Tue Oct 28 15:25:52 UTC 2025 I: starting to build libbpp-seq/forky/amd64 on jenkins on '2025-10-28 15:25' Tue Oct 28 15:25:52 UTC 2025 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_11/71457/console.log Tue Oct 28 15:25:52 UTC 2025 I: Downloading source for forky/libbpp-seq=2.4.1-14 --2025-10-28 15:25:52-- http://deb.debian.org/debian/pool/main/libb/libbpp-seq/libbpp-seq_2.4.1-14.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 2290 (2.2K) [text/prs.lines.tag] Saving to: ‘libbpp-seq_2.4.1-14.dsc’ 0K .. 100% 282M=0s 2025-10-28 15:25:52 (282 MB/s) - ‘libbpp-seq_2.4.1-14.dsc’ saved [2290/2290] Tue Oct 28 15:25:52 UTC 2025 I: libbpp-seq_2.4.1-14.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: libbpp-seq Binary: libbpp-seq-dev, libbpp-seq12t64 Architecture: any Version: 2.4.1-14 Maintainer: Debian Med Packaging Team Uploaders: Julien Dutheil , Andreas Tille Homepage: http://biopp.univ-montp2.fr/wiki/index.php/Main_Page Standards-Version: 4.7.2 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 3ee8629f64030f62bed2e22fb72c2c0b2cc602db 12432 libbpp-seq_2.4.1-14.debian.tar.xz Checksums-Sha256: dbfcb04803e4b7f08f9f159da8a947c91906c3ca8b20683ac193f6dc524d4655 322620 libbpp-seq_2.4.1.orig.tar.gz b700351c21a97e7399743c4d07b198fc9126c5871fc57fe9390d3c01c26bd162 12432 libbpp-seq_2.4.1-14.debian.tar.xz Files: bdafc80aab9591ff79556138d6555941 322620 libbpp-seq_2.4.1.orig.tar.gz 56772e172ac7fdf00152cfb9639194f0 12432 libbpp-seq_2.4.1-14.debian.tar.xz Dgit: 79cf787f8208fd4aac0a394b255b0546972f3c9e debian archive/debian/2.4.1-14 https://git.dgit.debian.org/libbpp-seq -----BEGIN PGP SIGNATURE----- iQJIBAEBCgAyFiEEj5GyJ8fW8rGUjII2eTz2fo8NEdoFAmja9KcUHGVtb2xsaWVy QGRlYmlhbi5vcmcACgkQeTz2fo8NEdorjA//RZZUW4kAaVBsDtWNW0nF38pgiYrB CMZtPZFY14qaqj2Ky8pQc3MHVJAaquIEc8UeIzaE8IUKtXkrg22e6jWiLMDQ/aaa gBdvYW/w87eTKXNI7+tUBkiLfoGAUhRVV/YotGV8UDhtLMCNWcvPPHARzWI2jCi5 PRWUfeJXx+ZQ8C6TkpuIT2qlpFUeD72YhhPkOtxLEaTqfYDGLgSbY3+6N9kSse6c 2vwMjaVLkzut/yqmzAb/egy5VI2VC7Z/PC2TO3FSZ6B+4y6/6aBNTHmP98E6aypz 3OldWf1XK/oCgAWcf6hBCCsA43pbYyYYskkRU+jW6muqp24EcLv1LBlWph1/xpis +rFZuJFudYy3PDqFdRT8T9hHlFOYJShLiSR6wykeOD/Co+bBfJYN6rCAK2LbE31f skBGtdFNVF+LuFtPLXQsajRCdGU1KYC367X6RRfcFTM5weTBbu5CxLrYIeXf1gPN xVb5u0iTgs0QySe48TKMf5AsO+QS/3qpEH/vJdB09BqJp9NI0K0eESY6kGHrAXT2 NZ5Li7MFnEutEwi5ni8F3GeL3G/jYlxzjj5fb0ew/FDB+SMMrrMo0ntdk06SdgEA pY9cD/cMUmFdwqPazSaauyGz3DgJTo3cBppFp5S64Y2rxMlGaFCve5OHgQXK7Ubs bUE7ycB3lBBZj8U= =N+Hr -----END PGP SIGNATURE----- Tue Oct 28 15:25:52 UTC 2025 I: Checking whether the package is not for us Tue Oct 28 15:25:52 UTC 2025 I: Starting 1st build on remote node ionos1-amd64.debian.net. Tue Oct 28 15:25:52 UTC 2025 I: Preparing to do remote build '1' on ionos1-amd64.debian.net. Tue Oct 28 15:31:37 UTC 2025 I: Deleting $TMPDIR on ionos1-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Tue Oct 28 03:25:53 -12 2025 I: pbuilder-time-stamp: 1761665153 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/forky-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_2.4.1-14.dsc] I: copying [./libbpp-seq_2.4.1.orig.tar.gz] I: copying [./libbpp-seq_2.4.1-14.debian.tar.xz] I: Extracting source dpkg-source: warning: cannot verify inline signature for ./libbpp-seq_2.4.1-14.dsc: no acceptable signature found 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_2.4.1-14.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 dpkg-source: info: applying cmake-4.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/417681/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='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=40 ' DISTRIBUTION='forky' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='c499f6dd8ffa4cee9a9ca7f69adb3c0e' 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='417681' 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.8kq9DyWC/pbuilderrc_oLid --distribution forky --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/forky-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.8kq9DyWC/b1 --logfile b1/build.log libbpp-seq_2.4.1-14.dsc' SUDO_GID='110' SUDO_HOME='/var/lib/jenkins' SUDO_UID='105' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://46.16.76.132:3128' I: uname -a Linux ionos1-amd64 6.12.48+deb13-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.12.48-1 (2025-09-20) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Aug 10 12:30 /bin -> usr/bin I: user script /srv/workspace/pbuilder/417681/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: amd64 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 ... 19902 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} 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} libngtcp2-16{a} libngtcp2-crypto-ossl0{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} libxml2-16{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, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 33.5 MB of archives. After unpacking 127 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian forky/main amd64 libexpat1 amd64 2.7.3-1 [112 kB] Get: 2 http://deb.debian.org/debian forky/main amd64 libproc2-0 amd64 2:4.0.4-9 [65.6 kB] Get: 3 http://deb.debian.org/debian forky/main amd64 procps amd64 2:4.0.4-9 [882 kB] Get: 4 http://deb.debian.org/debian forky/main amd64 sensible-utils all 0.0.26 [27.0 kB] Get: 5 http://deb.debian.org/debian forky/main amd64 libmagic-mgc amd64 1:5.46-5 [338 kB] Get: 6 http://deb.debian.org/debian forky/main amd64 libmagic1t64 amd64 1:5.46-5 [109 kB] Get: 7 http://deb.debian.org/debian forky/main amd64 file amd64 1:5.46-5 [43.6 kB] Get: 8 http://deb.debian.org/debian forky/main amd64 gettext-base amd64 0.23.1-2+b1 [244 kB] Get: 9 http://deb.debian.org/debian forky/main amd64 libuchardet0 amd64 0.0.8-2 [68.5 kB] Get: 10 http://deb.debian.org/debian forky/main amd64 groff-base amd64 1.23.0-9 [1187 kB] Get: 11 http://deb.debian.org/debian forky/main amd64 bsdextrautils amd64 2.41.2-1 [95.2 kB] Get: 12 http://deb.debian.org/debian forky/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 13 http://deb.debian.org/debian forky/main amd64 man-db amd64 2.13.1-1 [1469 kB] Get: 14 http://deb.debian.org/debian forky/main amd64 m4 amd64 1.4.20-2 [325 kB] Get: 15 http://deb.debian.org/debian forky/main amd64 autoconf all 2.72-3.1 [494 kB] Get: 16 http://deb.debian.org/debian forky/main amd64 autotools-dev all 20240727.1 [60.2 kB] Get: 17 http://deb.debian.org/debian forky/main amd64 automake all 1:1.18.1-2 [877 kB] Get: 18 http://deb.debian.org/debian forky/main amd64 autopoint all 0.23.1-2 [770 kB] Get: 19 http://deb.debian.org/debian forky/main amd64 cmake-data all 4.1.1+really3.31.6-2 [2268 kB] Get: 20 http://deb.debian.org/debian forky/main amd64 libxml2-16 amd64 2.14.6+dfsg-0.1 [651 kB] Get: 21 http://deb.debian.org/debian forky/main amd64 libarchive13t64 amd64 3.7.4-4+b1 [349 kB] Get: 22 http://deb.debian.org/debian forky/main amd64 libnghttp3-9 amd64 1.12.0-1 [68.4 kB] Get: 23 http://deb.debian.org/debian forky/main amd64 libngtcp2-16 amd64 1.16.0-1 [136 kB] Get: 24 http://deb.debian.org/debian forky/main amd64 libbrotli1 amd64 1.1.0-2+b7 [307 kB] Get: 25 http://deb.debian.org/debian forky/main amd64 libkrb5support0 amd64 1.21.3-5 [33.0 kB] Get: 26 http://deb.debian.org/debian forky/main amd64 libcom-err2 amd64 1.47.2-3+b3 [25.0 kB] Get: 27 http://deb.debian.org/debian forky/main amd64 libk5crypto3 amd64 1.21.3-5 [81.5 kB] Get: 28 http://deb.debian.org/debian forky/main amd64 libkeyutils1 amd64 1.6.3-6 [9456 B] Get: 29 http://deb.debian.org/debian forky/main amd64 libkrb5-3 amd64 1.21.3-5 [326 kB] Get: 30 http://deb.debian.org/debian forky/main amd64 libgssapi-krb5-2 amd64 1.21.3-5 [138 kB] Get: 31 http://deb.debian.org/debian forky/main amd64 libunistring5 amd64 1.3-2 [477 kB] Get: 32 http://deb.debian.org/debian forky/main amd64 libidn2-0 amd64 2.3.8-4 [110 kB] Get: 33 http://deb.debian.org/debian forky/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-10 [19.8 kB] Get: 34 http://deb.debian.org/debian forky/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-10 [57.8 kB] Get: 35 http://deb.debian.org/debian forky/main amd64 libldap2 amd64 2.6.10+dfsg-1 [194 kB] Get: 36 http://deb.debian.org/debian forky/main amd64 libnghttp2-14 amd64 1.64.0-1.1+b1 [76.2 kB] Get: 37 http://deb.debian.org/debian forky/main amd64 libngtcp2-crypto-ossl0 amd64 1.16.0-1 [27.5 kB] Get: 38 http://deb.debian.org/debian forky/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 39 http://deb.debian.org/debian forky/main amd64 libffi8 amd64 3.5.2-2 [25.5 kB] Get: 40 http://deb.debian.org/debian forky/main amd64 libp11-kit0 amd64 0.25.9-2 [443 kB] Get: 41 http://deb.debian.org/debian forky/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB] Get: 42 http://deb.debian.org/debian forky/main amd64 libgnutls30t64 amd64 3.8.10-3 [1493 kB] Get: 43 http://deb.debian.org/debian forky/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-3 [58.3 kB] Get: 44 http://deb.debian.org/debian forky/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 45 http://deb.debian.org/debian forky/main amd64 libcurl4t64 amd64 8.17.0~rc2-1 [408 kB] Get: 46 http://deb.debian.org/debian forky/main amd64 libjsoncpp26 amd64 1.9.6-4 [89.4 kB] Get: 47 http://deb.debian.org/debian forky/main amd64 librhash1 amd64 1.4.6-1 [137 kB] Get: 48 http://deb.debian.org/debian forky/main amd64 libuv1t64 amd64 1.51.0-2 [155 kB] Get: 49 http://deb.debian.org/debian forky/main amd64 cmake amd64 4.1.1+really3.31.6-2 [12.2 MB] Get: 50 http://deb.debian.org/debian forky/main amd64 d-shlibs all 0.109 [11.1 kB] Get: 51 http://deb.debian.org/debian forky/main amd64 libdebhelper-perl all 13.28 [92.4 kB] Get: 52 http://deb.debian.org/debian forky/main amd64 libtool all 2.5.4-7 [540 kB] Get: 53 http://deb.debian.org/debian forky/main amd64 dh-autoreconf all 21 [12.2 kB] Get: 54 http://deb.debian.org/debian forky/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 55 http://deb.debian.org/debian forky/main amd64 libfile-stripnondeterminism-perl all 1.15.0-1 [19.9 kB] Get: 56 http://deb.debian.org/debian forky/main amd64 dh-strip-nondeterminism all 1.15.0-1 [8812 B] Get: 57 http://deb.debian.org/debian forky/main amd64 libelf1t64 amd64 0.193-3 [192 kB] Get: 58 http://deb.debian.org/debian forky/main amd64 dwz amd64 0.16-2 [108 kB] Get: 59 http://deb.debian.org/debian forky/main amd64 gettext amd64 0.23.1-2+b1 [1680 kB] Get: 60 http://deb.debian.org/debian forky/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 61 http://deb.debian.org/debian forky/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 62 http://deb.debian.org/debian forky/main amd64 debhelper all 13.28 [941 kB] Get: 63 http://deb.debian.org/debian forky/main amd64 libbpp-core4t64 amd64 2.4.1-14 [623 kB] Get: 64 http://deb.debian.org/debian forky/main amd64 libbpp-core-dev amd64 2.4.1-14 [964 kB] Fetched 33.5 MB in 3s (11.4 MB/s) Preconfiguring packages ... Selecting previously unselected package libexpat1:amd64. (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 ... 19902 files and directories currently installed.) Preparing to unpack .../00-libexpat1_2.7.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.7.3-1) ... Selecting previously unselected package libproc2-0:amd64. Preparing to unpack .../01-libproc2-0_2%3a4.0.4-9_amd64.deb ... Unpacking libproc2-0:amd64 (2:4.0.4-9) ... Selecting previously unselected package procps. Preparing to unpack .../02-procps_2%3a4.0.4-9_amd64.deb ... Unpacking procps (2:4.0.4-9) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../03-sensible-utils_0.0.26_all.deb ... Unpacking sensible-utils (0.0.26) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../04-libmagic-mgc_1%3a5.46-5_amd64.deb ... Unpacking libmagic-mgc (1:5.46-5) ... Selecting previously unselected package libmagic1t64:amd64. Preparing to unpack .../05-libmagic1t64_1%3a5.46-5_amd64.deb ... Unpacking libmagic1t64:amd64 (1:5.46-5) ... Selecting previously unselected package file. Preparing to unpack .../06-file_1%3a5.46-5_amd64.deb ... Unpacking file (1:5.46-5) ... Selecting previously unselected package gettext-base. Preparing to unpack .../07-gettext-base_0.23.1-2+b1_amd64.deb ... Unpacking gettext-base (0.23.1-2+b1) ... Selecting previously unselected package libuchardet0:amd64. Preparing to unpack .../08-libuchardet0_0.0.8-2_amd64.deb ... 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Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up man-db (2.13.1-1) ... Not building database; man-db/auto-update is not 'true'. Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libcurl4t64:amd64 (8.17.0~rc2-1) ... Setting up debhelper (13.28) ... Setting up cmake (4.1.1+really3.31.6-2) ... Processing triggers for libc-bin (2.41-12) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.37.1.2-1). Solving dependencies... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 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_2.4.1-14_source.changes dpkg-buildpackage: info: source package libbpp-seq dpkg-buildpackage: info: source version 2.4.1-14 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Étienne Mollier dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 debian/rules clean dh clean dh_clean debian/rules binary dh binary dh_update_autotools_config dh_autoreconf dh_auto_configure cd obj-x86_64-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/x86_64-linux-gnu .. -- The CXX compiler identification is GNU 15.2.0 -- 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/x86_64-linux-gnu/libbpp-core.a -- shared lib: /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 -- includes: /usr/include -- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE) -- Configuring done (1.1s) -- 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-x86_64-linux-gnu dh_auto_build cd obj-x86_64-linux-gnu && make -j40 INSTALL="install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libbpp-seq-2.4.1 -B/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu/CMakeFiles /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/bpp-seq-static.dir/build.make src/CMakeFiles/bpp-seq-static.dir/depend 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-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/bpp-seq-static.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src/CMakeFiles/bpp-seq-shared.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make -f src/CMakeFiles/bpp-seq-shared.dir/build.make src/CMakeFiles/bpp-seq-shared.dir/build 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-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' [ 0%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/AbstractAlphabet.cpp.o [ 2%] Building CXX object 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/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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-x86_64-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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-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 [ 7%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o [ 9%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o [ 9%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o [ 9%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DefaultAlphabet.cpp.o [ 10%] 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-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS 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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 [ 11%] 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-x86_64-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 -fcf-protection -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 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src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/LetterAlphabet.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/CaseMaskedAlphabet.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS -I/build/reproducible-path/libbpp-seq-2.4.1/src -g -O2 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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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd 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CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/IntegerAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/IntegerAlphabet.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/c++ -Dbpp_seq_shared_EXPORTS 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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 [ 16%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o [ 16%] 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-x86_64-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 -fcf-protection -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 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src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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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-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -Wall -Weffc++ -Wshadow -Wconversion -MD -MT src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -MF CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o.d -o CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o -c /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Alphabet/WordAlphabet.cpp cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 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src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o [ 21%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o [ 18%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Alphabet/DNA.cpp.o [ 21%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 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src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 23%] 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-x86_64-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 -fcf-protection -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 [ 23%] 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-x86_64-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 -fcf-protection -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 [ 24%] 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-x86_64-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 -fcf-protection -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 [ 24%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/CodonSiteTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 24%] 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-x86_64-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 -fcf-protection -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 [ 25%] 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-x86_64-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 -fcf-protection -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 [ 26%] 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-x86_64-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 -fcf-protection -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 [ 26%] 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-x86_64-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 -fcf-protection -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 [ 27%] 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-x86_64-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 -fcf-protection -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 [ 27%] 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-x86_64-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 -fcf-protection -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 [ 28%] 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-x86_64-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 -fcf-protection -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/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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 29%] 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-x86_64-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 -fcf-protection -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 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/App/../Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 30%] 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-x86_64-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 -fcf-protection -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 [ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/CodonSiteTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 30%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/AlignedSequenceContainer.cpp.o [ 30%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerExceptions.cpp.o [ 31%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 31%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/MapSequenceContainer.cpp.o [ 32%] 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-x86_64-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 -fcf-protection -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 [ 33%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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/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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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/AbstractSequenceContainer.cpp:41: /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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 33%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SequenceContainerTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 34%] 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-x86_64-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 -fcf-protection -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 [ 34%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Container/SiteContainerIterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 35%] 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-x86_64-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 -fcf-protection -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 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 35%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Container/SiteContainerTools.cpp.o [ 36%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 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: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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 37%] 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-x86_64-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 -fcf-protection -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 [ 38%] 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-x86_64-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 -fcf-protection -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 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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: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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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: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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 38%] 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-x86_64-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 -fcf-protection -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 [ 39%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DNAToRNA.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 39%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/DistanceMatrix.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 39%] 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-x86_64-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 -fcf-protection -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 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 40%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DNAToRNA.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 40%] 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-x86_64-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 -fcf-protection -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 [ 41%] 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-x86_64-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 -fcf-protection -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 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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: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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 41%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/DistanceMatrix.cpp.o [ 42%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o [ 42%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 43%] 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-x86_64-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 -fcf-protection -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 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 43%] 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-x86_64-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 -fcf-protection -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 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 44%] 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-x86_64-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 -fcf-protection -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 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: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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 44%] 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-x86_64-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 -fcf-protection -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 [ 45%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/GeneticCode/YeastMitochondrialGeneticCode.cpp.o [ 46%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 46%] 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-x86_64-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 -fcf-protection -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 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/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, 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++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, 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++/15/bits/new_allocator.h:151:73: 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++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 47%] 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-x86_64-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 -fcf-protection -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/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/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, 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++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, 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++/15/bits/new_allocator.h:151:73: 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++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 47%] 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-x86_64-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 -fcf-protection -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 [ 48%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/GeneticCode.cpp.o [ 48%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceReaderFormat.cpp.o [ 49%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/GeneticCode/InvertebrateMitochondrialGeneticCode.cpp.o [ 50%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 50%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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/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/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, 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++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, 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++/15/bits/new_allocator.h:151:73: 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++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 51%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/BppOSequenceStreamReaderFormat.cpp.o [ 52%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 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/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, 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++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, 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++/15/bits/new_allocator.h:151:73: 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++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 52%] 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-x86_64-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 -fcf-protection -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/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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 53%] 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-x86_64-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 -fcf-protection -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 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 53%] 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-x86_64-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 -fcf-protection -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 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 54%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Fasta.cpp.o [ 54%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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: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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, 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++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, 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++/15/bits/new_allocator.h:151:73: 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++/15/bits/new_allocator.h:151:73: 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/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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ 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/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, 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++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, 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++/15/bits/new_allocator.h:151:73: 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++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 55%] 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-x86_64-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 -fcf-protection -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/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/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, 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++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, 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++/15/bits/new_allocator.h:151:73: 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++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 55%] 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-x86_64-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 -fcf-protection -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 [ 56%] 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-x86_64-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 -fcf-protection -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 [ 56%] 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-x86_64-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 -fcf-protection -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 [ 57%] 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-x86_64-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 -fcf-protection -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/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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 58%] 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-x86_64-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 -fcf-protection -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 [ 58%] 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-x86_64-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 -fcf-protection -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/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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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/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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 58%] 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-x86_64-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 -fcf-protection -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 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 59%] 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-x86_64-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 -fcf-protection -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 [ 59%] 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-x86_64-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 -fcf-protection -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 [ 60%] 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-x86_64-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 -fcf-protection -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 [ 61%] 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-x86_64-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 -fcf-protection -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 [ 62%] 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-x86_64-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 -fcf-protection -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 [ 62%] 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-x86_64-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 -fcf-protection -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 [ 62%] 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-x86_64-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 -fcf-protection -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 [ 63%] 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-x86_64-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 -fcf-protection -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 [ 63%] 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-x86_64-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 -fcf-protection -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 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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/x86_64-linux-gnu/c++/15/bits/c++allocator.h:33, from /usr/include/c++/15/bits/allocator.h:46, from /usr/include/c++/15/string:45, 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++/15/bits/alloc_traits.h:614:28, 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++/15/bits/stl_vector.h:387:33, inlined from 'void std::_Vector_base<_Tp, _Alloc>::_M_create_storage(std::size_t) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:405:44, 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++/15/bits/stl_vector.h:341:26, inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = int; _Alloc = std::allocator]' at /usr/include/c++/15/bits/stl_vector.h:587:47, 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++/15/bits/new_allocator.h:151:73: 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++/15/bits/new_allocator.h:151:73: note: at offset 8 into object of size 8 allocated by 'operator new' 151 | return static_cast<_Tp*>(_GLIBCXX_OPERATOR_NEW(__n * sizeof(_Tp))); | ^ [ 64%] 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-x86_64-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 -fcf-protection -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 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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: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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 65%] 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-x86_64-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 -fcf-protection -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 [ 65%] 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-x86_64-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 -fcf-protection -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 [ 66%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Io/Mase.cpp.o [ 66%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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/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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 66%] 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-x86_64-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 -fcf-protection -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/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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 67%] 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-x86_64-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 -fcf-protection -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 [ 68%] 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-x86_64-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 -fcf-protection -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 [ 68%] 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-x86_64-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 -fcf-protection -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 [ 69%] 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-x86_64-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 -fcf-protection -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 [ 70%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Io/Stockholm.cpp.o [ 70%] 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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 70%] 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-x86_64-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 -fcf-protection -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 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 70%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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/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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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/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: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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 71%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Sequence.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 72%] 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-x86_64-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 -fcf-protection -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/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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 73%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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/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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 73%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequencePositionIterators.cpp.o [ 74%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 75%] 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-x86_64-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 -fcf-protection -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 [ 75%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWalker.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 76%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 76%] 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-x86_64-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 -fcf-protection -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 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: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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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: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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 77%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/NucleicAcidsReplication.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 77%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Sequence.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 77%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 78%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 79%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQuality.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 79%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp: In static member function 'static bpp::Sequence* bpp::SequenceTools::subtractHaplotype(const bpp::Sequence&, const bpp::Sequence&, std::string, unsigned int)': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp:556:13: warning: ignoring return value of '_FIter std::remove(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = int]', declared with attribute 'nodiscard' [-Wunused-result] 556 | remove(nucs.begin(), nucs.end(), h.getValue(i)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/algorithm:63, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../SymbolList.h:49, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Sequence.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:44, 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/SequenceTools.h:49, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp:42: /usr/include/c++/15/bits/stl_algo.h:772:5: note: declared here 772 | remove(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~ [ 80%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceTools.cpp.o [ 80%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequencePositionIterators.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 81%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotation.cpp.o [ 81%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWalker.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 82%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Site.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 82%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 82%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithAnnotationTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 83%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQuality.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 84%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SiteTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 85%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/StringSequenceTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 85%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolList.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 86%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SequenceWithQualityTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 86%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Site.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 87%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteExceptions.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 88%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/SymbolListTools.cpp.o [ 88%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SiteTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 89%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/StringSequenceTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 89%] Building CXX object src/CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Transliterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 89%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolList.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 90%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/SymbolListTools.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp: In static member function 'static bpp::Sequence* bpp::SequenceTools::subtractHaplotype(const bpp::Sequence&, const bpp::Sequence&, std::string, unsigned int)': /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp:556:13: warning: ignoring return value of '_FIter std::remove(_FIter, _FIter, const _Tp&) [with _FIter = __gnu_cxx::__normal_iterator >; _Tp = int]', declared with attribute 'nodiscard' [-Wunused-result] 556 | remove(nucs.begin(), nucs.end(), h.getValue(i)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/c++/15/algorithm:63, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../SymbolList.h:49, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Sequence.h:44, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/GeneticCode/../Transliterator.h:44, 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/SequenceTools.h:49, from /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/SequenceTools.cpp:42: /usr/include/c++/15/bits/stl_algo.h:772:5: note: declared here 772 | remove(_ForwardIterator __first, _ForwardIterator __last, | ^~~~~~ [ 90%] Building CXX object src/CMakeFiles/bpp-seq-static.dir/Bpp/Seq/Transliterator.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 [ 91%] Linking CXX shared library libbpp-seq.so cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/NumericAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/ProteicAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNA.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/RNY.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/Alphabet/WordAlphabet.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex1Entry.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/AAIndex2Entry.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/BLOSUM50.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/DefaultNucleotideScore.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/GranthamAAChemicalDistance.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/MiyataAAChemicalDistance.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/AlphabetIndex/SimpleScore.cpp.o" "CMakeFiles/bpp-seq-shared.dir/Bpp/Seq/App/SequenceApplicationTools.cpp.o" "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" 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"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/Bp[ 92%] Linking CXX static library libbpp-seq.a cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/src && /usr/bin/cmake -P CMakeFiles/bpp-seq-static.dir/cmake_clean_target.cmake cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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" 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"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-pOAlphabetIndex2Format.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/x86_64-linux-gnu/libbpp-core.so.4.1.0 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-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 -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/depend make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/depend make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/depend 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-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_alignment_scores.dir/DependInfo.cmake "--color=" make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/depend make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_alphabets.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_bowker.dir/DependInfo.cmake "--color=" 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-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_io.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_containers.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_sequences.dir/DependInfo.cmake "--color=" make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test/CMakeFiles/test_walker.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_walker.dir/build.make test/CMakeFiles/test_walker.dir/build make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_bowker.dir/build.make test/CMakeFiles/test_bowker.dir/build make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_io.dir/build.make test/CMakeFiles/test_io.dir/build make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make -f test/CMakeFiles/test_alignment_scores.dir/build.make test/CMakeFiles/test_alignment_scores.dir/build make -f test/CMakeFiles/test_alphabets.dir/build.make test/CMakeFiles/test_alphabets.dir/build make -f test/CMakeFiles/test_containers.dir/build.make test/CMakeFiles/test_containers.dir/build make -f test/CMakeFiles/test_sequences.dir/build.make test/CMakeFiles/test_sequences.dir/build make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' [ 94%] Building CXX object test/CMakeFiles/test_walker.dir/test_walker.cpp.o [ 94%] Building CXX object test/CMakeFiles/test_bowker.dir/test_bowker.cpp.o [ 98%] Building CXX object test/CMakeFiles/test_containers.dir/test_containers.cpp.o [ 98%] Building CXX object test/CMakeFiles/test_io.dir/test_io.cpp.o [ 98%] Building CXX object test/CMakeFiles/test_alignment_scores.dir/test_alignment_scores.cpp.o [ 98%] Building CXX object test/CMakeFiles/test_alphabets.dir/test_alphabets.cpp.o [ 98%] Building CXX object test/CMakeFiles/test_sequences.dir/test_sequences.cpp.o cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -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 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: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; | ^~~~~~~~ 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; | ^~~~~~~~ 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ /build/reproducible-path/libbpp-seq-2.4.1/src/Bpp/Seq/Container/OrderedSequenceContainer.h:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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_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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 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:199:18: note: by 'virtual int& bpp::OrderedSequenceContainer::operator()(size_t, size_t)' 199 | virtual int& operator()(size_t sequenceIndex, size_t elementIndex) = 0; | ^~~~~~~~ [ 98%] Linking CXX executable test_containers cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_containers.dir/link.txt --verbose=1 [ 99%] Linking CXX executable test_walker cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_walker.dir/link.txt --verbose=1 [ 99%] Linking CXX executable test_sequences cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' [ 99%] Built target test_containers [ 99%] Linking CXX executable test_alphabets cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alphabets.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' [ 99%] Built target test_walker /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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' [ 99%] Built target test_sequences /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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' [ 99%] Built target test_alphabets [ 99%] Linking CXX executable test_bowker cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_bowker.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' [ 99%] Built target test_bowker [ 99%] Linking CXX executable test_io cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_io.dir/link.txt --verbose=1 [100%] Linking CXX executable test_alignment_scores cd /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/test && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_alignment_scores.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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 /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 -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -Wl,-z,relro -Wl,-z,now -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-x86_64-linux-gnu/src ../src/libbpp-seq.so.12.0.0 /usr/lib/x86_64-linux-gnu/libbpp-core.so.4.1.0 make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' [100%] Built target test_io [100%] Built target test_alignment_scores 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-x86_64-linux-gnu' [100%] Built target bpp-seq-static make[2]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' dh_auto_test cd obj-x86_64-linux-gnu && make -j40 test ARGS\+=--verbose ARGS\+=-j40 make[1]: Entering directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' Running tests... /usr/bin/ctest --force-new-ctest-process --verbose -j40 UpdateCTestConfiguration from :/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl UpdateCTestConfiguration from :/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Parse Config file:/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu/DartConfiguration.tcl Test project /build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-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-x86_64-linux-gnu/test/test_walker 7: Working Directory: /build/reproducible-path/libbpp-seq-2.4.1/test 7: Test timeout computed to be: 60000 4: 47 4: ----AUGCCG---GCGU----UUU----G--G-CCGACGUGUUUU-- 4: ---GAAGGCG---G-GU----UUU----GC-GACCGACG--UUUU-- 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 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 1/7 Test #4: test_containers .................. Passed 0.01 sec 2/7 Test #1: test_alignment_scores ............ Passed 0.01 sec 3/7 Test #2: test_alphabets ................... Passed 0.01 sec 3: 2 0.919699 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 4/7 Test #6: test_sequences ................... Passed 0.00 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 5: example.fasta contains 100 sequences 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 0.30 sec 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 5: 100 1209 6/7 Test #5: test_io .......................... Passed 0.32 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%0.0088 0.0506 0.1024 0.5138 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%0.0112 0.0472 0.0934 0.5132 7/7 Test #3: test_bowker ...................... Passed 14.35 sec 100% tests passed, 0 tests failed out of 7 Total Test time (real) = 14.47 sec make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-linux-gnu' create-stamp debian/debhelper-build-stamp dh_prep dh_auto_install cd obj-x86_64-linux-gnu && make -j40 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-x86_64-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/libbpp-seq-2.4.1 -B/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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-x86_64-linux-gnu' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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/x86_64-linux-gnu/cmake/bpp-seq/bpp-seq-config.cmake -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/bpp-seq/bpp-seq-config-version.cmake -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-seq.a -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-seq.so.12 -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/x86_64-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/SequenceWithQuality.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/StreamSequenceIterator.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/Clustal.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/Io/BppOSequenceWriterFormat.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/SequenceFileIndex.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/Dcse.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/OSequence.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/AbstractOSequence.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/MaseTools.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/ISequence.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/BppOAlignmentWriterFormat.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/BppOSequenceStreamReaderFormat.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/Mase.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/ISequenceStream.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/BppOSequenceReaderFormat.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/IoSequence.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/PhredPhd.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/NucleicAcidsReplication.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/StringSequenceTools.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/SymbolListTools.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/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/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/GeneticCode/GeneticCode.h -- 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/StandardGeneticCode.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/SequenceWithAnnotation.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/SiteTools.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/AlphabetIndex -- 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/BLOSUM50.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/AAVolumeIndex.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/AAIndex2Entry.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/AASEAInf10Index.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/AlphabetIndex/AAChenGuHuangHydrophobicityIndex.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/AlphabetIndex2.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/AAChouFasmanAHelixIndex.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/AlphabetIndex1.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/AAChouFasmanBSheetIndex.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/SimpleIndexDistance.h -- 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/AAMassIndex.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/AASEASup30Index.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/CodonSiteTools.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/ProteicAlphabetState.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/LetterAlphabet.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/NucleicAlphabetState.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/Alphabet.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/NumericAlphabet.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/AbstractAlphabet.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/NucleicAlphabet.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/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/DNA.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/LexicalAlphabet.h -- 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/SiteIterator.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/DNAToRNA.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/Container -- 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/AlignedSequenceContainer.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/SiteContainerTools.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/AbstractSequenceContainer.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/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/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/SiteContainerExceptions.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/SiteExceptions.h -- 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/SequenceExceptions.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/Sequence.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/CoreSite.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/SequenceWithQualityTools.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/lib/x86_64-linux-gnu/cmake/bpp-seq/bpp-seq-targets.cmake -- Installing: /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/bpp-seq/bpp-seq-targets-none.cmake make[1]: Leaving directory '/build/reproducible-path/libbpp-seq-2.4.1/obj-x86_64-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/x86_64-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/x86_64-linux-gnu install -d -m 755 debian/libbpp-seq12t64/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-seq.a debian/libbpp-seq-dev/usr/lib/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-seq.so debian/libbpp-seq-dev/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-seq.so.12 debian/libbpp-seq12t64/usr/lib/x86_64-linux-gnu mv /build/reproducible-path/libbpp-seq-2.4.1/debian/tmp/usr/lib/x86_64-linux-gnu/libbpp-seq.so.12.0.0 debian/libbpp-seq12t64/usr/lib/x86_64-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/x86_64-linux-gnu mv debian/tmp/usr/lib/x86_64-linux-gnu/cmake debian/libbpp-seq-dev/usr/lib/x86_64-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 dh_installdeb dh_gencontrol dh_md5sums dh_builddeb dpkg-deb: building package 'libbpp-seq12t64-dbgsym' in '../libbpp-seq12t64-dbgsym_2.4.1-14_amd64.deb'. dpkg-deb: building package 'libbpp-seq-dev' in '../libbpp-seq-dev_2.4.1-14_amd64.deb'. dpkg-deb: building package 'libbpp-seq12t64' in '../libbpp-seq12t64_2.4.1-14_amd64.deb'. dpkg-genbuildinfo --build=binary -O../libbpp-seq_2.4.1-14_amd64.buildinfo dpkg-genchanges --build=binary -O../libbpp-seq_2.4.1-14_amd64.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/417681 and its subdirectories I: Current time: Tue Oct 28 03:31:37 -12 2025 I: pbuilder-time-stamp: 1761665497 Tue Oct 28 15:31:37 UTC 2025 I: 1st build successful. Starting 2nd build on remote node ionos15-amd64.debian.net. Tue Oct 28 15:31:37 UTC 2025 I: Preparing to do remote build '2' on ionos15-amd64.debian.net. Tue Oct 28 15:37:45 UTC 2025 I: Deleting $TMPDIR on ionos15-amd64.debian.net. Tue Oct 28 15:37:45 UTC 2025 I: libbpp-seq_2.4.1-14_amd64.changes: Format: 1.8 Date: Mon, 29 Sep 2025 23:01:22 +0200 Source: libbpp-seq Binary: libbpp-seq-dev libbpp-seq12t64 libbpp-seq12t64-dbgsym Architecture: amd64 Version: 2.4.1-14 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team Changed-By: Étienne Mollier Description: libbpp-seq-dev - Bio++ Sequence library development files libbpp-seq12t64 - Bio++ Sequence library Closes: 1113121 Changes: libbpp-seq (2.4.1-14) unstable; urgency=medium . * Team upload. * cmake-4.patch: new: bump cmake requirement to 3.10. (Closes: #1113121) * d/control: declare standards compliance to version 4.7.2. * d/copyright: remove the old FSF address. * d/watch: bump to v5 Github template. * d/*lintian-overrides: remove unused soname override. * d/s/lintian-overrides: glob d/control line number. This stabilises the override match when d/control varies. * d/control: remove redundant Rules-Requires-Root: no. Checksums-Sha1: 4ddbe7e8f7d19fc3c1cf72c56fa71869bc20c005 740216 libbpp-seq-dev_2.4.1-14_amd64.deb 4fa1155bf41dcea25d7a5c8fadeb793a44558489 9979816 libbpp-seq12t64-dbgsym_2.4.1-14_amd64.deb 29cb650805c11b66dff6d1f5a74f86c4add4b85b 509700 libbpp-seq12t64_2.4.1-14_amd64.deb 3cfaec4ba11aeef3b64e532ddaffb0eca5ef5850 6621 libbpp-seq_2.4.1-14_amd64.buildinfo Checksums-Sha256: 49f310e35b9636555efb46375cfaa0f940a4ebc9b7861cc92321987b7c96df57 740216 libbpp-seq-dev_2.4.1-14_amd64.deb 718b18043674e298323429943f2ab92e4b706cac543f37f5ee21be9766a60ffa 9979816 libbpp-seq12t64-dbgsym_2.4.1-14_amd64.deb 8bf3a4758851217c5d64f8098b8d75d783e48076e7e756b88ff8da415dd609a8 509700 libbpp-seq12t64_2.4.1-14_amd64.deb 6128480c08264f593dfd2335aa188cc1ea7c3e717eb4031355a46ce2f422ce83 6621 libbpp-seq_2.4.1-14_amd64.buildinfo Files: 7746522781c72d823793fddf2fdc658a 740216 libdevel optional libbpp-seq-dev_2.4.1-14_amd64.deb fbddf79cdbe419d7329ec453efcff210 9979816 debug optional libbpp-seq12t64-dbgsym_2.4.1-14_amd64.deb 11cb3e14dd0f23ee377a1fb7f1db5053 509700 libs optional libbpp-seq12t64_2.4.1-14_amd64.deb 2cfbd194ed57df9b18a842a5752d952c 6621 science optional libbpp-seq_2.4.1-14_amd64.buildinfo Tue Oct 28 15:37:46 UTC 2025 I: W: /var/lib/schroot/session/jenkins-reproducible-forky-diffoscope-fdb8602a-07d5-4bac-9fb2-0f62595123e8: Failed to stat file: No such file or directory diffoscope 306 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_11-71457.service; invocation ID: 72e2ef30d06845b0bab1a36f1809b711 # Profiling output for: /usr/bin/diffoscope --html /srv/reproducible-results/rbuild-debian/r-b-build.8kq9DyWC/libbpp-seq_2.4.1-14.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.8kq9DyWC/libbpp-seq_2.4.1-14.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.8kq9DyWC/libbpp-seq_2.4.1-14.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.8kq9DyWC/b1/libbpp-seq_2.4.1-14_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.8kq9DyWC/b2/libbpp-seq_2.4.1-14_amd64.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/SUCCESS Service runtime: 197ms CPU time consumed: 173ms Memory peak: 17.8M (swap: 0B) Tue Oct 28 15:37:46 UTC 2025 I: W: /var/lib/schroot/session/jenkins-reproducible-forky-diffoscope-fdb8602a-07d5-4bac-9fb2-0f62595123e8: Failed to stat file: No such file or directory diffoscope 306 found no differences in the changes files, and a .buildinfo file also exists. Tue Oct 28 15:37:46 UTC 2025 I: libbpp-seq from forky built successfully and reproducibly on amd64. Tue Oct 28 15:37:47 UTC 2025 I: Removing signed libbpp-seq_2.4.1-14_amd64.buildinfo.asc files: removed './b1/libbpp-seq_2.4.1-14_amd64.buildinfo.asc' removed './b2/libbpp-seq_2.4.1-14_amd64.buildinfo.asc'