:arm64 (1:5.46-2) ... Selecting previously unselected package file. Preparing to unpack .../05-file_1%3a5.46-2_arm64.deb ... Unpacking file (1:5.46-2) ... Selecting previously unselected package gettext-base. Preparing to unpack .../06-gettext-base_0.23.1-1_arm64.deb ... Unpacking gettext-base (0.23.1-1) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../07-libuchardet0_0.0.8-1+b2_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.8-1+b2) ... Selecting previously unselected package groff-base. Preparing to unpack .../08-groff-base_1.23.0-7_arm64.deb ... Unpacking groff-base (1.23.0-7) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../09-bsdextrautils_2.40.4-5_arm64.deb ... Unpacking bsdextrautils (2.40.4-5) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../10-libpipeline1_1.5.8-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.8-1) ... Selecting previously unselected package man-db. Preparing to unpack .../11-man-db_2.13.0-1_arm64.deb ... Unpacking man-db (2.13.0-1) ... Selecting previously unselected package m4. Preparing to unpack .../12-m4_1.4.19-7_arm64.deb ... Unpacking m4 (1.4.19-7) ... 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. 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Setting up automake (1:1.17-3) ... update-alternatives: using /usr/bin/automake-1.17 to provide /usr/bin/automake (automake) in auto mode Setting up libfile-stripnondeterminism-perl (1.14.1-2) ... Setting up gettext (0.23.1-1) ... Setting up libtool (2.5.4-4) ... Setting up libidn2-0:arm64 (2.3.8-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up dh-autoreconf (20) ... Setting up libp11-kit0:arm64 (0.25.5-3) ... Setting up libgssapi-krb5-2:arm64 (1.21.3-5) ... Setting up dh-strip-nondeterminism (1.14.1-2) ... Setting up groff-base (1.23.0-7) ... Setting up libarchive13t64:arm64 (3.7.4-1.1) ... Setting up libgnutls30t64:arm64 (3.8.9-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpsl5t64:arm64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libcurl4t64:arm64 (8.13.0~rc2-1) ... Setting up debhelper (13.24.1) ... 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Building tag database... -> Finished parsing the build-deps I: Building the package I: Running cd /build/reproducible-path/libbpp-seq-2.4.1/ && 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 > ../libbpp-seq_2.4.1-13_source.changes dpkg-buildpackage: info: source package libbpp-seq dpkg-buildpackage: info: source version 2.4.1-13 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andreas Tille dpkg-source --before-build . dpkg-buildpackage: info: host architecture arm64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-aarch64-linux-gnu && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/aarch64-linux-gnu .. CMake Deprecation Warning at CMakeLists.txt:8 (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 CXX compiler identification is GNU 14.2.0 -- 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 -- bpp-core 4.1.0 found: -- static lib: /usr/lib/aarch64-linux-gnu/libbpp-core.a -- shared lib: /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 -- includes: /usr/include -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done (0.7s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu dh_auto_build cd obj-aarch64-linux-gnu && make -j12 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libbpp-seq-2.4.1 -B/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/CMakeFiles /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/src /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/bpp-seq-static.dir/DependInfo.cmake "--color=" make -f src/CMakeFiles/bpp-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/src /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src/CMakeFiles/bpp-seq-shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f src/CMakeFiles/bpp-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 0%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AbstractAlphabet.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetTools.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp [ 2%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o [ 3%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetExceptions.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong 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-fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp [ 5%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/AlphabetTools.cpp [ 6%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DNA.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/BinaryAlphabet.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp [ 7%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp [ 7%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp [ 8%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp [ 8%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp [ 9%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CodonAlphabet.cpp [ 9%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat 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CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp [ 10%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNA.cpp [ 11%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNY.cpp [ 11%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 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-Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/DefaultAlphabet.cpp [ 13%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp [ 13%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp [ 13%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp [ 14%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LetterAlphabet.cpp [ 15%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp [ 15%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/LexicalAlphabet.cpp [ 16%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/NumericAlphabet.cpp [ 17%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/ProteicAlphabet.cpp [ 18%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp [ 18%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp [ 19%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp [ 19%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp [ 20%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.cpp [ 20%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNA.cpp [ 21%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/RNY.cpp [ 21%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.h:48, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.h:49: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 22%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp [ 22%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp [ 23%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp [ 23%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 24%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp [ 24%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/WordAlphabet.cpp [ 25%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 25%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerExceptions.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.h:50, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.h:51: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 26%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp [ 26%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp [ 27%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp [ 27%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 28%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp [ 29%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp [ 29%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp [ 30%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DNAToRNA.cpp [ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 30%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DistanceMatrix.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 31%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp [ 31%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp [ 32%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.cpp [ 33%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o [ 34%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp [ 34%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:72:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 72 | v[2] = 50; In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, inlined from 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:70:27: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::_ZTv0_n104_NK3bpp34EchinodermMitochondrialGeneticCode18getStopCodonsAsIntEv() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:72:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 72 | v[2] = 50; /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 34%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp [ 35%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp [ 36%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/AlphabetIndex/SimpleScore.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, inlined from 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:71:27: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::_ZTv0_n104_NK3bpp36InvertebrateMitochondrialGeneticCode18getStopCodonsAsIntEv() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::MoldMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, inlined from 'virtual std::vector bpp::MoldMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:71:27: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::MoldMitochondrialGeneticCode::_ZTv0_n104_NK3bpp28MoldMitochondrialGeneticCode18getStopCodonsAsIntEv() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 37%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.h:48, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/VectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/SequenceApplicationTools.h:49: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 37%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/CodonSiteTools.cpp [ 37%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp [ 38%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp [ 39%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp [ 39%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp [ 40%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 40%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp [ 40%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 41%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 42%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp [ 42%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AlignedSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 43%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp [ 43%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::YeastMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, inlined from 'virtual std::vector bpp::YeastMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:71:27: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::YeastMitochondrialGeneticCode::_ZTv0_n104_NK3bpp29YeastMitochondrialGeneticCode18getStopCodonsAsIntEv() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/MapSequenceContainer.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 44%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp [ 44%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 45%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Dcse.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.cpp [ 46%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp [ 46%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp [ 47%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 47%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp [ 47%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerIterator.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 48%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp [ 49%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerExceptions.cpp [ 49%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o [ 49%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 50%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.h:50, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainerTools.h:51: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 51%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp [ 52%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerIterator.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 52%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainerTools.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSequenceContainer.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/AbstractSequenceContainer.h:46: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 53%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPhd.cpp [ 53%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp [ 54%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DNAToRNA.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 54%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/DistanceMatrix.cpp [ 54%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPoly.cpp [ 55%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 56%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp [ 57%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.cpp [ 57%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/StreamSequenceIterator.cpp [ 57%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/OSequence.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractOAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/OSequence.h:45: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 58%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/NucleicAcidsReplication.cpp [ 58%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Sequence.cpp [ 59%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.cpp [ 60%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceExceptions.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp:39: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:72:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 72 | v[2] = 50; In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:43: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, inlined from 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:70:27: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::EchinodermMitochondrialGeneticCode::_ZTv0_n104_NK3bpp34EchinodermMitochondrialGeneticCode18getStopCodonsAsIntEv() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h:72:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 72 | v[2] = 50; /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 60%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequencePositionIterators.cpp [ 61%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp [ 61%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWalker.cpp [ 62%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithAnnotation.cpp [ 62%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithAnnotationTools.cpp [ 63%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQuality.cpp [ 64%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQualityTools.cpp [ 64%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Site.cpp [ 64%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp [ 65%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteExceptions.cpp [ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp [ 66%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp [ 66%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp [ 67%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/StringSequenceTools.cpp [ 67%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:44: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, inlined from 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:71:27: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolList.cpp /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::InvertebrateMitochondrialGeneticCode::_ZTv0_n104_NK3bpp36InvertebrateMitochondrialGeneticCode18getStopCodonsAsIntEv() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 68%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::MoldMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:44: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, inlined from 'virtual std::vector bpp::MoldMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:71:27: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::MoldMitochondrialGeneticCode::_ZTv0_n104_NK3bpp28MoldMitochondrialGeneticCode18getStopCodonsAsIntEv() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 69%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.cpp [ 70%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp [ 70%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Transliterator.cpp [ 70%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp [ 71%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::YeastMitochondrialGeneticCode::getStopCodonsAsInt() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; In file included from /usr/include/aarch64-linux-gnu/c++/14/bits/c++allocator.h:33, from /usr/include/c++/14/bits/allocator.h:46, from /usr/include/c++/14/string:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Alphabet/Alphabet.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/GeneticCode.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:44: In member function '_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*) [with _Tp = int]', inlined from 'static _Tp* std::allocator_traits >::allocate(allocator_type&, size_type) [with _Tp = int]' at /usr/include/c++/14/bits/alloc_traits.h:515:28, inlined from 'std::_Vector_base<_Tp, _Alloc>::pointer std::_Vector_base<_Tp, _Alloc>::_M_allocate(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:380:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:398:44, inlined from 'std::_Vector_base<_Tp, _Alloc>::_Vector_base(std::size_t, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:334:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/14/bits/stl_vector.h:557:47, inlined from 'virtual std::vector bpp::YeastMitochondrialGeneticCode::getStopCodonsAsInt() const' at /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:71:27: /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h: In member function 'virtual std::vector bpp::YeastMitochondrialGeneticCode::_ZTv0_n104_NK3bpp29YeastMitochondrialGeneticCode18getStopCodonsAsIntEv() const': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h:73:12: warning: array subscript 2 is outside array bounds of 'int [2]' [-Warray-bounds=] 73 | v[2] = 50; /usr/include/c++/14/bits/new_allocator.h:151:55: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 71%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 72%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 72%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp [ 73%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp [ 73%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 74%] Linking CXX static library libbpp-seq.a cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/bpp-seq-static.dir/cmake_clean_target.cmake In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-seq-static.dir/link.txt --verbose=1 /usr/bin/ar qc libbpp-seq.a "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNA.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/RNY.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Clustal.cpp.o" "CMakeFiles/bpp-seq-[ 75%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp [ 75%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.cpp static.dir/Bpp/Seq/Io/Dcse.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Fasta.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/GenBank.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/MaseTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/NexusTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPhd.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/PhredPoly.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Phylip.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Stockholm.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o" "CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o" /usr/bin/ranlib libbpp-seq.a make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 75%] Built target bpp-seq-static [ 75%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.cpp [ 76%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp [ 77%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Clustal.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 78%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Dcse.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/GenBank.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/IoSequenceFactory.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 78%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Mase.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 79%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/MaseTools.h:44: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 80%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPhd.cpp [ 80%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusTools.cpp [ 80%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/PhredPoly.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/NexusIoSequence.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 81%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp [ 81%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.cpp [ 82%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/StreamSequenceIterator.cpp [ 82%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/NucleicAcidsReplication.cpp [ 83%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Sequence.cpp [ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceExceptions.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/AlignedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractIAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Phylip.cpp:40: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/OSequence.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractOAlignment.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Stockholm.cpp:42: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/OSequence.h:45: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequencePositionIterators.cpp [ 85%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp [ 85%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWalker.cpp [ 86%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithAnnotation.cpp [ 86%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithAnnotationTools.cpp [ 87%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQuality.cpp [ 87%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceWithQualityTools.cpp [ 88%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Site.cpp [ 88%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteExceptions.cpp [ 89%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SiteTools.cpp [ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/StringSequenceTools.cpp [ 90%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolList.cpp [ 91%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SymbolListTools.cpp [ 91%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o -MF CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o.d -o CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Transliterator.cpp [ 92%] Linking CXX shared library libbpp-seq.so cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/bpp-seq-shared.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,--dependency-file=CMakeFiles/bpp-seq-shared.dir/link.d -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libbpp-seq.so.12 -o libbpp-seq.so.12.0.0 "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AlphabetTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/BinaryAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/CodonAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DNA.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LexicalAlphabet.cpp.o" 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"CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AbstractSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/CompressedVectorSiteContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSequenceContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/VectorSiteContainer.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/StandardGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentReaderFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlignmentWriterFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex1Format.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOAlphabetIndex2Format.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceWriterFormat.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Clustal.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Dcse.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/GenBank.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/IoSequenceFactory.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Mase.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/MaseTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusIoSequence.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/NexusTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPhd.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/PhredPoly.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Phylip.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/StreamSequenceIterator.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o" /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src && /usr/bin/cmake -E cmake_symlink_library libbpp-seq.so.12.0.0 libbpp-seq.so.12 libbpp-seq.so make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 92%] Built target bpp-seq-shared make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_alignment_scores.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_alphabets.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_bowker.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/depend make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/build cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_containers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_io.dir/build.make test/CMakeFiles/test_io.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/depend cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_io.dir/DependInfo.cmake "--color=" [ 92%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -MF CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o.d -o CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_alignment_scores.cpp make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_sequences.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build [ 93%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o make -f test/CMakeFiles/test_walker.dir/build.make test/CMakeFiles/test_walker.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/libbpp-seq-2.4.1 /build/reproducible-path/libbpp-seq-2.4.1/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/CMakeFiles/test_walker.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -MF CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o.d -o CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_alphabets.cpp make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_io.dir/build.make test/CMakeFiles/test_io.dir/build [ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/build cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o -MF CMakeFiles/test_bowker.dir/test_bowker.cpp.o.d -o CMakeFiles/test_bowker.dir/test_bowker.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_bowker.cpp make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make -f test/CMakeFiles/test_walker.dir/build.make test/CMakeFiles/test_walker.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 95%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_containers.dir/test_containers.cpp.o -MF CMakeFiles/test_containers.dir/test_containers.cpp.o.d -o CMakeFiles/test_containers.dir/test_containers.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_containers.cpp [ 96%] Building CXX object test/CMakeFiles/test_sequences.dir/test_sequences.cpp.o [ 97%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_io.dir/test_io.cpp.o -MF CMakeFiles/test_io.dir/test_io.cpp.o.d -o CMakeFiles/test_io.dir/test_io.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_io.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_sequences.dir/test_sequences.cpp.o -MF CMakeFiles/test_sequences.dir/test_sequences.cpp.o.d -o CMakeFiles/test_sequences.dir/test_sequences.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_sequences.cpp [ 98%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/c++ -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -fPIE -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT test/CMakeFiles/test_walker.dir/test_walker.cpp.o -MF CMakeFiles/test_walker.dir/test_walker.cpp.o.d -o CMakeFiles/test_walker.dir/test_walker.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/test/test_walker.cpp In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/test/test_alignment_scores.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:47, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/AbstractISequence.h:43, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/Fasta.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/test/test_io.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/ISequence.h:48: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Io/../Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ In file included from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:45, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/VectorSiteContainer.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/test/test_containers.cpp:41: /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:300:24: warning: 'virtual const int& bpp::SequenceContainer::operator()(const std::string&, size_t) const' was hidden [-Woverloaded-virtual=] 300 | virtual const int& operator()(const std::string& sequenceName, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/SequenceContainer.h:288:18: warning: 'virtual int& bpp::SequenceContainer::operator()(const std::string&, size_t)' was hidden [-Woverloaded-virtual=] 288 | virtual int& operator()(const std::string& sequenceName, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:211:24: note: by 'bpp::OrderedSequenceContainer::operator()' 211 | virtual const int& operator()(size_t sequenceIndex, size_t elementIndex) const = 0; | ^~~~~~~~ [ 98%] Linking CXX executable test_alphabets cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alphabets.dir/link.txt --verbose=1 [ 99%] Linking CXX executable test_walker cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_walker.dir/link.txt --verbose=1 [ 99%] Linking CXX executable test_containers cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_containers.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_walker.dir/link.d CMakeFiles/test_walker.dir/test_walker.cpp.o -o test_walker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_alphabets.dir/link.d CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o -o test_alphabets -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 [ 99%] Built target test_walker make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 99%] Built target test_alphabets /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_containers.dir/link.d CMakeFiles/test_containers.dir/test_containers.cpp.o -o test_containers -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 99%] Built target test_containers [ 99%] Linking CXX executable test_sequences cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_sequences.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_sequences.dir/link.d CMakeFiles/test_sequences.dir/test_sequences.cpp.o -o test_sequences -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [ 99%] Built target test_sequences [100%] Linking CXX executable test_alignment_scores cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alignment_scores.dir/link.txt --verbose=1 [100%] Linking CXX executable test_bowker cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.dir/link.txt --verbose=1 [100%] Linking CXX executable test_io cd /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_io.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_alignment_scores.dir/link.d CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o -o test_alignment_scores -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [100%] Built target test_alignment_scores /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_bowker.dir/link.d CMakeFiles/test_bowker.dir/test_bowker.cpp.o -o test_bowker -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/libbpp-seq-2.4.1=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -mbranch-protection=standard -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -rdynamic -Wl,--dependency-file=CMakeFiles/test_io.dir/link.d CMakeFiles/test_io.dir/test_io.cpp.o -o test_io -Wl,-rpath,/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/aarch64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' [100%] Built target test_bowker [100%] Built target test_io make[2]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' dh_auto_test cd obj-aarch64-linux-gnu && make -j12 test ARGS\+=--verbose ARGS\+=-j12 make[1]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j12 UpdateCTestConfiguration from :/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu Constructing a list of tests Done constructing a list of tests Updating test list for fixtures Added 0 tests to meet fixture requirements Checking test dependency graph... Checking test dependency graph end Connected to MAKE jobserver test 1 Start 1: test_alignment_scores 1: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/test_alignment_scores 1: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 1: Test timeout computed to be: 60000 test 2 Start 2: test_alphabets 2: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/test_alphabets 2: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 2: Test timeout computed to be: 60000 test 3 Start 3: test_bowker 3: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/test_bowker 3: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 3: Test timeout computed to be: 60000 test 4 Start 4: test_containers 4: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/test_containers 4: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 4: Test timeout computed to be: 60000 test 5 Start 5: test_io 5: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/test_io 5: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 5: Test timeout computed to be: 60000 test 6 Start 6: test_sequences 6: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/test_sequences 6: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 6: Test timeout computed to be: 60000 test 7 Start 7: test_walker 7: Test command: /build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu/test/test_walker 7: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 7: Test timeout computed to be: 60000 1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 1: 0 0 0 1 1 1 1 1 1 1 0 0 0 1 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 0 0 1: 0 0 0 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1 0 1 1 1 1 1 1 1 0 1 0 1 1 1 1 1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.333333 0.333333 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.333333 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1: 0.000000 0.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 1.000000 0.000000 0.000000 0.333333 1.000000 1.000000 1.000000 1.000000 3: 2 0.919699 4: 47 4: ----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU-- 4: ---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU-- 4: [>>> ] 8% [>>>> ] 12% [>>>>>> ] 17% [>>>>>>>> ] 21% [>>>>>>>>> ] 25% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 38% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>>>> ] 51% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 72% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 80% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 85% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 93% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100% 4: 30 4: -AUGCCGGCGUUUUG-G-CCGACGUGUUUU 4: GAAGGCGG-GUUUUGCGACCGACG--UUUU 5: example.fasta contains 100 sequences 6: --- Strict match --- 6: ATTT: 0 6: TCG: 3 6: GATC: 29 6: CGTC: 33 6: CWCAT: 19 6: --- Degenerated match --- 6: CTCAT: 19 6: AAGCA: 16 1/7 Test #1: test_alignment_scores ............ Passed 0.11 sec 2/7 Test #2: test_alphabets ................... Passed 0.10 sec 3/7 Test #4: test_containers .................. Passed 0.06 sec 4/7 Test #6: test_sequences ................... Passed 0.03 sec 7: 0 A 4 7: 1 U 5 7: 2 G 6 7: 3 C 7 7: 4 C 8 7: 5 G 9 7: 6 G 13 7: 7 C 14 7: 8 G 15 7: 9 U 16 7: 10 U 21 7: 11 U 22 7: 12 U 23 7: 13 G 28 7: 14 G 31 7: 15 C 33 7: 16 C 34 7: 17 G 35 7: 18 A 36 7: 19 C 37 7: 20 G 38 7: 21 U 39 7: 22 G 40 7: 23 U 41 7: 24 U 42 7: 25 U 43 7: 26 U 44 7: 7: 0 7: 4 7: 26 7: 44 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 4 7: 26 7: 44 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 4 7: 26 7: 44 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: _________________________________________________ 7: 0 - 0 7: 1 - 0 7: 2 - 0 7: 3 - 0 7: 4 A 0 7: 5 U 1 7: 6 G 2 7: 7 C 3 7: 8 C 4 7: 9 G 5 7: 10 - 5 7: 11 - 5 7: 12 - 5 7: 13 G 6 7: 14 C 7 7: 15 G 8 7: 16 U 9 7: 17 - 9 7: 18 - 9 7: 19 - 9 7: 20 - 9 7: 21 U 10 7: 22 U 11 7: 23 U 12 7: 24 - 12 7: 25 - 12 7: 26 - 12 7: 27 - 12 7: 28 G 13 7: 29 - 13 7: 30 - 13 7: 31 G 14 7: 32 - 14 7: 33 C 15 7: 34 C 16 7: 35 G 17 7: 36 A 18 7: 37 C 19 7: 38 G 20 7: 39 U 21 7: 40 G 22 7: 41 U 23 7: 42 U 24 7: 43 U 25 7: 44 U 26 7: 45 - 26 7: 46 - 26 7: 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 7: 0 7: 0 7: 46 7: 26 7: [ ] 0% [= ] 2% [== ] 5% [=== ] 8% [==== ] 10% [===== ] 13% [====== ] 16% [======= ] 18% [======== ] 21% [========= ] 24% [========== ] 27% [=========== ] 29% [============ ] 32% [============= ] 35% [============== ] 37% [=============== ] 40% [================ ] 43% [================= ] 45% [================== ] 48% [=================== ] 51% [==================== ] 54% [===================== ] 56% [====================== ] 59% [======================= ] 62% [======================== ] 64% [========================= ] 67% [========================== ] 70% [=========================== ] 72% [============================ ] 75% [============================= ] 78% [============================== ] 81% [=============================== ] 83% [================================ ] 86% [================================= ] 89% [================================== ] 91% [=================================== ] 94% [==================================== ] 97% [======================================] 100% 5/7 Test #7: test_walker ...................... Passed 0.02 sec 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 6/7 Test #5: test_io .......................... Passed 0.06 sec 3: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0078 0.0442 0.0916 0.491 3: [ ] 0% [> ] 2% [>> ] 5% [>>> ] 7% [>>>> ] 10% [>>>>> ] 13% [>>>>>> ] 15% [>>>>>>> ] 18% [>>>>>>>> ] 21% [>>>>>>>>> ] 23% [>>>>>>>>>> ] 26% [>>>>>>>>>>> ] 29% [>>>>>>>>>>>> ] 31% [>>>>>>>>>>>>> ] 34% [>>>>>>>>>>>>>> ] 36% [>>>>>>>>>>>>>>> ] 39% [>>>>>>>>>>>>>>>> ] 42% [>>>>>>>>>>>>>>>>> ] 44% [>>>>>>>>>>>>>>>>>> ] 47% [>>>>>>>>>>>>>>>>>>> ] 50% [>>>>>>>>>>>>>>>>>>>> ] 52% [>>>>>>>>>>>>>>>>>>>>> ] 55% [>>>>>>>>>>>>>>>>>>>>>> ] 58% [>>>>>>>>>>>>>>>>>>>>>>> ] 60% [>>>>>>>>>>>>>>>>>>>>>>>> ] 63% [>>>>>>>>>>>>>>>>>>>>>>>>> ] 66% [>>>>>>>>>>>>>>>>>>>>>>>>>> ] 68% [>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 71% [>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 73% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 76% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 79% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 81% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 84% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 87% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 89% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 92% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 95% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ] 97% [>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>] 100%0.0096 0.0518 0.0994 0.4886 7/7 Test #3: test_bowker ...................... Passed 29.06 sec 100% tests passed, 0 tests failed out of 7 Total Test time (real) = 29.10 sec make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-aarch64-linux-gnu && make -j12 install DESTDIR=/build/reproducible-path/libbpp-seq-2.4.1/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libbpp-seq-2.4.1 -B/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/bpp-seq/bpp-seq-config.cmake -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/bpp-seq/bpp-seq-config-version.cmake -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libbpp-seq.a -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libbpp-seq.so.12 -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libbpp-seq.so -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Transliterator.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SymbolListTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SymbolList.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/StringSequenceTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SiteTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SiteIterator.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SiteExceptions.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Site.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithQualityTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithQuality.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithAnnotationTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWithAnnotation.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceWalker.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequencePositionIterators.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceIterator.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/SequenceExceptions.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Sequence.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/NucleicAcidsReplication.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Mase.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/StreamSequenceIterator.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Stockholm.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/SequenceFileIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Phylip.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/PhredPoly.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/PhredPhd.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/OSequenceStream.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/OSequence.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/NexusTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/NexusIoSequence.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/MaseTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/IoSequenceStream.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/IoSequenceFactory.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/IoSequence.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/ISequenceStream.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/ISequence.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/GenBank.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Fasta.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Dcse.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/Clustal.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceWriterFormat.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOSequenceReaderFormat.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlphabetIndex2Format.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlphabetIndex1Format.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlignmentWriterFormat.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/BppOAlignmentReaderFormat.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractOSequence.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractOAlignment.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractISequence.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Io/AbstractIAlignment.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/VertebrateMitochondrialGeneticCode.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/StandardGeneticCode.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/MoldMitochondrialGeneticCode.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/GeneticCode.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/EchinodermMitochondrialGeneticCode.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/GeneticCode/AscidianMitochondrialGeneticCode.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/DistanceMatrix.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/DNAToRNA.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/CoreSite.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/CoreSequence.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/VectorSiteContainer.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/VectorSequenceContainer.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerIterator.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainerExceptions.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SiteContainer.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SequenceContainerTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SequenceContainerIterator.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SequenceContainerExceptions.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/SequenceContainer.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/OrderedSequenceContainer.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/MapSequenceContainer.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/CompressedVectorSiteContainer.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/AlignedSequenceContainer.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Container/AbstractSequenceContainer.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/CodonSiteTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/App -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/App/SequenceApplicationTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/UserAlphabetIndex1.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/SimpleScore.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/SimpleIndexDistance.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/KleinAANetChargeIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAVolumeIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAPolarityIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/BLOSUM50.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex2.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AlphabetIndex1.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAVolumeIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASurfaceIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEASup30Index.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEAInf10Index.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AASEA1030Index.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAMassIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAIndex2Entry.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAIndex1Entry.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanTurnIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanBSheetIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChouFasmanAHelixIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/AlphabetIndex/AAChargeIndex.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/WordAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/RNY.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/RNA.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/ProteicAlphabetState.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/ProteicAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NumericAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NucleicAlphabetState.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/NucleicAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/LexicalAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/LetterAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/IntegerAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/DefaultAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/DNA.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/CodonAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/CaseMaskedAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/BinaryAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetTools.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetState.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetNumericState.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AlphabetExceptions.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/Alphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/include/Bpp/Seq/Alphabet/AbstractAlphabet.h -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/bpp-seq/bpp-seq-targets.cmake -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/cmake/bpp-seq/bpp-seq-targets-none.cmake make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-aarch64-linux-gnu' debian/rules override_dh_install make[1]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1' dh_install d-shlibmove --commit \ --t64 \ --multiarch \ --devunversioned \ --exclude-la \ --movedev debian/tmp/usr/include/* usr/include \ --movedev debian/tmp/usr/lib/*/cmake usr/lib/aarch64-linux-gnu \ debian/tmp/usr/lib/*/*.so Library package automatic movement utility --> libbpp-core-dev package exists. set -e install -d -m 755 debian/libbpp-seq-dev/usr/lib/aarch64-linux-gnu install -d -m 755 debian/libbpp-seq12t64/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libbpp-seq.a debian/libbpp-seq-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/libbpp-seq.so debian/libbpp-seq-dev/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libbpp-seq.so.12 debian/libbpp-seq12t64/usr/lib/aarch64-linux-gnu mv /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/aarch64-linux-gnu/libbpp-seq.so.12.0.0 debian/libbpp-seq12t64/usr/lib/aarch64-linux-gnu PKGDEV=libbpp-seq-dev PKGSHL=libbpp-seq12t64 install -d -m 755 debian/libbpp-seq-dev/usr/include mv debian/tmp/usr/include/Bpp debian/libbpp-seq-dev/usr/include install -d -m 755 debian/libbpp-seq-dev/usr/lib/aarch64-linux-gnu mv debian/tmp/usr/lib/aarch64-linux-gnu/cmake debian/libbpp-seq-dev/usr/lib/aarch64-linux-gnu make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1' dh_installdocs dh_installchangelogs dh_lintian dh_perl dh_link dh_strip_nondeterminism dh_compress dh_fixperms dh_missing dh_dwz -a dh_strip -a dh_makeshlibs -a dh_shlibdeps -a dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 from: /lib/ld-linux-aarch64.so.1 dpkg-shlibdeps: warning: diversions involved - output may be incorrect diversion by libc6 to: /lib/ld-linux-aarch64.so.1.usr-is-merged dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbpp-seq12t64-dbgsym' in '../libbpp-seq12t64-dbgsym_2.4.1-13_arm64.deb'. dpkg-deb: building package 'libbpp-seq-dev' in '../libbpp-seq-dev_2.4.1-13_arm64.deb'. dpkg-deb: building package 'libbpp-seq12t64' in '../libbpp-seq12t64_2.4.1-13_arm64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-seq_2.4.1-13_arm64.buildinfo dpkg-genchanges --build=binary -O../libbpp-seq_2.4.1-13_arm64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration 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/4068209 and its subdirectories I: Current time: Tue Mar 18 05:21:32 -12 2025 I: pbuilder-time-stamp: 1742318492 Tue Mar 18 17:21:39 UTC 2025 I: 1st build successful. Starting 2nd build on remote node codethink03-arm64.debian.net. Tue Mar 18 17:21:39 UTC 2025 I: Preparing to do remote build '2' on codethink03-arm64.debian.net. Tue Mar 18 17:23:45 UTC 2025 I: Deleting $TMPDIR on codethink03-arm64.debian.net. Tue Mar 18 17:23:45 UTC 2025 I: libbpp-seq_2.4.1-13_arm64.changes: Format: 1.8 Date: Wed, 07 Aug 2024 10:57:57 +0200 Source: libbpp-seq Binary: libbpp-seq-dev libbpp-seq12t64 libbpp-seq12t64-dbgsym Architecture: arm64 Version: 2.4.1-13 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Andreas Tille Description: libbpp-seq-dev - Bio++ Sequence library development files libbpp-seq12t64 - Bio++ Sequence library Closes: 1075153 Changes: libbpp-seq (2.4.1-13) unstable; urgency=medium . * Since every GCC version bump ends up in a bug caused by the need to update symbols files we stop providing symbols for this library Closes: #1075153 * lintian-override for no-symbols-control-file Checksums-Sha1: 5d8529d4f6e4e94f1acb2e6bb7b344b71cb3aea7 10381968 libbpp-seq-dev_2.4.1-13_arm64.deb fd59bc97b3d4179ca48165f311511876bb99170a 9670324 libbpp-seq12t64-dbgsym_2.4.1-13_arm64.deb 5935eb028078057450c683f7a2d4f673e23d1760 451908 libbpp-seq12t64_2.4.1-13_arm64.deb 63886a7c53dcbb52e339ffaec7782c1ae6410bb8 6562 libbpp-seq_2.4.1-13_arm64.buildinfo Checksums-Sha256: 0babc60cebb7bf77e225aeb5895af1038ce7cdc2a58557a6ffb821e0f8b7a118 10381968 libbpp-seq-dev_2.4.1-13_arm64.deb 6894a29f752319a89daa427f4205380ebae8e8b037f79e5e7ed986892ccbd058 9670324 libbpp-seq12t64-dbgsym_2.4.1-13_arm64.deb 332e295afea19951aed7a299675c1800c98c307e97e55a0cdac3af868563ccac 451908 libbpp-seq12t64_2.4.1-13_arm64.deb 5e0d461bb512fd6a637f4c1e0192795435936ab09f9b55c0b06454108a8391e3 6562 libbpp-seq_2.4.1-13_arm64.buildinfo Files: 7ed61ed64b6f5902b4ffe4e83ed8a66f 10381968 libdevel optional libbpp-seq-dev_2.4.1-13_arm64.deb 39b2176b2e53e771f1c4dff4d9fdf527 9670324 debug optional libbpp-seq12t64-dbgsym_2.4.1-13_arm64.deb 796b87bfbcde845afb81377225de6fcb 451908 libs optional libbpp-seq12t64_2.4.1-13_arm64.deb ba3313cac27437f43d6822588d175e35 6562 science optional libbpp-seq_2.4.1-13_arm64.buildinfo Tue Mar 18 17:23:47 UTC 2025 I: diffoscope 289 will be used to compare the two builds: Running as unit: rb-diffoscope-arm64_7-62564.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.6T2sEiXC/libbpp-seq_2.4.1-13.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.6T2sEiXC/libbpp-seq_2.4.1-13.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.6T2sEiXC/libbpp-seq_2.4.1-13.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.6T2sEiXC/b1/libbpp-seq_2.4.1-13_arm64.changes /srv/reproducible-results/rbuild-debian/r-b-build.6T2sEiXC/b2/libbpp-seq_2.4.1-13_arm64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call diffoscope.comparators.binary.FilesystemFile ## main (total time: 0.003s) 0.003s 2 calls outputs 0.000s 1 call cleanup Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 224ms CPU time consumed: 224ms Tue Mar 18 17:23:47 UTC 2025 I: diffoscope 289 found no differences in the changes files, and a .buildinfo file also exists. Tue Mar 18 17:23:47 UTC 2025 I: libbpp-seq from unstable built successfully and reproducibly on arm64. Tue Mar 18 17:23:48 UTC 2025 I: Submitting .buildinfo files to external archives: Tue Mar 18 17:23:48 UTC 2025 I: Submitting 8.0K b1/libbpp-seq_2.4.1-13_arm64.buildinfo.asc Tue Mar 18 17:23:49 UTC 2025 I: Submitting 8.0K b2/libbpp-seq_2.4.1-13_arm64.buildinfo.asc Tue Mar 18 17:23:50 UTC 2025 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Tue Mar 18 17:23:50 UTC 2025 I: Done submitting .buildinfo files. Tue Mar 18 17:23:50 UTC 2025 I: Removing signed libbpp-seq_2.4.1-13_arm64.buildinfo.asc files: removed './b1/libbpp-seq_2.4.1-13_arm64.buildinfo.asc' removed './b2/libbpp-seq_2.4.1-13_arm64.buildinfo.asc'